diff --git a/assets/import_mixs_slots_regardless.tsv b/assets/import_mixs_slots_regardless.tsv deleted file mode 100644 index ddcdd44eea..0000000000 --- a/assets/import_mixs_slots_regardless.tsv +++ /dev/null @@ -1,490 +0,0 @@ -source class source file or URL slot section column order destination class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml abs_air_humidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml add_recov_method placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml additional_info placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml address placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml adj_room placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml aero_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml agrochem_addition placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_PM_concen placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_temp_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml al_sat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml al_sat_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml alkalinity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml alkalinity_method placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml alkyl_diethers placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml alt placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml aminopept_act placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ammonium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml amount_light placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ances_data placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml annual_precpt placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml annual_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml antibiotic_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml api placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml arch_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml aromatics_pc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml asphaltenes_pc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml atmospheric_data placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml avg_dew_point placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml avg_occup placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml avg_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bac_prod placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bac_resp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bacteria_carb_prod placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml barometric_press placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml basin placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bathroom_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bedroom_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml benzene placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biochem_oxygen_dem placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biocide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biocide_admin_method placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biol_stat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biomass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biotic_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml biotic_relationship placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bishomohopanol placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml blood_press_diast placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml blood_press_syst placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bromide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml build_docs placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml build_occup_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml building_setting placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_age placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_set placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml calcium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_dioxide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_monoxide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_nitro_ratio placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_area placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_finish_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_texture placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_thermal_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chem_administration placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chem_mutagen placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chem_oxygen_dem placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chem_treat_method placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chem_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chimera_check placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chloride placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml chlorophyll placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml climate_environment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml collection_date placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml conduc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml cool_syst_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml crop_rotation placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml cult_root_med placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml cur_land_use placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml cur_vegetation placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml cur_vegetation_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml date_last_rain placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml density placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml depos_env placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml depth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml dew_point placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diether_lipids placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_carb_dioxide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_hydrogen placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_inorg_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_inorg_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_inorg_phosp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_iron placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_org_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_org_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_oxygen placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml diss_oxygen_fluid placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_comp_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_direct placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_move placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_size placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_type_metal placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_type_wood placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml door_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml down_par placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml drainage_class placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml drawings placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml efficiency_percent placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml elev placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml elevator placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml emulsions placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml env_broad_scale placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml env_local_scale placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml env_medium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml escalator placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ethylbenzene placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml exp_duct placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml exp_pipe placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml experimental_factor placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ext_door placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ext_wall_orient placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ext_window_orient placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml extreme_event placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fao_class placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fertilizer_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml field placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml filter_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fire placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fireplace_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml flooding placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_age placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_area placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_finish_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_thermal_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml floor_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fluor placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml freq_clean placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml freq_cook placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml fungicide_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml furniture placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml gaseous_environment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml gaseous_substances placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml gender_restroom placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml genetic_mod placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml geo_loc_name placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml glucosidase_act placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml gravidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml gravity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml growth_facil placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml growth_habit placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml growth_hormone_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hall_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml handidness placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hc_produced placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hcr placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hcr_fw_salinity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hcr_geol_age placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hcr_pressure placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml hcr_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heat_cool_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heat_deliv_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heat_sys_deliv_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heat_system_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heavy_metals placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml heavy_metals_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml height_carper_fiber placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml herbicide_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml horizon_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_age placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_body_habitat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_body_product placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_body_site placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_body_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_color placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_common_name placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_diet placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_disease_stat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_dry_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_family_relation placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_genotype placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_growth_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_height placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_last_meal placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_length placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_life_stage placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_phenotype placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_sex placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_shape placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_subject_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_subspecf_genlin placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_substrate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_symbiont placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_taxid placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_tot_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml host_wet_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml humidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml humidity_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml indoor_space placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml indoor_surf placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml indust_eff_percent placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml inorg_particles placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml inside_lux placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml int_wall_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml iw_bt_date_well placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml iwf placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml last_clean placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml lat_lon placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml light_intensity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml light_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml light_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml link_addit_analys placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml link_class_info placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml link_climate_info placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml lithology placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml local_class placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml local_class_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml magnesium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml max_occup placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml mean_frict_vel placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml mean_peak_frict_vel placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml mech_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml mechanical_damage placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml methane placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml micro_biomass_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml microbial_biomass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml mineral_nutr_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml misc_param placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml n_alkanes placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml nitrate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml nitrite placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml non_min_nutr_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml nucl_acid_amp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml nucl_acid_ext placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml number_pets placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml number_plants placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml number_resident placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml occup_density_samp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml occup_document placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml occup_samp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml org_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml org_count_qpcr_info placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml org_matter placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml org_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml org_particles placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml organism_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml owc_tvdss placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml oxy_stat_samp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml oxygen placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml part_org_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml part_org_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml particle_class placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pcr_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pcr_primers placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml permeability placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml perturbation placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pesticide_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml petroleum_hydrocarb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ph placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ph_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ph_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml phaeopigments placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml phosphate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml phosplipid_fatt_acid placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml photon_flux placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml plant_growth_med placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml plant_product placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml plant_sex placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml plant_struc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pollutants placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pool_dna_extracts placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml porosity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml potassium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pour_point placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pre_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pres_animal_insect placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml pressure placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml prev_land_use_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml previous_land_use placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml primary_prod placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml primary_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml prod_rate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml prod_start_date placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml profile_position placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml quad_pos placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml radiation_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml rainfall_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml reactor_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml redox_potential placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml rel_air_humidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml rel_humidity_out placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml rel_samp_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml reservoir placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml resins_pc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_air_exch_rate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_architec_elem placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_condt placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_connected placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_dim placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_door_dist placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_door_share placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_hallway placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_moist_dam_hist placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_net_area placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_occup placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_samp_pos placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_vol placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_wall_share placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml room_window_count placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_carbon placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_macronutr placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_micronutr placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_ph placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_regl placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_solid placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml root_med_suppl placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml salinity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml salinity_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml salt_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_capt_status placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_collec_device placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_collec_method placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_collect_point placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_dis_stage placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_floor placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_loc_corr_rate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_mat_process placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_md placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_name placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_preserv placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_room_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_size placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_sort_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_store_dur placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_store_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_store_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_subtype placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_taxon_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_time_out placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_transport_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_tvdss placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_vol_we_dna_ext placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_weather placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml samp_well_name placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml saturates_pc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml season placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml season_environment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml season_precpt placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml season_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml season_use placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml secondary_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sediment_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml seq_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml seq_quality_check placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sewage_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml shad_dev_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml shading_device_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml shading_device_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml shading_device_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml shading_device_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sieving placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml silicate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml size_frac placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml size_frac_low placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml size_frac_up placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml slope_aspect placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml slope_gradient placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sludge_retent_time placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sodium placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soil_horizon placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soil_text_measure placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soil_texture_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soil_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soil_type_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml solar_irradiance placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soluble_inorg_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soluble_org_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml soluble_react_phosp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml source_mat_id placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml space_typ_state placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml specific placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml specific_humidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sr_dep_env placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sr_geol_age placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sr_kerog_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sr_lithology placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml standing_water_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml store_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml substructure_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sulfate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sulfate_fw placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml sulfide placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_air_cont placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_humidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_material placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_moisture placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_moisture_ph placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml surf_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml suspend_part_matter placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml suspend_solids placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tan placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml target_gene placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml target_subfragment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml temp_out placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tertiary_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tidal_stage placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tillage placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tiss_cult_growth_med placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml toluene placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_depth_water_col placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_diss_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_inorg_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_iron placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_nitro placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_nitro_cont_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_nitro_content placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_org_c_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_org_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_part_carb placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_phosp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_phosphate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tot_sulfur placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml train_line placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml train_stat_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml train_stop_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml turbidity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tvdss_of_hcr_press placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml tvdss_of_hcr_temp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml typ_occup_density placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ventilation_rate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ventilation_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml vfa placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml vfa_fw placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml vis_media placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml viscosity placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml volatile_org_comp placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_area placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_const_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_finish_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_height placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_surf_treatment placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_texture placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_thermal_mass placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wall_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wastewater_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_cont_soil_meth placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_content placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_current placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_cut placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_feat_size placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_feat_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_prod_rate placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml water_temp_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml watering_regm placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml weekday placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml win placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wind_direction placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml wind_speed placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_cond placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_cover placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_horiz_pos placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_loc placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_mat placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_open_freq placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_size placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_status placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_type placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_vert_pos placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml window_water_mold placeholder_class -soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml xylene placeholder_class diff --git a/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv b/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv new file mode 100644 index 0000000000..108985774f --- /dev/null +++ b/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv @@ -0,0 +1,485 @@ +source class source file or URL column order section slot destination class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml abs_air_humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml add_recov_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml additional_info placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml address placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml adj_room placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aero_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml agrochem_addition placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_PM_concen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_temp_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml al_sat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml al_sat_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkalinity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkalinity_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkyl_diethers placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aminopept_act placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ammonium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml amount_light placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ances_data placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml annual_precpt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml annual_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml antibiotic_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml api placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml arch_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aromatics_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml asphaltenes_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml atmospheric_data placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_dew_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_occup placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bac_prod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bac_resp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bacteria_carb_prod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml barometric_press placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml basin placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bathroom_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bedroom_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml benzene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biochem_oxygen_dem placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biocide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biocide_admin_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biol_stat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biomass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biotic_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biotic_relationship placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bishomohopanol placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml blood_press_diast placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml blood_press_syst placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bromide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml build_docs placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml build_occup_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml building_setting placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_set placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml calcium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_dioxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_monoxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_nitro_ratio placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_finish_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_texture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_thermal_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_administration placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_mutagen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_oxygen_dem placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_treat_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chimera_check placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chloride placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chlorophyll placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml climate_environment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml collection_date placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml conduc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cool_syst_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml crop_rotation placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cult_root_med placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_land_use placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_vegetation placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_vegetation_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml date_last_rain placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml density placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml depos_env placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml depth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml dew_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diether_lipids placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_carb_dioxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_hydrogen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_phosp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_iron placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_org_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_oxygen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_oxygen_fluid placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_comp_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_direct placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_move placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_type_metal placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_type_wood placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml door_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml down_par placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml drainage_class placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml drawings placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml efficiency_percent placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml elev placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml elevator placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml emulsions placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml env_broad_scale placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml env_local_scale placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml env_medium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml escalator placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ethylbenzene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml exp_duct placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml exp_pipe placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml experimental_factor placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ext_door placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ext_wall_orient placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ext_window_orient placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml extreme_event placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fao_class placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fertilizer_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml field placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml filter_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fire placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fireplace_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml flooding placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_finish_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_thermal_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml floor_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fluor placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml freq_clean placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml freq_cook placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml fungicide_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml furniture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml gaseous_environment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml gaseous_substances placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml gender_restroom placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml genetic_mod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml geo_loc_name placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml glucosidase_act placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml gravidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml gravity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml growth_facil placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml growth_habit placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml growth_hormone_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hall_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml handidness placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hc_produced placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hcr placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hcr_fw_salinity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hcr_geol_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hcr_pressure placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml hcr_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heat_cool_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heat_deliv_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heat_sys_deliv_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heat_system_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heavy_metals placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml heavy_metals_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml height_carper_fiber placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml herbicide_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml horizon_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_body_habitat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_body_product placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_body_site placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_body_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_color placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_common_name placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_diet placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_dry_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_genotype placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_growth_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_height placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_last_meal placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_length placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_life_stage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_phenotype placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_sex placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_shape placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_subject_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_subspecf_genlin placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_substrate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_symbiont placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_taxid placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_tot_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml host_wet_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml humidity_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml indoor_space placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml indoor_surf placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml indust_eff_percent placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml inorg_particles placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml inside_lux placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml int_wall_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml iw_bt_date_well placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml iwf placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml last_clean placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml lat_lon placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml light_intensity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml light_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml light_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml link_addit_analys placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml link_class_info placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml link_climate_info placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml lithology placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml local_class placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml local_class_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml magnesium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml max_occup placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml mean_frict_vel placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml mean_peak_frict_vel placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml mech_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml mechanical_damage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml methane placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml micro_biomass_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml microbial_biomass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml mineral_nutr_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml misc_param placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml n_alkanes placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml nitrate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml nitrite placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml non_min_nutr_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml nucl_acid_amp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml nucl_acid_ext placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml number_pets placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml number_plants placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml number_resident placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml occup_density_samp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml occup_document placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml occup_samp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml org_count_qpcr_info placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml org_matter placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml org_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml org_particles placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml organism_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml owc_tvdss placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml oxy_stat_samp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml oxygen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml part_org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml part_org_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml particle_class placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pcr_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pcr_primers placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml permeability placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml perturbation placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pesticide_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml petroleum_hydrocarb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ph placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ph_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ph_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml phaeopigments placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml phosphate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml phosplipid_fatt_acid placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml photon_flux placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml plant_growth_med placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml plant_product placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml plant_sex placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml plant_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pollutants placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pool_dna_extracts placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml porosity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml potassium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pour_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pre_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pres_animal_insect placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml pressure placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml prev_land_use_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml previous_land_use placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml primary_prod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml primary_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml prod_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml prod_start_date placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml profile_position placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml quad_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml radiation_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml rainfall_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml reactor_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml redox_potential placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml rel_air_humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml rel_humidity_out placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml rel_samp_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml reservoir placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml resins_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_air_exch_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_architec_elem placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_condt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_connected placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_dim placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_door_dist placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_door_share placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_hallway placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_moist_dam_hist placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_net_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_occup placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_samp_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_vol placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_wall_share placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml room_window_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_carbon placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_macronutr placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_micronutr placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_ph placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_regl placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_solid placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml root_med_suppl placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml salinity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml salt_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_capt_status placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_collect_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_dis_stage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_floor placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_loc_corr_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_mat_process placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_md placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_name placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_preserv placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_room_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_sort_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_store_dur placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_store_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_store_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_subtype placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_taxon_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_time_out placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_transport_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_tvdss placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_vol_we_dna_ext placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_weather placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_well_name placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml saturates_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml season placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml season_environment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml season_precpt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml season_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml season_use placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml secondary_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sediment_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml seq_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml seq_quality_check placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sewage_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml shad_dev_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml shading_device_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml shading_device_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml shading_device_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml shading_device_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sieving placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml silicate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml size_frac placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml size_frac_low placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml size_frac_up placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml slope_aspect placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml slope_gradient placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sludge_retent_time placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sodium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soil_horizon placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soil_texture_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soil_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soil_type_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml solar_irradiance placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soluble_inorg_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soluble_org_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml soluble_react_phosp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml source_mat_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml space_typ_state placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml specific placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml specific_humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sr_dep_env placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sr_geol_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sr_kerog_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sr_lithology placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml standing_water_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml store_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml substructure_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sulfate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sulfate_fw placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml sulfide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_air_cont placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_material placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_moisture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_moisture_ph placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml surf_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml suspend_part_matter placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml suspend_solids placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tan placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml target_gene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml target_subfragment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml temp_out placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tertiary_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tidal_stage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tillage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tiss_cult_growth_med placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml toluene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_depth_water_col placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_diss_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_inorg_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_iron placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro_cont_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro_content placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_org_c_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_part_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_phosp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_phosphate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_sulfur placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_line placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_stat_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_stop_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml turbidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tvdss_of_hcr_press placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tvdss_of_hcr_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml typ_occup_density placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ventilation_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ventilation_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vfa placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vfa_fw placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vis_media placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml viscosity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml volatile_org_comp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_const_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_finish_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_height placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_surf_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_texture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_thermal_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wastewater_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_cont_soil_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_content placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_current placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_cut placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_feat_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_feat_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_prod_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_temp_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml watering_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml weekday placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml win placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wind_direction placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wind_speed placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_cover placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_horiz_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_open_freq placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_status placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_vert_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml xylene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml samp_collect_method placeholder_class \ No newline at end of file diff --git a/assets/other_mixs_yaml_files/mixs_template.yaml b/assets/other_mixs_yaml_files/mixs_template.yaml index eeb092caaa..81091624e9 100644 --- a/assets/other_mixs_yaml_files/mixs_template.yaml +++ b/assets/other_mixs_yaml_files/mixs_template.yaml @@ -5,7 +5,6 @@ id: https://w3id.org/nmdc/mixs subsets: mixs_environmental_triad: title: MIxS Environmental Triad - mixs extension: { } notes: - removed several MIxS terms/slots that were sharing slot uris; commented out Biosample assignments diff --git a/assets/yq-for-mixs_subset_modified.txt b/assets/yq-for-mixs_subset_modified.txt index 56ceda3b30..c5186d6898 100644 --- a/assets/yq-for-mixs_subset_modified.txt +++ b/assets/yq-for-mixs_subset_modified.txt @@ -1,28 +1,46 @@ + +'.slots.abs_air_humidity.range |= "QuantityValue"' '.slots.agrochem_addition.range |= "TextValue"' '.slots.air_temp_regm.range |= "TextValue"' +'.slots.ammonium.range |= "QuantityValue"' '.slots.antibiotic_regm.range |= "TextValue"' '.slots.aromatics_pc.range |= "TextValue"' '.slots.asphaltenes_pc.range |= "TextValue"' '.slots.atmospheric_data.range |= "TextValue"' '.slots.avg_occup.range |= "TextValue"' +'.slots.avg_temp.range |= "QuantityValue"' '.slots.bathroom_count.range |= "TextValue"' '.slots.bedroom_count.range |= "TextValue"' '.slots.biocide_admin_method.range |= "TextValue"' '.slots.biomass.range |= "TextValue"' +'.slots.calcium.range |= "QuantityValue"' +'.slots.carb_nitro_ratio.range |= "QuantityValue"' '.slots.chem_administration.range |= "ControlledTermValue"' '.slots.chem_mutagen.range |= "TextValue"' '.slots.chem_treat_method.range |= "string"' +'.slots.chloride.range |= "QuantityValue"' +'.slots.chlorophyll.range |= "QuantityValue"' '.slots.collection_date.range |= "TimestampValue"' +'.slots.conduc.range |= "QuantityValue"' '.slots.cool_syst_id.range |= "TextValue"' +'.slots.cur_vegetation.range |= "QuantityValue"' +'.slots.cur_vegetation.range |= "TextValue"' '.slots.date_last_rain.range |= "TimestampValue"' +'.slots.depth.range |= "QuantityValue"' '.slots.diether_lipids.range |= "TextValue"' +'.slots.diss_inorg_carb.range |= "QuantityValue"' +'.slots.diss_inorg_nitro.range |= "QuantityValue"' +'.slots.diss_iron.range |= "QuantityValue"' +'.slots.diss_org_carb.range |= "QuantityValue"' +'.slots.diss_oxygen.range |= "QuantityValue"' '.slots.elevator.range |= "TextValue"' '.slots.emulsions.range |= "TextValue"' '.slots.env_broad_scale.range |= "ControlledIdentifiedTermValue"' '.slots.env_local_scale.range |= "ControlledIdentifiedTermValue"' -'.slots.env_medium.range |= "ControlledIdentifiedTermValue"' +'.slots.env_medium.range |= "ControlledIdentifiedTermValue"' '.slots.escalator.range |= "TextValue"' '.slots.exp_pipe.range |= "QuantityValue"' +'.slots.experimental_factor.multivalued |= false' '.slots.experimental_factor.range |= "ControlledTermValue"' '.slots.ext_door.range |= "TextValue"' '.slots.extreme_event.range |= "TimestampValue"' @@ -35,6 +53,7 @@ '.slots.fungicide_regm.range |= "TextValue"' '.slots.gaseous_environment.range |= "TextValue"' '.slots.gaseous_substances.range |= "TextValue"' +'.slots.gravidity.range |= "TextValue"' '.slots.gravity.range |= "TextValue"' '.slots.growth_facil.range |= "ControlledTermValue"' '.slots.growth_hormone_regm.range |= "TextValue"' @@ -46,41 +65,52 @@ '.slots.heat_system_id.range |= "TextValue"' '.slots.heavy_metals.range |= "TextValue"' '.slots.herbicide_regm.range |= "TextValue"' +'.slots.host_age.range |= "QuantityValue"' '.slots.host_body_product.range |= "ControlledTermValue"' '.slots.host_body_site.range |= "ControlledTermValue"' -'.slots.host_family_relation.range |= "string"' +'.slots.host_dry_mass.range |= "QuantityValue"' +'.slots.host_height.range |= "QuantityValue"' +'.slots.host_life_stage.range |= "TextValue"' '.slots.host_phenotype.range |= "ControlledTermValue"' '.slots.host_subspecf_genlin.range |= "string"' '.slots.host_symbiont.range |= "string"' +'.slots.humidity.range |= "QuantityValue"' '.slots.humidity_regm.range |= "TextValue"' '.slots.inorg_particles.range |= "TextValue"' '.slots.iw_bt_date_well.range |= "TimestampValue"' '.slots.last_clean.range |= "TimestampValue"' '.slots.lat_lon.range |= "GeolocationValue"' '.slots.light_regm.range |= "TextValue"' +'.slots.magnesium.range |= "QuantityValue"' '.slots.max_occup.range |= "QuantityValue"' '.slots.micro_biomass_meth.range |= "string"' '.slots.mineral_nutr_regm.range |= "TextValue"' '.slots.misc_param.range |= "TextValue"' '.slots.n_alkanes.range |= "TextValue"' +'.slots.nitrate.range |= "QuantityValue"' +'.slots.nitro.range |= "QuantityValue"' '.slots.non_min_nutr_regm.range |= "string"' '.slots.number_pets.range |= "QuantityValue"' '.slots.number_plants.range |= "QuantityValue"' '.slots.number_resident.range |= "QuantityValue"' '.slots.occup_density_samp.range |= "QuantityValue"' '.slots.occup_samp.range |= "QuantityValue"' +'.slots.org_carb.range |= "QuantityValue"' '.slots.org_count_qpcr_info.range |= "string"' '.slots.org_particles.range |= "TextValue"' '.slots.organism_count.range |= "QuantityValue"' '.slots.particle_class.range |= "TextValue"' '.slots.permeability.range |= "TextValue"' +'.slots.perturbation.range |= "TextValue"' '.slots.pesticide_regm.range |= "TextValue"' '.slots.phaeopigments.range |= "TextValue"' '.slots.phosplipid_fatt_acid.range |= "TextValue"' +'.slots.photon_flux.range |= "QuantityValue"' '.slots.plant_growth_med.range |= "ControlledTermValue"' '.slots.plant_struc.range |= "ControlledTermValue"' '.slots.pollutants.range |= "TextValue"' '.slots.porosity.range |= "TextValue"' +'.slots.potassium.range |= "QuantityValue"' '.slots.pres_animal_insect.range |= "string"' '.slots.prev_land_use_meth.range |= "string"' '.slots.prod_start_date.range |= "TimestampValue"' @@ -101,14 +131,14 @@ '.slots.root_med_regl.range |= "TextValue"' '.slots.root_med_suppl.range |= "TextValue"' '.slots.salt_regm.range |= "TextValue"' -'.slots.samp_collec_device.range |= "string"' -'.slots.samp_collec_method.range |= "string"' '.slots.samp_loc_corr_rate.range |= "TextValue"' '.slots.samp_mat_process.range |= "ControlledTermValue"' '.slots.samp_md.range |= "QuantityValue"' '.slots.samp_name.range |= "string"' '.slots.samp_preserv.range |= "TextValue"' '.slots.samp_room_id.range |= "TextValue"' +'.slots.samp_size.range |= "QuantityValue"' +'.slots.samp_store_temp.range |= "QuantityValue"' '.slots.samp_time_out.range |= "TextValue"' '.slots.samp_transport_cond.range |= "TextValue"' '.slots.samp_tvdss.range |= "TextValue"' @@ -116,16 +146,31 @@ '.slots.shad_dev_water_mold.range |= "string"' '.slots.sieving.range |= "TextValue"' '.slots.size_frac.range |= "TextValue"' +'.slots.sodium.range |= "QuantityValue"' '.slots.soil_texture_meth.range |= "string"' +'.slots.solar_irradiance.multivalued |= false' +'.slots.solar_irradiance.range |= "QuantityValue"' '.slots.soluble_inorg_mat.range |= "TextValue"' '.slots.soluble_org_mat.range |= "TextValue"' +'.slots.soluble_react_phosp.range |= "QuantityValue"' +'.slots.source_mat_id.multivalued |= false' +'.slots.source_mat_id.range |= "TextValue"' +'.slots.store_cond.range |= "TextValue"' +'.slots.sulfate.range |= "QuantityValue"' '.slots.suspend_solids.range |= "TextValue"' +'.slots.temp.range |= "QuantityValue"' +'.slots.tot_carb.range |= "QuantityValue"' +'.slots.tot_nitro.range |= "QuantityValue"' '.slots.tot_nitro_cont_meth.range |= "string"' +'.slots.tot_nitro_content.range |= "QuantityValue"' +'.slots.tot_org_carb.range |= "QuantityValue"' +'.slots.tot_phosp.range |= "QuantityValue"' '.slots.viscosity.range |= "TextValue"' '.slots.volatile_org_comp.range |= "TextValue"' '.slots.water_cont_soil_meth.range |= "string"' '.slots.water_temp_regm.range |= "TextValue"' '.slots.watering_regm.range |= "TextValue"' +'.slots.wind_speed.range |= "QuantityValue"' '.slots.window_open_freq.range |= "TextValue"' '.slots.window_size.range |= "TextValue"' @@ -155,7 +200,7 @@ 'del(.slots.["has unit"])' # add "M horizon" to soil_horizon_enum -'.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}' +'.enums.SOIL_HORIZON_ENUM.permissible_values.["M horizon"] = {}' # as of 2024-01-30: # ValueError: Conflicting URIs (https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml, https://w3id.org/linkml/types) for item: date @@ -167,3 +212,27 @@ make: *** [Makefile:102: gen-project] Error 1 '.slots.fire.range |= "string"' '.slots.flooding.range |= "string"' '.slots.water_content.range |= "string"' + +'del(.slots[].required)' +'del(.slots[].in_subset)' +'del(.subsets)' + +'.slots.samp_collec_method = .slots.samp_collect_method' +'.slots.samp_collec_method.notes += "cloned from MIxS 6.2 samp_collect_method"' +'del(.slots.samp_collect_method)' +'.slots.samp_collec_method.range |= "string"' +'del(.slots.samp_collec_method.pattern)' +'del(.slots.samp_collec_method.structured_pattern)' + +'.slots.samp_collec_device = .slots.samp_collect_device' +'.slots.samp_collec_device.notes += "cloned from MIxS 6.2 samp_collect_device"' +'del(.slots.samp_collect_device)' +'.slots.samp_collec_device.range |= "string"' +'del(.slots.samp_collec_device.pattern)' +'del(.slots.samp_collec_device.structured_pattern)' + +'del(.slots.micro_biomass_meth.pattern)' +'del(.slots.micro_biomass_meth.structured_pattern)' + +'del(.slots.water_content.pattern)' +'del(.slots.water_content.structured_pattern)' diff --git a/nmdc_schema/generate_import_slots_regardless.py b/nmdc_schema/generate_import_slots_regardless.py deleted file mode 100644 index 1a1faf5f19..0000000000 --- a/nmdc_schema/generate_import_slots_regardless.py +++ /dev/null @@ -1,54 +0,0 @@ -import csv -import click - - -class ImportSlotsRegardless: - mixs_slots_used_in_schema_tsv = "../assets/mixs_slots_used_in_schema.tsv" - mixs_slots_used_in_schema = list() - - static_value_dict = { - "source class": "soil MIMS", - # "source file or URL": "https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/model/schema/mixs.yaml", - "source file or URL": "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml", - "slot": "", - "section": "", - "column order": "", - "destination class": "placeholder_class" - } - - def populate_mixs_slots_used_in_schema(self, input_file): - with open(input_file, 'r') as file: - self.mixs_slots_used_in_schema = [line.strip().split('\t')[0] for line in file] - - def make_import_slots_regardless_rows(self, input_file): - self.populate_mixs_slots_used_in_schema(input_file) - import_slots_regardless_rows = list() - - for slot in self.mixs_slots_used_in_schema: - final_dict = self.static_value_dict.copy() - final_dict["slot"] = slot - import_slots_regardless_rows.append(final_dict) - - return import_slots_regardless_rows - - def write_import_slots_regardless_rows(self, output_file, input_file): - fieldnames = list(self.static_value_dict.keys()) - slots_regardless_rows = self.make_import_slots_regardless_rows(input_file) - with open(output_file, 'w', newline='') as output_file: - writer = csv.DictWriter(output_file, fieldnames=fieldnames, delimiter='\t') - writer.writeheader() - for row in slots_regardless_rows: - writer.writerow(row) - - -@click.command() -@click.option("--input_file", required=True, help="input file path from get-mixs-slots-used-in-schema") -@click.option("--output_file", required=True, help="output file path for sheets_and_friends") -def main(output_file, input_file): - import_slots = ImportSlotsRegardless() - import_slots.write_import_slots_regardless_rows(output_file, input_file) - click.echo("Import slots regardless file generated successfully.") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_mixs_slots.py b/nmdc_schema/get_mixs_slots.py deleted file mode 100644 index 87669c2f2b..0000000000 --- a/nmdc_schema/get_mixs_slots.py +++ /dev/null @@ -1,47 +0,0 @@ -import csv -import pprint -import urllib.request - -import csv -import io -import urllib.request -from typing import List - - -class MIxSSlotsGetter: - # switch to retrieving from GSC' mixs.yaml - def any_mixs_sheet_getter(self, url): - response = urllib.request.urlopen(url) - tsv_file = io.StringIO(response.read().decode('utf-8')) - - rows = [] - - # Parse the file using DictReader - reader = csv.DictReader(tsv_file, delimiter='\t') - for row in reader: - rows.append(row) - - return rows - - def extract_vals_from_rows(self, rows, var_name): - slots = [] - for row in rows: - if var_name in row and row[var_name] != '': - slots.append(row[var_name]) - slots.sort() - return slots - - def get_unique_slot_names(self, - var_name: str = "Structured comment name", - url_list: List[str] = ( - "https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?gid=178015749&format=tsv", - "https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?gid=750683809&format=tsv" - )): - slot_names = set() - for url in url_list: - parsed = self.any_mixs_sheet_getter(url) - per_page_slots = self.extract_vals_from_rows(parsed, var_name) - slot_names.update(per_page_slots) - slot_names = list(slot_names) - slot_names.sort() - return slot_names diff --git a/nmdc_schema/get_mixs_slots_matching_slot_list.py b/nmdc_schema/get_mixs_slots_matching_slot_list.py deleted file mode 100644 index 09c977aec3..0000000000 --- a/nmdc_schema/get_mixs_slots_matching_slot_list.py +++ /dev/null @@ -1,50 +0,0 @@ -from typing import List - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - -import click - - -class IntersectionMixsSlotsGetter: - mixs_term_getter: MIxSSlotsGetter = MIxSSlotsGetter() - mixs_slotnames: List[str] = mixs_term_getter.get_unique_slot_names() - slot_list = [] - - def get_intersection_mixs_slots(self, slot_list_file) -> List[str]: - print(f"slot_list_file: {slot_list_file}") - with open(slot_list_file, 'r') as file: - self.slot_list = [line.strip().split('\t')[0] for line in file] - - used_mixs_slots = list(set(self.mixs_slotnames) & set(self.slot_list)) - used_mixs_slots.sort() - return used_mixs_slots - - -@click.command() -@click.option('--slot_list_file', - '-s', - type=click.Path(exists=True), - required=True, - help='Provide a single-column TSV file listing desired slots.') -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -def main(slot_list_file, output_file): - print(f"slot_list_file: {slot_list_file}") - print(f"output_file: {output_file}") - - intersection_mixs_slot_getter = IntersectionMixsSlotsGetter() - intersection_mixs_slots = intersection_mixs_slot_getter.get_intersection_mixs_slots(slot_list_file) - - with output_file: - for slot in intersection_mixs_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file.name}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_mixs_slots_used_in_schema.py b/nmdc_schema/get_mixs_slots_used_in_schema.py deleted file mode 100644 index f0d578b202..0000000000 --- a/nmdc_schema/get_mixs_slots_used_in_schema.py +++ /dev/null @@ -1,40 +0,0 @@ -from typing import List - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - -import click - - -class UsedMixsSlotsGetter: - mixs_term_getter: MIxSSlotsGetter = MIxSSlotsGetter() - mixs_slotnames: List[str] = mixs_term_getter.get_unique_slot_names() - - schema_slots_getter: SchemaSlotsGetter = SchemaSlotsGetter() - schema_slots: List[str] = schema_slots_getter.get_schema_slots() - - def get_used_mixs_slots(self) -> List[str]: - used_mixs_slots = list(set(self.mixs_slotnames) & set(self.schema_slots)) - used_mixs_slots.sort() - return used_mixs_slots - - -@click.command() -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -def main(output_file): - used_mixs_slot_getter = UsedMixsSlotsGetter() - used_mixs_slots = used_mixs_slot_getter.get_used_mixs_slots() - - with output_file: - for slot in used_mixs_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file.name}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_slots_from_class.py b/nmdc_schema/get_slots_from_class.py deleted file mode 100644 index cb8b2024a8..0000000000 --- a/nmdc_schema/get_slots_from_class.py +++ /dev/null @@ -1,44 +0,0 @@ -import pprint -from typing import List - -import click - -from nmdc_schema.get_nmdc_view import ViewGetter - - -class ClassSlotsGetter: - @staticmethod - def get_class_slots(class_name) -> List[str]: - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - nmdc_class = nmdc_view.induced_class(class_name) - class_slots = nmdc_class.attributes - - class_slot_names = [v.name for k, v in class_slots.items()] - class_slot_names.sort() - return class_slot_names - - -@click.command() -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -@click.option('--class_name', - '-c', - required=True, - help='For what class do you want to retrieve slots?.') -def main(output_file, class_name): - class_slot_getter = ClassSlotsGetter() - class_used_slots = class_slot_getter.get_class_slots(class_name) - - with output_file: - for slot in class_used_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_slots_from_view.py b/nmdc_schema/get_slots_from_view.py deleted file mode 100644 index e808aad7a4..0000000000 --- a/nmdc_schema/get_slots_from_view.py +++ /dev/null @@ -1,16 +0,0 @@ -import pprint -from typing import List - -from nmdc_schema.get_nmdc_view import ViewGetter - - -class SchemaSlotsGetter: - def get_schema_slots(self) -> List[str]: - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - - schema_slots = nmdc_view.all_slots() - schema_slot_names = [v.name for k, v in schema_slots.items()] - schema_slot_names.sort() - return schema_slot_names - diff --git a/nmdc_schema/gold-to-mixs.sssom.tsv b/nmdc_schema/gold-to-mixs.sssom.tsv deleted file mode 100644 index 60c2cb5ea9..0000000000 --- a/nmdc_schema/gold-to-mixs.sssom.tsv +++ /dev/null @@ -1,129 +0,0 @@ -#license: https://creativecommons.org/publicdomain/zero/1.0/ -#mapping_date: 2020-06-36 -#mapping_provider: https://microbiomedata.org/ -#creator_label: -# - Jagadish Sundaramurthi -# - Bill Duncan -#curie_map: -# gold.vocab: "https://microbiomedata/schema/ddl/" -# mixs: "https://microbiomedata/schema/mixs#" -# skos: "http://www.w3.org/2004/02/skos/core#" -subject_id subject_label predicate_id object_id object_label match_type subject_source object_source confidence comment -gold.vocab:altitude altitude skos:exactMatch mixs:alt alt SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:growth_temperature growth_temperature skos:exactMatch mixs:temp temp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:salinity_concentration salinity_concentration skos:exactMatch mixs:salinity salinity SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:oxygen_concentration oxygen_concentration skos:exactMatch mixs:diss_oxygen diss_oxygen SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:ph ph skos:exactMatch mixs:ph ph SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:geographic_location geographic_location skos:exactMatch mixs:geo_loc_name geo_loc_name SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:nitrate_concentration nitrate_concentration skos:exactMatch mixs:nitrate nitrate SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:chlorophyll_concentration chlorophyll_concentration skos:exactMatch mixs:chlorophyll chlorophyll SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:sample_volume sample_volume skos:exactMatch mixs:samp_vol_we_dna_ext samp_vol_we_dna_ext SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:sampling_strategy sampling_strategy skos:exactMatch mixs:samp_collect_device samp_collect_device SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_curr_land_use soil_curr_land_use skos:exactMatch mixs:cur_land_use cur_land_use SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_curr_vegetation soil_curr_vegetation skos:exactMatch mixs:cur_vegetation cur_vegetation SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_curr_vegetation_method soil_curr_vegetation_method skos:exactMatch mixs:cur_vegetation_meth cur_vegetation_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_prev_land_use soil_prev_land_use skos:exactMatch mixs:previous_land_use previous_land_use SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_prev_land_use_meth soil_prev_land_use_meth skos:exactMatch mixs:previous_land_use_meth previous_land_use_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_crop_rotation soil_crop_rotation skos:exactMatch mixs:crop_rotation crop_rotation SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_agrochem_addition soil_agrochem_addition skos:exactMatch mixs:agrochem_addition agrochem_addition SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_tillage soil_tillage skos:exactMatch mixs:tillage tillage SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_fire soil_fire skos:exactMatch mixs:fire fire SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_flooding soil_flooding skos:exactMatch mixs:flooding flooding SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_extreme_event soil_extreme_event skos:exactMatch mixs:extreme_event extreme_event SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_horizon soil_horizon skos:exactMatch mixs:horizon horizon SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_horizon_method soil_horizon_method skos:exactMatch mixs:horizon_meth horizon_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_seiving soil_seiving skos:exactMatch mixs:sieving sieving SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_water_content soil_water_content skos:exactMatch mixs:water_content water_content SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_water_content_soil_meth soil_water_content_soil_meth skos:exactMatch mixs:water_content_soil_meth water_content_soil_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:sample_weight_dna_ext sample_weight_dna_ext skos:exactMatch mixs:samp_vol_we_dna_ext samp_vol_we_dna_ext SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_sample_weight_dna_ext soil_sample_weight_dna_ext skos:exactMatch mixs:samp_vol_we_dna_ext samp_vol_we_dna_ext SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_sample_weight_dna_ext water_sample_weight_dna_ext skos:exactMatch mixs:samp_vol_we_dna_ext samp_vol_we_dna_ext SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_pool_dna_extracts soil_pool_dna_extracts skos:exactMatch mixs:pool_dna_extracts pool_dna_extracts SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_store_condition soil_store_condition skos:exactMatch mixs:store_cond store_cond SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_link_climate_info soil_link_climate_info skos:exactMatch mixs:link_climate_info link_climate_info SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_temp soil_annual_season_temp skos:closeMatch mixs:annual_temp annual_temp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_temp soil_annual_season_temp skos:closeMatch mixs:season_temp season_temp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_precpt soil_annual_season_precpt skos:closeMatch mixs:season_precpt season_precpt SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_precpt soil_annual_season_precpt skos:closeMatch mixs:annual_precpt annual_precpt SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_link_class_info soil_link_class_info skos:exactMatch mixs:link_class_info link_class_info SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_fao_class soil_fao_class skos:exactMatch mixs:fao_class fao_class SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_local_class soil_local_class skos:exactMatch mixs:local_class local_class SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_local_class_method soil_local_class_method skos:exactMatch mixs:local_class_meth local_class_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_type soil_type skos:exactMatch mixs:soil_type soil_type SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_type_method soil_type_method skos:exactMatch mixs:soil_type_meth soil_type_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_slope_gradient soil_slope_gradient skos:exactMatch mixs:slope_gradient slope_gradient SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_slope_aspect soil_slope_aspect skos:exactMatch mixs:slope_aspect slope_aspect SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_profile_position soil_profile_position skos:exactMatch mixs:profile_position profile_position SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_drainage_class soil_drainage_class skos:exactMatch mixs:drainage_class drainage_class SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_texture soil_texture skos:exactMatch mixs:texture texture SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_texture_method soil_texture_method skos:exactMatch mixs:texture_meth texture_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_ph soil_ph skos:exactMatch mixs:ph ph SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_ph_method soil_ph_method skos:exactMatch mixs:ph_meth ph_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_tot_org_carbon soil_tot_org_carbon skos:exactMatch mixs:tot_org_carb tot_org_carb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:tot_org_carbon tot_org_carbon skos:exactMatch mixs:tot_org_carb tot_org_carb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_tot_org_c_method soil_tot_org_c_method skos:exactMatch mixs:tot_org_c_meth tot_org_c_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_tot_nitrogen soil_tot_nitrogen skos:exactMatch mixs:tot_nitro_content tot_nitro_content SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:tot_nitrogen tot_nitrogen skos:exactMatch mixs:tot_nitro_content tot_nitro_content SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_tot_n_method soil_tot_n_method skos:exactMatch mixs:tot_nitro_content_meth tot_nitro_content_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_microbial_biomass soil_microbial_biomass skos:exactMatch mixs:microbial_biomass microbial_biomass SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_microbial_biomass_method soil_microbial_biomass_method skos:exactMatch mixs:microbial_biomass_meth microbial_biomass_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_link_addit_analys soil_link_addit_analys skos:exactMatch mixs:link_addit_analys link_addit_analys SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_salinity_method soil_salinity_method skos:exactMatch mixs:salinity_meth salinity_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_heavy_metals soil_heavy_metals skos:exactMatch mixs:heavy_metals heavy_metals SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_heavy_metals_method soil_heavy_metals_method skos:exactMatch mixs:heavy_metals_meth heavy_metals_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_aluminium_sat soil_aluminium_sat skos:exactMatch mixs:al_sat al_sat SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_aluminium_sat_method soil_aluminium_sat_method skos:exactMatch mixs:al_sat_meth al_sat_meth SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_misc_param soil_misc_param skos:exactMatch mixs:misc_param misc_param SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_ph water_ph skos:exactMatch mixs:ph ph SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_alkalinity water_alkalinity skos:exactMatch mixs:alkalinity alkalinity SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_alkalinity_method water_alkalinity_method skos:exactMatch mixs:alkalinity_method alkalinity_method SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_alkyl_diethers water_alkyl_diethers skos:exactMatch mixs:alkyl_diethers alkyl_diethers SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_aminopept_act water_aminopept_act skos:exactMatch mixs:aminopept_act aminopept_act SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_ammonium water_ammonium skos:exactMatch mixs:ammonium ammonium SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_bacterial_carbon_prod water_bacterial_carbon_prod skos:exactMatch mixs:bacteria_carb_prod bacteria_carb_prod SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_bishomohopanol water_bishomohopanol skos:exactMatch mixs:bishomohopanol bishomohopanol SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_bromide water_bromide skos:exactMatch mixs:bromide bromide SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_calcium water_calcium skos:exactMatch mixs:calcium calcium SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_carbon_nitrog_ratio water_carbon_nitrog_ratio skos:exactMatch mixs:carb_nitro_ratio carb_nitro_ratio SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_chem_administration water_chem_administration skos:exactMatch mixs:chem_administration chem_administration SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_chloride water_chloride skos:exactMatch mixs:chloride chloride SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_density water_density skos:exactMatch mixs:density density SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diether_lipids water_diether_lipids skos:exactMatch mixs:diether_lipids diether_lipids SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_carbon_dioxide water_diss_carbon_dioxide skos:exactMatch mixs:diss_carb_dioxide diss_carb_dioxide SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_hydrogen water_diss_hydrogen skos:exactMatch mixs:diss_hydrogen diss_hydrogen SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_inorg_carbon water_diss_inorg_carbon skos:exactMatch mixs:diss_inorg_carb diss_inorg_carb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_inorg_nitro water_diss_inorg_nitro skos:exactMatch mixs:diss_inorg_nitro diss_inorg_nitro SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_inorg_phosphorus water_diss_inorg_phosphorus skos:exactMatch mixs:diss_inorg_phosp diss_inorg_phosp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_org_carbon water_diss_org_carbon skos:exactMatch mixs:diss_org_carb diss_org_carb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_diss_org_nitrogen water_diss_org_nitrogen skos:exactMatch mixs:diss_org_nitro diss_org_nitro SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_glucosidase_activity water_glucosidase_activity skos:exactMatch mixs:glucosidase_act glucosidase_act SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_magnesium water_magnesium skos:exactMatch mixs:magnesium magnesium SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_mean_frict_vel water_mean_frict_vel skos:exactMatch mixs:mean_frict_vel mean_frict_vel SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_mean_peak_frict_vel water_mean_peak_frict_vel skos:exactMatch mixs:mean_peak_frict_vel mean_peak_frict_vel SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_misc_parameter water_misc_parameter skos:exactMatch mixs:misc_param misc_param SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_n_alkanes water_n_alkanes skos:exactMatch mixs:n_alkanes n_alkanes SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_nitrite water_nitrite skos:exactMatch mixs:nitrite nitrite SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_org_matter water_org_matter skos:exactMatch mixs:org_matter org_matter SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_org_nitrogen water_org_nitrogen skos:exactMatch mixs:org_nitro org_nitro SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_organism_count water_organism_count skos:exactMatch mixs:organism_count organism_count SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_oxy_stat_sample water_oxy_stat_sample skos:exactMatch mixs:oxy_stat_samp oxy_stat_samp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_part_org_carbon water_part_org_carbon skos:exactMatch mixs:part_org_carb part_org_carb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_perturbation water_perturbation skos:exactMatch mixs:perturbation perturbation SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_petroleum_hydrocarbon water_petroleum_hydrocarbon skos:exactMatch mixs:petroleum_hydrocarb petroleum_hydrocarb SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_phaeopigments water_phaeopigments skos:exactMatch mixs:phaeopigments phaeopigments SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_phosplipid_fatt_acid water_phosplipid_fatt_acid skos:exactMatch mixs:phosplipid_fatt_acid phosplipid_fatt_acid SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_potassium water_potassium skos:exactMatch mixs:potassium potassium SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_redox_potential water_redox_potential skos:exactMatch mixs:redox_potential redox_potential SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_samp_store_dur water_samp_store_dur skos:exactMatch mixs:samp_store_dur samp_store_dur SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_samp_store_loc water_samp_store_loc skos:exactMatch mixs:samp_store_loc samp_store_loc SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_samp_store_temp water_samp_store_temp skos:exactMatch mixs:samp_store_temp samp_store_temp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_size_frac_low water_size_frac_low skos:exactMatch mixs:size_frac_low size_frac_low SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_size_frac_up water_size_frac_up skos:exactMatch mixs:size_frac_up size_frac_up SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_sodium water_sodium skos:exactMatch mixs:sodium sodium SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_sulfate water_sulfate skos:exactMatch mixs:sulfate sulfate SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_sulfide water_sulfide skos:exactMatch mixs:sulfide sulfide SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_tidal_stage water_tidal_stage skos:exactMatch mixs:tidal_stage tidal_stage SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_tot_depth_water_col water_tot_depth_water_col skos:exactMatch mixs:tot_depth_water_col tot_depth_water_col SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_tot_diss_nitro water_tot_diss_nitro skos:exactMatch mixs:tot_diss_nitro tot_diss_nitro SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_tot_phosphorus water_tot_phosphorus skos:exactMatch mixs:tot_phosp tot_phosp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:water_turbidity water_turbidity skos:exactMatch mixs:turbidity turbidity SSSOMC:HumanCurated gold.vocab mixs 1 . \ No newline at end of file diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index 00ef32abdd..888b44f3da 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-06-21T09:39:03 +# Generation date: 2024-07-18T12:38:28 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc @@ -298,7 +298,7 @@ class MetatranscriptomeAnnotationActivityId(WorkflowExecutionActivityId): pass -class MetatranscriptomeActivityId(WorkflowExecutionActivityId): +class MetatranscriptomeExpressionAnalysisId(WorkflowExecutionActivityId): pass @@ -414,7 +414,9 @@ class Database(YAMLRoot): metagenome_assembly_set: Optional[Union[Dict[Union[str, MetagenomeAssemblyId], Union[dict, "MetagenomeAssembly"]], List[Union[dict, "MetagenomeAssembly"]]]] = empty_dict() metagenome_sequencing_activity_set: Optional[Union[Dict[Union[str, MetagenomeSequencingActivityId], Union[dict, "MetagenomeSequencingActivity"]], List[Union[dict, "MetagenomeSequencingActivity"]]]] = empty_dict() metaproteomics_analysis_activity_set: Optional[Union[Dict[Union[str, MetaproteomicsAnalysisActivityId], Union[dict, "MetaproteomicsAnalysisActivity"]], List[Union[dict, "MetaproteomicsAnalysisActivity"]]]] = empty_dict() - metatranscriptome_activity_set: Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]] = empty_dict() + metatranscriptome_annotation_set: Optional[Union[Dict[Union[str, MetatranscriptomeAnnotationActivityId], Union[dict, "MetatranscriptomeAnnotationActivity"]], List[Union[dict, "MetatranscriptomeAnnotationActivity"]]]] = empty_dict() + metatranscriptome_assembly_set: Optional[Union[Dict[Union[str, MetatranscriptomeAssemblyId], Union[dict, "MetatranscriptomeAssembly"]], List[Union[dict, "MetatranscriptomeAssembly"]]]] = empty_dict() + metatranscriptome_expression_analysis_set: Optional[Union[Dict[Union[str, MetatranscriptomeExpressionAnalysisId], Union[dict, "MetatranscriptomeExpressionAnalysis"]], List[Union[dict, "MetatranscriptomeExpressionAnalysis"]]]] = empty_dict() nom_analysis_activity_set: Optional[Union[Dict[Union[str, NomAnalysisActivityId], Union[dict, "NomAnalysisActivity"]], List[Union[dict, "NomAnalysisActivity"]]]] = empty_dict() omics_processing_set: Optional[Union[Dict[Union[str, OmicsProcessingId], Union[dict, "OmicsProcessing"]], List[Union[dict, "OmicsProcessing"]]]] = empty_dict() planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict() @@ -461,7 +463,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self._normalize_inlined_as_list(slot_name="metaproteomics_analysis_activity_set", slot_type=MetaproteomicsAnalysisActivity, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="metatranscriptome_activity_set", slot_type=MetatranscriptomeActivity, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="metatranscriptome_annotation_set", slot_type=MetatranscriptomeAnnotationActivity, key_name="id", keyed=True) + + self._normalize_inlined_as_list(slot_name="metatranscriptome_assembly_set", slot_type=MetatranscriptomeAssembly, key_name="id", keyed=True) + + self._normalize_inlined_as_list(slot_name="metatranscriptome_expression_analysis_set", slot_type=MetatranscriptomeExpressionAnalysis, key_name="id", keyed=True) self._normalize_inlined_as_list(slot_name="nom_analysis_activity_set", slot_type=NomAnalysisActivity, key_name="id", keyed=True) @@ -1048,7 +1054,8 @@ class Biosample(MaterialEntity): env_broad_scale: Union[dict, "ControlledIdentifiedTermValue"] = None env_local_scale: Union[dict, "ControlledIdentifiedTermValue"] = None env_medium: Union[dict, "ControlledIdentifiedTermValue"] = None - host_disease_stat: Optional[Union[dict, "TextValue"]] = None + samp_collec_method: Optional[str] = None + samp_collec_device: Optional[str] = None neon_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list() host_taxid: Optional[Union[dict, "ControlledIdentifiedTermValue"]] = None embargoed: Optional[Union[bool, Bool]] = None @@ -1063,79 +1070,79 @@ class Biosample(MaterialEntity): emsl_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list() igsn_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list() abs_air_humidity: Optional[Union[dict, "QuantityValue"]] = None - add_recov_method: Optional[Union[dict, "TextValue"]] = None + add_recov_method: Optional[str] = None additional_info: Optional[Union[dict, "TextValue"]] = None - address: Optional[Union[dict, "TextValue"]] = None + address: Optional[str] = None adj_room: Optional[Union[dict, "TextValue"]] = None - aero_struc: Optional[Union[dict, "TextValue"]] = None + aero_struc: Optional[Union[str, "AEROSTRUCENUM"]] = None agrochem_addition: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - air_PM_concen: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - air_temp: Optional[Union[dict, "QuantityValue"]] = None + air_PM_concen: Optional[Union[str, List[str]]] = empty_list() + air_temp: Optional[Union[dict, "TextValue"]] = None air_temp_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - al_sat: Optional[Union[dict, "QuantityValue"]] = None + al_sat: Optional[Union[dict, "TextValue"]] = None al_sat_meth: Optional[Union[dict, "TextValue"]] = None - alkalinity: Optional[Union[dict, "QuantityValue"]] = None + alkalinity: Optional[Union[dict, "TextValue"]] = None alkalinity_method: Optional[Union[dict, "TextValue"]] = None - alkyl_diethers: Optional[Union[dict, "QuantityValue"]] = None - alt: Optional[Union[dict, "QuantityValue"]] = None - aminopept_act: Optional[Union[dict, "QuantityValue"]] = None + alkyl_diethers: Optional[Union[dict, "TextValue"]] = None + alt: Optional[Union[dict, "TextValue"]] = None + aminopept_act: Optional[Union[dict, "TextValue"]] = None ammonium: Optional[Union[dict, "QuantityValue"]] = None ammonium_nitrogen: Optional[Union[dict, "QuantityValue"]] = None - amount_light: Optional[Union[dict, "QuantityValue"]] = None + amount_light: Optional[Union[dict, "TextValue"]] = None ances_data: Optional[Union[dict, "TextValue"]] = None - annual_precpt: Optional[Union[dict, "QuantityValue"]] = None - annual_temp: Optional[Union[dict, "QuantityValue"]] = None + annual_precpt: Optional[Union[dict, "TextValue"]] = None + annual_temp: Optional[Union[dict, "TextValue"]] = None antibiotic_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - api: Optional[Union[dict, "QuantityValue"]] = None - arch_struc: Optional[Union[str, "ArchStrucEnum"]] = None + api: Optional[Union[dict, "TextValue"]] = None + arch_struc: Optional[Union[str, "ARCHSTRUCENUM"]] = None aromatics_pc: Optional[Union[dict, "TextValue"]] = None asphaltenes_pc: Optional[Union[dict, "TextValue"]] = None atmospheric_data: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - avg_dew_point: Optional[Union[dict, "QuantityValue"]] = None + avg_dew_point: Optional[Union[dict, "TextValue"]] = None avg_occup: Optional[Union[dict, "TextValue"]] = None avg_temp: Optional[Union[dict, "QuantityValue"]] = None - bac_prod: Optional[Union[dict, "QuantityValue"]] = None - bac_resp: Optional[Union[dict, "QuantityValue"]] = None - bacteria_carb_prod: Optional[Union[dict, "QuantityValue"]] = None - barometric_press: Optional[Union[dict, "QuantityValue"]] = None + bac_prod: Optional[Union[dict, "TextValue"]] = None + bac_resp: Optional[Union[dict, "TextValue"]] = None + bacteria_carb_prod: Optional[Union[dict, "TextValue"]] = None + barometric_press: Optional[Union[dict, "TextValue"]] = None basin: Optional[Union[dict, "TextValue"]] = None bathroom_count: Optional[Union[dict, "TextValue"]] = None bedroom_count: Optional[Union[dict, "TextValue"]] = None - benzene: Optional[Union[dict, "QuantityValue"]] = None - biochem_oxygen_dem: Optional[Union[dict, "QuantityValue"]] = None - biocide: Optional[Union[dict, "TextValue"]] = None + benzene: Optional[Union[dict, "TextValue"]] = None + biochem_oxygen_dem: Optional[Union[dict, "TextValue"]] = None + biocide: Optional[str] = None biocide_admin_method: Optional[Union[dict, "TextValue"]] = None - biol_stat: Optional[Union[str, "BiolStatEnum"]] = None + biol_stat: Optional[str] = None biomass: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - biotic_regm: Optional[Union[dict, "TextValue"]] = None - biotic_relationship: Optional[Union[str, "BioticRelationshipEnum"]] = None - bishomohopanol: Optional[Union[dict, "QuantityValue"]] = None - blood_press_diast: Optional[Union[dict, "QuantityValue"]] = None - blood_press_syst: Optional[Union[dict, "QuantityValue"]] = None - bromide: Optional[Union[dict, "QuantityValue"]] = None - build_docs: Optional[Union[str, "BuildDocsEnum"]] = None - build_occup_type: Optional[Union[Union[str, "BuildOccupTypeEnum"], List[Union[str, "BuildOccupTypeEnum"]]]] = empty_list() - building_setting: Optional[Union[str, "BuildingSettingEnum"]] = None - built_struc_age: Optional[Union[dict, "QuantityValue"]] = None - built_struc_set: Optional[Union[dict, "TextValue"]] = None + biotic_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() + biotic_relationship: Optional[Union[str, "BIOTICRELATIONSHIPENUM"]] = None + bishomohopanol: Optional[Union[dict, "TextValue"]] = None + blood_press_diast: Optional[Union[dict, "TextValue"]] = None + blood_press_syst: Optional[Union[dict, "TextValue"]] = None + bromide: Optional[Union[dict, "TextValue"]] = None + build_docs: Optional[Union[str, "BUILDDOCSENUM"]] = None + build_occup_type: Optional[Union[Union[str, "BUILDOCCUPTYPEENUM"], List[Union[str, "BUILDOCCUPTYPEENUM"]]]] = empty_list() + building_setting: Optional[Union[str, "BUILDINGSETTINGENUM"]] = None + built_struc_age: Optional[Union[dict, "TextValue"]] = None + built_struc_set: Optional[Union[str, "BUILTSTRUCSETENUM"]] = None built_struc_type: Optional[Union[dict, "TextValue"]] = None calcium: Optional[Union[dict, "QuantityValue"]] = None - carb_dioxide: Optional[Union[dict, "QuantityValue"]] = None - carb_monoxide: Optional[Union[dict, "QuantityValue"]] = None + carb_dioxide: Optional[Union[dict, "TextValue"]] = None + carb_monoxide: Optional[Union[dict, "TextValue"]] = None carb_nitro_ratio: Optional[Union[dict, "QuantityValue"]] = None - ceil_area: Optional[Union[dict, "QuantityValue"]] = None - ceil_cond: Optional[Union[str, "CeilCondEnum"]] = None - ceil_finish_mat: Optional[Union[str, "CeilFinishMatEnum"]] = None - ceil_struc: Optional[Union[dict, "TextValue"]] = None - ceil_texture: Optional[Union[str, "CeilTextureEnum"]] = None - ceil_thermal_mass: Optional[Union[dict, "QuantityValue"]] = None - ceil_type: Optional[Union[str, "CeilTypeEnum"]] = None - ceil_water_mold: Optional[Union[dict, "TextValue"]] = None + ceil_area: Optional[Union[dict, "TextValue"]] = None + ceil_cond: Optional[Union[str, "SHAREDENUM3"]] = None + ceil_finish_mat: Optional[Union[str, "CEILFINISHMATENUM"]] = None + ceil_struc: Optional[Union[str, "CEILSTRUCENUM"]] = None + ceil_texture: Optional[Union[str, "SHAREDENUM4"]] = None + ceil_thermal_mass: Optional[Union[dict, "TextValue"]] = None + ceil_type: Optional[Union[str, "CEILTYPEENUM"]] = None + ceil_water_mold: Optional[Union[str, "SHAREDENUM1"]] = None chem_administration: Optional[Union[Union[dict, "ControlledTermValue"], List[Union[dict, "ControlledTermValue"]]]] = empty_list() chem_mutagen: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - chem_oxygen_dem: Optional[Union[dict, "QuantityValue"]] = None + chem_oxygen_dem: Optional[Union[dict, "TextValue"]] = None chem_treat_method: Optional[str] = None - chem_treatment: Optional[Union[dict, "TextValue"]] = None + chem_treatment: Optional[str] = None chimera_check: Optional[Union[dict, "TextValue"]] = None chloride: Optional[Union[dict, "QuantityValue"]] = None chlorophyll: Optional[Union[dict, "QuantityValue"]] = None @@ -1143,256 +1150,251 @@ class Biosample(MaterialEntity): collection_date: Optional[Union[dict, "TimestampValue"]] = None conduc: Optional[Union[dict, "QuantityValue"]] = None cool_syst_id: Optional[Union[dict, "TextValue"]] = None - core_field: Optional[str] = None - crop_rotation: Optional[Union[dict, "TextValue"]] = None - cult_root_med: Optional[Union[dict, "TextValue"]] = None - cur_land_use: Optional[Union[str, "CurLandUseEnum"]] = None + crop_rotation: Optional[str] = None + cult_root_med: Optional[str] = None + cur_land_use: Optional[str] = None cur_vegetation: Optional[Union[dict, "TextValue"]] = None cur_vegetation_meth: Optional[Union[dict, "TextValue"]] = None date_last_rain: Optional[Union[dict, "TimestampValue"]] = None - density: Optional[Union[dict, "QuantityValue"]] = None - depos_env: Optional[Union[str, "DeposEnvEnum"]] = None + density: Optional[Union[dict, "TextValue"]] = None + depos_env: Optional[Union[str, "DEPOSENVENUM"]] = None depth: Optional[Union[dict, "QuantityValue"]] = None - dew_point: Optional[Union[dict, "QuantityValue"]] = None + dew_point: Optional[Union[dict, "TextValue"]] = None diether_lipids: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - diss_carb_dioxide: Optional[Union[dict, "QuantityValue"]] = None - diss_hydrogen: Optional[Union[dict, "QuantityValue"]] = None + diss_carb_dioxide: Optional[Union[dict, "TextValue"]] = None + diss_hydrogen: Optional[Union[dict, "TextValue"]] = None diss_inorg_carb: Optional[Union[dict, "QuantityValue"]] = None diss_inorg_nitro: Optional[Union[dict, "QuantityValue"]] = None - diss_inorg_phosp: Optional[Union[dict, "QuantityValue"]] = None + diss_inorg_phosp: Optional[Union[dict, "TextValue"]] = None diss_iron: Optional[Union[dict, "QuantityValue"]] = None diss_org_carb: Optional[Union[dict, "QuantityValue"]] = None - diss_org_nitro: Optional[Union[dict, "QuantityValue"]] = None + diss_org_nitro: Optional[Union[dict, "TextValue"]] = None diss_oxygen: Optional[Union[dict, "QuantityValue"]] = None - diss_oxygen_fluid: Optional[Union[dict, "QuantityValue"]] = None + diss_oxygen_fluid: Optional[Union[dict, "TextValue"]] = None dna_cont_well: Optional[str] = None - door_comp_type: Optional[Union[str, "DoorCompTypeEnum"]] = None - door_cond: Optional[Union[str, "DoorCondEnum"]] = None - door_direct: Optional[Union[str, "DoorDirectEnum"]] = None - door_loc: Optional[Union[str, "DoorLocEnum"]] = None - door_mat: Optional[Union[str, "DoorMatEnum"]] = None - door_move: Optional[Union[str, "DoorMoveEnum"]] = None - door_size: Optional[Union[dict, "QuantityValue"]] = None - door_type: Optional[Union[str, "DoorTypeEnum"]] = None - door_type_metal: Optional[Union[str, "DoorTypeMetalEnum"]] = None - door_type_wood: Optional[Union[str, "DoorTypeWoodEnum"]] = None - door_water_mold: Optional[Union[dict, "TextValue"]] = None - down_par: Optional[Union[dict, "QuantityValue"]] = None - drainage_class: Optional[Union[str, "DrainageClassEnum"]] = None - drawings: Optional[Union[str, "DrawingsEnum"]] = None + door_comp_type: Optional[Union[str, "DOORCOMPTYPEENUM"]] = None + door_cond: Optional[Union[str, "SHAREDENUM2"]] = None + door_direct: Optional[Union[str, "DOORDIRECTENUM"]] = None + door_loc: Optional[Union[str, "SHAREDENUM0"]] = None + door_mat: Optional[Union[str, "DOORMATENUM"]] = None + door_move: Optional[Union[str, "DOORMOVEENUM"]] = None + door_size: Optional[Union[dict, "TextValue"]] = None + door_type: Optional[Union[str, "DOORTYPEENUM"]] = None + door_type_metal: Optional[Union[str, "DOORTYPEMETALENUM"]] = None + door_type_wood: Optional[str] = None + door_water_mold: Optional[Union[str, "SHAREDENUM1"]] = None + down_par: Optional[Union[dict, "TextValue"]] = None + drainage_class: Optional[Union[str, "DRAINAGECLASSENUM"]] = None + drawings: Optional[Union[str, "DRAWINGSENUM"]] = None ecosystem: Optional[str] = None ecosystem_category: Optional[str] = None ecosystem_subtype: Optional[str] = None ecosystem_type: Optional[str] = None - efficiency_percent: Optional[Union[dict, "QuantityValue"]] = None + efficiency_percent: Optional[Union[dict, "TextValue"]] = None elev: Optional[float] = None elevator: Optional[Union[dict, "TextValue"]] = None emulsions: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() env_package: Optional[Union[dict, "TextValue"]] = None - environment_field: Optional[str] = None escalator: Optional[Union[dict, "TextValue"]] = None - ethylbenzene: Optional[Union[dict, "QuantityValue"]] = None - exp_duct: Optional[Union[dict, "QuantityValue"]] = None + ethylbenzene: Optional[Union[dict, "TextValue"]] = None + exp_duct: Optional[Union[dict, "TextValue"]] = None exp_pipe: Optional[Union[dict, "QuantityValue"]] = None experimental_factor: Optional[Union[dict, "ControlledTermValue"]] = None ext_door: Optional[Union[dict, "TextValue"]] = None - ext_wall_orient: Optional[Union[str, "ExtWallOrientEnum"]] = None - ext_window_orient: Optional[Union[str, "ExtWindowOrientEnum"]] = None + ext_wall_orient: Optional[Union[str, "SHAREDENUM0"]] = None + ext_window_orient: Optional[Union[str, "SHAREDENUM0"]] = None extreme_event: Optional[str] = None - fao_class: Optional[Union[str, "FaoClassEnum"]] = None + fao_class: Optional[Union[str, "FAOCLASSENUM"]] = None fertilizer_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() field: Optional[Union[dict, "TextValue"]] = None - filter_type: Optional[Union[Union[str, "FilterTypeEnum"], List[Union[str, "FilterTypeEnum"]]]] = empty_list() + filter_type: Optional[Union[Union[str, "FILTERTYPEENUM"], List[Union[str, "FILTERTYPEENUM"]]]] = empty_list() fire: Optional[str] = None - fireplace_type: Optional[Union[dict, "TextValue"]] = None + fireplace_type: Optional[Union[str, "FIREPLACETYPEENUM"]] = None flooding: Optional[str] = None - floor_age: Optional[Union[dict, "QuantityValue"]] = None - floor_area: Optional[Union[dict, "QuantityValue"]] = None - floor_cond: Optional[Union[str, "FloorCondEnum"]] = None + floor_age: Optional[Union[dict, "TextValue"]] = None + floor_area: Optional[Union[dict, "TextValue"]] = None + floor_cond: Optional[Union[str, "SHAREDENUM3"]] = None floor_count: Optional[Union[dict, "TextValue"]] = None - floor_finish_mat: Optional[Union[str, "FloorFinishMatEnum"]] = None - floor_struc: Optional[Union[str, "FloorStrucEnum"]] = None - floor_thermal_mass: Optional[Union[dict, "QuantityValue"]] = None - floor_water_mold: Optional[Union[str, "FloorWaterMoldEnum"]] = None - fluor: Optional[Union[dict, "QuantityValue"]] = None + floor_finish_mat: Optional[str] = None + floor_struc: Optional[Union[str, "FLOORSTRUCENUM"]] = None + floor_thermal_mass: Optional[Union[dict, "TextValue"]] = None + floor_water_mold: Optional[Union[str, "FLOORWATERMOLDENUM"]] = None + fluor: Optional[Union[dict, "TextValue"]] = None freq_clean: Optional[Union[dict, "QuantityValue"]] = None freq_cook: Optional[Union[dict, "QuantityValue"]] = None fungicide_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - furniture: Optional[Union[str, "FurnitureEnum"]] = None + furniture: Optional[Union[str, "FURNITUREENUM"]] = None gaseous_environment: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() gaseous_substances: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - gender_restroom: Optional[Union[str, "GenderRestroomEnum"]] = None - genetic_mod: Optional[Union[dict, "TextValue"]] = None + gender_restroom: Optional[Union[str, "GENDERRESTROOMENUM"]] = None + genetic_mod: Optional[str] = None geo_loc_name: Optional[Union[dict, "TextValue"]] = None - glucosidase_act: Optional[Union[dict, "QuantityValue"]] = None + glucosidase_act: Optional[Union[dict, "TextValue"]] = None gravidity: Optional[Union[dict, "TextValue"]] = None gravity: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() growth_facil: Optional[Union[dict, "ControlledTermValue"]] = None - growth_habit: Optional[Union[str, "GrowthHabitEnum"]] = None + growth_habit: Optional[Union[str, "GROWTHHABITENUM"]] = None growth_hormone_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() hall_count: Optional[Union[dict, "TextValue"]] = None - handidness: Optional[Union[str, "HandidnessEnum"]] = None - hc_produced: Optional[Union[str, "HcProducedEnum"]] = None - hcr: Optional[Union[str, "HcrEnum"]] = None - hcr_fw_salinity: Optional[Union[dict, "QuantityValue"]] = None - hcr_geol_age: Optional[Union[str, "HcrGeolAgeEnum"]] = None + handidness: Optional[Union[str, "HANDIDNESSENUM"]] = None + hc_produced: Optional[Union[str, "HCPRODUCEDENUM"]] = None + hcr: Optional[Union[str, "HCRENUM"]] = None + hcr_fw_salinity: Optional[Union[dict, "TextValue"]] = None + hcr_geol_age: Optional[Union[str, "SHAREDENUM5"]] = None hcr_pressure: Optional[Union[dict, "TextValue"]] = None hcr_temp: Optional[Union[dict, "TextValue"]] = None - heat_cool_type: Optional[Union[Union[str, "HeatCoolTypeEnum"], List[Union[str, "HeatCoolTypeEnum"]]]] = empty_list() - heat_deliv_loc: Optional[Union[str, "HeatDelivLocEnum"]] = None + heat_cool_type: Optional[Union[Union[str, "HEATCOOLTYPEENUM"], List[Union[str, "HEATCOOLTYPEENUM"]]]] = empty_list() + heat_deliv_loc: Optional[Union[str, "SHAREDENUM0"]] = None heat_sys_deliv_meth: Optional[str] = None heat_system_id: Optional[Union[dict, "TextValue"]] = None heavy_metals: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() heavy_metals_meth: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - height_carper_fiber: Optional[Union[dict, "QuantityValue"]] = None + height_carper_fiber: Optional[Union[dict, "TextValue"]] = None herbicide_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() horizon_meth: Optional[Union[dict, "TextValue"]] = None host_age: Optional[Union[dict, "QuantityValue"]] = None host_body_habitat: Optional[Union[dict, "TextValue"]] = None host_body_product: Optional[Union[dict, "ControlledTermValue"]] = None host_body_site: Optional[Union[dict, "ControlledTermValue"]] = None - host_body_temp: Optional[Union[dict, "QuantityValue"]] = None + host_body_temp: Optional[Union[dict, "TextValue"]] = None host_color: Optional[Union[dict, "TextValue"]] = None host_common_name: Optional[Union[dict, "TextValue"]] = None host_diet: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() host_dry_mass: Optional[Union[dict, "QuantityValue"]] = None - host_family_relation: Optional[Union[str, List[str]]] = empty_list() host_genotype: Optional[Union[dict, "TextValue"]] = None host_growth_cond: Optional[Union[dict, "TextValue"]] = None host_height: Optional[Union[dict, "QuantityValue"]] = None - host_last_meal: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - host_length: Optional[Union[dict, "QuantityValue"]] = None + host_last_meal: Optional[Union[str, List[str]]] = empty_list() + host_length: Optional[Union[dict, "TextValue"]] = None host_life_stage: Optional[Union[dict, "TextValue"]] = None host_phenotype: Optional[Union[dict, "ControlledTermValue"]] = None - host_sex: Optional[Union[str, "HostSexEnum"]] = None + host_sex: Optional[str] = None host_shape: Optional[Union[dict, "TextValue"]] = None host_subject_id: Optional[Union[dict, "TextValue"]] = None host_subspecf_genlin: Optional[Union[str, List[str]]] = empty_list() host_substrate: Optional[Union[dict, "TextValue"]] = None host_symbiont: Optional[Union[str, List[str]]] = empty_list() - host_tot_mass: Optional[Union[dict, "QuantityValue"]] = None - host_wet_mass: Optional[Union[dict, "QuantityValue"]] = None + host_tot_mass: Optional[Union[dict, "TextValue"]] = None + host_wet_mass: Optional[Union[dict, "TextValue"]] = None humidity: Optional[Union[dict, "QuantityValue"]] = None humidity_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - indoor_space: Optional[Union[str, "IndoorSpaceEnum"]] = None - indoor_surf: Optional[Union[str, "IndoorSurfEnum"]] = None - indust_eff_percent: Optional[Union[dict, "QuantityValue"]] = None + indoor_space: Optional[Union[str, "INDOORSPACEENUM"]] = None + indoor_surf: Optional[Union[str, "INDOORSURFENUM"]] = None + indust_eff_percent: Optional[Union[dict, "TextValue"]] = None inorg_particles: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - inside_lux: Optional[Union[dict, "QuantityValue"]] = None - int_wall_cond: Optional[Union[str, "IntWallCondEnum"]] = None - investigation_field: Optional[str] = None + inside_lux: Optional[Union[dict, "TextValue"]] = None + int_wall_cond: Optional[Union[str, "SHAREDENUM3"]] = None iw_bt_date_well: Optional[Union[dict, "TimestampValue"]] = None - iwf: Optional[Union[dict, "QuantityValue"]] = None + iwf: Optional[float] = None last_clean: Optional[Union[dict, "TimestampValue"]] = None lat_lon: Optional[Union[dict, "GeolocationValue"]] = None lbc_thirty: Optional[Union[dict, "QuantityValue"]] = None lbceq: Optional[Union[dict, "QuantityValue"]] = None - light_intensity: Optional[Union[dict, "QuantityValue"]] = None + light_intensity: Optional[Union[dict, "TextValue"]] = None light_regm: Optional[Union[dict, "TextValue"]] = None - light_type: Optional[Union[Union[str, "LightTypeEnum"], List[Union[str, "LightTypeEnum"]]]] = empty_list() + light_type: Optional[Union[Union[str, "LIGHTTYPEENUM"], List[Union[str, "LIGHTTYPEENUM"]]]] = empty_list() link_addit_analys: Optional[Union[dict, "TextValue"]] = None - link_class_info: Optional[Union[dict, "TextValue"]] = None + link_class_info: Optional[str] = None link_climate_info: Optional[Union[dict, "TextValue"]] = None - lithology: Optional[Union[str, "LithologyEnum"]] = None - local_class: Optional[Union[dict, "TextValue"]] = None + lithology: Optional[Union[str, "LITHOLOGYENUM"]] = None + local_class: Optional[str] = None local_class_meth: Optional[Union[dict, "TextValue"]] = None magnesium: Optional[Union[dict, "QuantityValue"]] = None manganese: Optional[Union[dict, "QuantityValue"]] = None max_occup: Optional[Union[dict, "QuantityValue"]] = None - mean_frict_vel: Optional[Union[dict, "QuantityValue"]] = None - mean_peak_frict_vel: Optional[Union[dict, "QuantityValue"]] = None - mech_struc: Optional[Union[str, "MechStrucEnum"]] = None - mechanical_damage: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - methane: Optional[Union[dict, "QuantityValue"]] = None + mean_frict_vel: Optional[Union[dict, "TextValue"]] = None + mean_peak_frict_vel: Optional[Union[dict, "TextValue"]] = None + mech_struc: Optional[Union[str, "MECHSTRUCENUM"]] = None + mechanical_damage: Optional[Union[str, List[str]]] = empty_list() + methane: Optional[Union[dict, "TextValue"]] = None micro_biomass_meth: Optional[str] = None - microbial_biomass: Optional[Union[dict, "QuantityValue"]] = None + microbial_biomass: Optional[Union[dict, "TextValue"]] = None mineral_nutr_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() misc_param: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() n_alkanes: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() nitrate: Optional[Union[dict, "QuantityValue"]] = None nitrate_nitrogen: Optional[Union[dict, "QuantityValue"]] = None - nitrite: Optional[Union[dict, "QuantityValue"]] = None + nitrite: Optional[Union[dict, "TextValue"]] = None nitrite_nitrogen: Optional[Union[dict, "QuantityValue"]] = None nitro: Optional[Union[dict, "QuantityValue"]] = None non_min_nutr_regm: Optional[Union[str, List[str]]] = empty_list() nucl_acid_amp: Optional[Union[dict, "TextValue"]] = None nucl_acid_ext: Optional[Union[dict, "TextValue"]] = None - nucleic_acid_sequence_source_field: Optional[str] = None number_pets: Optional[Union[dict, "QuantityValue"]] = None number_plants: Optional[Union[dict, "QuantityValue"]] = None number_resident: Optional[Union[dict, "QuantityValue"]] = None occup_density_samp: Optional[Union[dict, "QuantityValue"]] = None - occup_document: Optional[Union[str, "OccupDocumentEnum"]] = None + occup_document: Optional[Union[str, "OCCUPDOCUMENTENUM"]] = None occup_samp: Optional[Union[dict, "QuantityValue"]] = None org_carb: Optional[Union[dict, "QuantityValue"]] = None org_count_qpcr_info: Optional[str] = None - org_matter: Optional[Union[dict, "QuantityValue"]] = None - org_nitro: Optional[Union[dict, "QuantityValue"]] = None + org_matter: Optional[Union[dict, "TextValue"]] = None + org_nitro: Optional[Union[dict, "TextValue"]] = None org_particles: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() organism_count: Optional[Union[Union[dict, "QuantityValue"], List[Union[dict, "QuantityValue"]]]] = empty_list() - owc_tvdss: Optional[Union[dict, "QuantityValue"]] = None - oxy_stat_samp: Optional[Union[str, "OxyStatSampEnum"]] = None - oxygen: Optional[Union[dict, "QuantityValue"]] = None - part_org_carb: Optional[Union[dict, "QuantityValue"]] = None - part_org_nitro: Optional[Union[dict, "QuantityValue"]] = None + owc_tvdss: Optional[Union[dict, "TextValue"]] = None + oxy_stat_samp: Optional[Union[str, "OXYSTATSAMPENUM"]] = None + oxygen: Optional[Union[dict, "TextValue"]] = None + part_org_carb: Optional[Union[dict, "TextValue"]] = None + part_org_nitro: Optional[Union[dict, "TextValue"]] = None particle_class: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - pcr_cond: Optional[Union[dict, "TextValue"]] = None - pcr_primers: Optional[Union[dict, "TextValue"]] = None + pcr_cond: Optional[str] = None + pcr_primers: Optional[str] = None permeability: Optional[Union[dict, "TextValue"]] = None perturbation: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() pesticide_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - petroleum_hydrocarb: Optional[Union[dict, "QuantityValue"]] = None + petroleum_hydrocarb: Optional[Union[dict, "TextValue"]] = None ph: Optional[float] = None ph_meth: Optional[Union[dict, "TextValue"]] = None ph_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() phaeopigments: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - phosphate: Optional[Union[dict, "QuantityValue"]] = None + phosphate: Optional[Union[dict, "TextValue"]] = None phosplipid_fatt_acid: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() photon_flux: Optional[Union[dict, "QuantityValue"]] = None plant_growth_med: Optional[Union[dict, "ControlledTermValue"]] = None - plant_product: Optional[Union[dict, "TextValue"]] = None - plant_sex: Optional[Union[str, "PlantSexEnum"]] = None + plant_product: Optional[str] = None + plant_sex: Optional[Union[str, "PLANTSEXENUM"]] = None plant_struc: Optional[Union[dict, "ControlledTermValue"]] = None pollutants: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - pool_dna_extracts: Optional[Union[dict, "TextValue"]] = None + pool_dna_extracts: Optional[str] = None porosity: Optional[Union[dict, "TextValue"]] = None potassium: Optional[Union[dict, "QuantityValue"]] = None - pour_point: Optional[Union[dict, "QuantityValue"]] = None - pre_treatment: Optional[Union[dict, "TextValue"]] = None + pour_point: Optional[Union[dict, "TextValue"]] = None + pre_treatment: Optional[str] = None pres_animal_insect: Optional[str] = None - pressure: Optional[Union[dict, "QuantityValue"]] = None + pressure: Optional[Union[dict, "TextValue"]] = None prev_land_use_meth: Optional[str] = None - previous_land_use: Optional[Union[dict, "TextValue"]] = None - primary_prod: Optional[Union[dict, "QuantityValue"]] = None - primary_treatment: Optional[Union[dict, "TextValue"]] = None - prod_rate: Optional[Union[dict, "QuantityValue"]] = None + previous_land_use: Optional[str] = None + primary_prod: Optional[Union[dict, "TextValue"]] = None + primary_treatment: Optional[str] = None + prod_rate: Optional[Union[dict, "TextValue"]] = None prod_start_date: Optional[Union[dict, "TimestampValue"]] = None - profile_position: Optional[Union[str, "ProfilePositionEnum"]] = None - quad_pos: Optional[Union[str, "QuadPosEnum"]] = None + profile_position: Optional[Union[str, "PROFILEPOSITIONENUM"]] = None + quad_pos: Optional[Union[str, "QUADPOSENUM"]] = None radiation_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() rainfall_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - reactor_type: Optional[Union[dict, "TextValue"]] = None - redox_potential: Optional[Union[dict, "QuantityValue"]] = None - rel_air_humidity: Optional[Union[dict, "QuantityValue"]] = None - rel_humidity_out: Optional[Union[dict, "QuantityValue"]] = None - rel_samp_loc: Optional[Union[str, "RelSampLocEnum"]] = None + reactor_type: Optional[str] = None + redox_potential: Optional[Union[dict, "TextValue"]] = None + rel_air_humidity: Optional[float] = None + rel_humidity_out: Optional[Union[dict, "TextValue"]] = None + rel_samp_loc: Optional[Union[str, "RELSAMPLOCENUM"]] = None reservoir: Optional[Union[dict, "TextValue"]] = None resins_pc: Optional[Union[dict, "TextValue"]] = None - room_air_exch_rate: Optional[Union[dict, "QuantityValue"]] = None + room_air_exch_rate: Optional[Union[dict, "TextValue"]] = None room_architec_elem: Optional[str] = None - room_condt: Optional[Union[str, "RoomCondtEnum"]] = None - room_connected: Optional[Union[str, "RoomConnectedEnum"]] = None + room_condt: Optional[Union[str, "ROOMCONDTENUM"]] = None + room_connected: Optional[Union[str, "ROOMCONNECTEDENUM"]] = None room_count: Optional[Union[dict, "TextValue"]] = None room_dim: Optional[Union[dict, "TextValue"]] = None room_door_dist: Optional[Union[dict, "TextValue"]] = None room_door_share: Optional[Union[dict, "TextValue"]] = None room_hallway: Optional[Union[dict, "TextValue"]] = None - room_loc: Optional[Union[str, "RoomLocEnum"]] = None + room_loc: Optional[Union[str, "ROOMLOCENUM"]] = None room_moist_dam_hist: Optional[int] = None room_net_area: Optional[Union[dict, "TextValue"]] = None room_occup: Optional[Union[dict, "QuantityValue"]] = None - room_samp_pos: Optional[Union[str, "RoomSampPosEnum"]] = None - room_type: Optional[Union[str, "RoomTypeEnum"]] = None + room_samp_pos: Optional[Union[str, "ROOMSAMPPOSENUM"]] = None + room_type: Optional[str] = None room_vol: Optional[Union[dict, "TextValue"]] = None room_wall_share: Optional[Union[dict, "TextValue"]] = None room_window_count: Optional[int] = None @@ -1404,15 +1406,12 @@ class Biosample(MaterialEntity): root_med_regl: Optional[Union[dict, "TextValue"]] = None root_med_solid: Optional[Union[dict, "TextValue"]] = None root_med_suppl: Optional[Union[dict, "TextValue"]] = None - salinity: Optional[Union[dict, "QuantityValue"]] = None - salinity_meth: Optional[Union[dict, "TextValue"]] = None + salinity: Optional[Union[dict, "TextValue"]] = None salt_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - samp_capt_status: Optional[Union[str, "SampCaptStatusEnum"]] = None - samp_collec_device: Optional[str] = None - samp_collec_method: Optional[str] = None - samp_collect_point: Optional[Union[str, "SampCollectPointEnum"]] = None - samp_dis_stage: Optional[Union[str, "SampDisStageEnum"]] = None - samp_floor: Optional[Union[str, "SampFloorEnum"]] = None + samp_capt_status: Optional[Union[str, "SAMPCAPTSTATUSENUM"]] = None + samp_collect_point: Optional[Union[str, "SAMPCOLLECTPOINTENUM"]] = None + samp_dis_stage: Optional[Union[str, "SAMPDISSTAGEENUM"]] = None + samp_floor: Optional[str] = None samp_loc_corr_rate: Optional[Union[dict, "TextValue"]] = None samp_mat_process: Optional[Union[dict, "ControlledTermValue"]] = None samp_md: Optional[Union[dict, "QuantityValue"]] = None @@ -1421,148 +1420,146 @@ class Biosample(MaterialEntity): samp_size: Optional[Union[dict, "QuantityValue"]] = None samp_sort_meth: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() samp_store_dur: Optional[Union[dict, "TextValue"]] = None - samp_store_loc: Optional[Union[dict, "TextValue"]] = None + samp_store_loc: Optional[str] = None samp_store_temp: Optional[Union[dict, "QuantityValue"]] = None - samp_subtype: Optional[Union[str, "SampSubtypeEnum"]] = None + samp_subtype: Optional[Union[str, "SAMPSUBTYPEENUM"]] = None samp_taxon_id: Optional[Union[dict, "ControlledIdentifiedTermValue"]] = None samp_time_out: Optional[Union[dict, "TextValue"]] = None samp_transport_cond: Optional[Union[dict, "TextValue"]] = None samp_tvdss: Optional[Union[dict, "TextValue"]] = None samp_type: Optional[Union[dict, "TextValue"]] = None - samp_vol_we_dna_ext: Optional[Union[dict, "QuantityValue"]] = None - samp_weather: Optional[Union[str, "SampWeatherEnum"]] = None + samp_vol_we_dna_ext: Optional[Union[dict, "TextValue"]] = None + samp_weather: Optional[Union[str, "SAMPWEATHERENUM"]] = None samp_well_name: Optional[Union[dict, "TextValue"]] = None saturates_pc: Optional[Union[dict, "TextValue"]] = None season: Optional[Union[dict, "TextValue"]] = None season_environment: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - season_precpt: Optional[Union[dict, "QuantityValue"]] = None - season_temp: Optional[Union[dict, "QuantityValue"]] = None - season_use: Optional[Union[str, "SeasonUseEnum"]] = None - secondary_treatment: Optional[Union[dict, "TextValue"]] = None - sediment_type: Optional[Union[str, "SedimentTypeEnum"]] = None + season_precpt: Optional[Union[dict, "TextValue"]] = None + season_temp: Optional[Union[dict, "TextValue"]] = None + season_use: Optional[Union[str, "SEASONUSEENUM"]] = None + secondary_treatment: Optional[str] = None + sediment_type: Optional[Union[str, "SEDIMENTTYPEENUM"]] = None seq_meth: Optional[Union[dict, "TextValue"]] = None - seq_quality_check: Optional[Union[dict, "TextValue"]] = None - sequencing_field: Optional[str] = None - sewage_type: Optional[Union[dict, "TextValue"]] = None + seq_quality_check: Optional[Union[str, "SEQQUALITYCHECKENUM"]] = None + sewage_type: Optional[str] = None shad_dev_water_mold: Optional[str] = None - shading_device_cond: Optional[Union[str, "ShadingDeviceCondEnum"]] = None - shading_device_loc: Optional[Union[dict, "TextValue"]] = None - shading_device_mat: Optional[Union[dict, "TextValue"]] = None - shading_device_type: Optional[Union[str, "ShadingDeviceTypeEnum"]] = None + shading_device_cond: Optional[Union[str, "SHAREDENUM2"]] = None + shading_device_loc: Optional[Union[str, "SHADINGDEVICELOCENUM"]] = None + shading_device_mat: Optional[str] = None + shading_device_type: Optional[Union[str, "SHADINGDEVICETYPEENUM"]] = None sieving: Optional[Union[dict, "TextValue"]] = None - silicate: Optional[Union[dict, "QuantityValue"]] = None + silicate: Optional[Union[dict, "TextValue"]] = None size_frac: Optional[Union[dict, "TextValue"]] = None - size_frac_low: Optional[Union[dict, "QuantityValue"]] = None - size_frac_up: Optional[Union[dict, "QuantityValue"]] = None - slope_aspect: Optional[Union[dict, "QuantityValue"]] = None - slope_gradient: Optional[Union[dict, "QuantityValue"]] = None - sludge_retent_time: Optional[Union[dict, "QuantityValue"]] = None + size_frac_low: Optional[Union[dict, "TextValue"]] = None + size_frac_up: Optional[Union[dict, "TextValue"]] = None + slope_aspect: Optional[Union[dict, "TextValue"]] = None + slope_gradient: Optional[Union[dict, "TextValue"]] = None + sludge_retent_time: Optional[Union[dict, "TextValue"]] = None sodium: Optional[Union[dict, "QuantityValue"]] = None - soil_horizon: Optional[Union[str, "SoilHorizonEnum"]] = None - soil_text_measure: Optional[Union[dict, "QuantityValue"]] = None + soil_horizon: Optional[Union[str, "SOILHORIZONENUM"]] = None soil_texture_meth: Optional[str] = None - soil_type: Optional[Union[dict, "TextValue"]] = None + soil_type: Optional[str] = None soil_type_meth: Optional[Union[dict, "TextValue"]] = None solar_irradiance: Optional[Union[dict, "QuantityValue"]] = None soluble_inorg_mat: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() soluble_org_mat: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() soluble_react_phosp: Optional[Union[dict, "QuantityValue"]] = None source_mat_id: Optional[Union[dict, "TextValue"]] = None - space_typ_state: Optional[Union[dict, "TextValue"]] = None - specific: Optional[Union[str, "SpecificEnum"]] = None + space_typ_state: Optional[Union[str, "SPACETYPSTATEENUM"]] = None + specific: Optional[Union[str, "SPECIFICENUM"]] = None specific_ecosystem: Optional[str] = None - specific_humidity: Optional[Union[dict, "QuantityValue"]] = None - sr_dep_env: Optional[Union[str, "SrDepEnvEnum"]] = None - sr_geol_age: Optional[Union[str, "SrGeolAgeEnum"]] = None - sr_kerog_type: Optional[Union[str, "SrKerogTypeEnum"]] = None - sr_lithology: Optional[Union[str, "SrLithologyEnum"]] = None + specific_humidity: Optional[Union[dict, "TextValue"]] = None + sr_dep_env: Optional[Union[str, "SRDEPENVENUM"]] = None + sr_geol_age: Optional[Union[str, "SHAREDENUM5"]] = None + sr_kerog_type: Optional[Union[str, "SRKEROGTYPEENUM"]] = None + sr_lithology: Optional[Union[str, "SRLITHOLOGYENUM"]] = None standing_water_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() store_cond: Optional[Union[dict, "TextValue"]] = None - substructure_type: Optional[Union[Union[str, "SubstructureTypeEnum"], List[Union[str, "SubstructureTypeEnum"]]]] = empty_list() + substructure_type: Optional[Union[Union[str, "SUBSTRUCTURETYPEENUM"], List[Union[str, "SUBSTRUCTURETYPEENUM"]]]] = empty_list() sulfate: Optional[Union[dict, "QuantityValue"]] = None - sulfate_fw: Optional[Union[dict, "QuantityValue"]] = None - sulfide: Optional[Union[dict, "QuantityValue"]] = None - surf_air_cont: Optional[Union[Union[str, "SurfAirContEnum"], List[Union[str, "SurfAirContEnum"]]]] = empty_list() - surf_humidity: Optional[Union[dict, "QuantityValue"]] = None - surf_material: Optional[Union[str, "SurfMaterialEnum"]] = None - surf_moisture: Optional[Union[dict, "QuantityValue"]] = None + sulfate_fw: Optional[Union[dict, "TextValue"]] = None + sulfide: Optional[Union[dict, "TextValue"]] = None + surf_air_cont: Optional[Union[Union[str, "SURFAIRCONTENUM"], List[Union[str, "SURFAIRCONTENUM"]]]] = empty_list() + surf_humidity: Optional[float] = None + surf_material: Optional[Union[str, "SURFMATERIALENUM"]] = None + surf_moisture: Optional[Union[dict, "TextValue"]] = None surf_moisture_ph: Optional[float] = None - surf_temp: Optional[Union[dict, "QuantityValue"]] = None - suspend_part_matter: Optional[Union[dict, "QuantityValue"]] = None + surf_temp: Optional[Union[dict, "TextValue"]] = None + suspend_part_matter: Optional[Union[dict, "TextValue"]] = None suspend_solids: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - tan: Optional[Union[dict, "QuantityValue"]] = None + tan: Optional[Union[dict, "TextValue"]] = None target_gene: Optional[Union[dict, "TextValue"]] = None target_subfragment: Optional[Union[dict, "TextValue"]] = None temp: Optional[Union[dict, "QuantityValue"]] = None - temp_out: Optional[Union[dict, "QuantityValue"]] = None - tertiary_treatment: Optional[Union[dict, "TextValue"]] = None - tidal_stage: Optional[Union[str, "TidalStageEnum"]] = None - tillage: Optional[Union[Union[str, "TillageEnum"], List[Union[str, "TillageEnum"]]]] = empty_list() + temp_out: Optional[Union[dict, "TextValue"]] = None + tertiary_treatment: Optional[str] = None + tidal_stage: Optional[Union[str, "TIDALSTAGEENUM"]] = None + tillage: Optional[Union[Union[str, "TILLAGEENUM"], List[Union[str, "TILLAGEENUM"]]]] = empty_list() tiss_cult_growth_med: Optional[Union[dict, "TextValue"]] = None - toluene: Optional[Union[dict, "QuantityValue"]] = None + toluene: Optional[Union[dict, "TextValue"]] = None tot_carb: Optional[Union[dict, "QuantityValue"]] = None - tot_depth_water_col: Optional[Union[dict, "QuantityValue"]] = None - tot_diss_nitro: Optional[Union[dict, "QuantityValue"]] = None - tot_inorg_nitro: Optional[Union[dict, "QuantityValue"]] = None - tot_iron: Optional[Union[dict, "QuantityValue"]] = None + tot_depth_water_col: Optional[Union[dict, "TextValue"]] = None + tot_diss_nitro: Optional[Union[dict, "TextValue"]] = None + tot_inorg_nitro: Optional[Union[dict, "TextValue"]] = None + tot_iron: Optional[Union[dict, "TextValue"]] = None tot_nitro: Optional[Union[dict, "QuantityValue"]] = None tot_nitro_cont_meth: Optional[str] = None tot_nitro_content: Optional[Union[dict, "QuantityValue"]] = None tot_org_c_meth: Optional[Union[dict, "TextValue"]] = None tot_org_carb: Optional[Union[dict, "QuantityValue"]] = None - tot_part_carb: Optional[Union[dict, "QuantityValue"]] = None + tot_part_carb: Optional[Union[dict, "TextValue"]] = None tot_phosp: Optional[Union[dict, "QuantityValue"]] = None - tot_phosphate: Optional[Union[dict, "QuantityValue"]] = None - tot_sulfur: Optional[Union[dict, "QuantityValue"]] = None - train_line: Optional[Union[str, "TrainLineEnum"]] = None - train_stat_loc: Optional[Union[str, "TrainStatLocEnum"]] = None - train_stop_loc: Optional[Union[str, "TrainStopLocEnum"]] = None - turbidity: Optional[Union[dict, "QuantityValue"]] = None - tvdss_of_hcr_press: Optional[Union[dict, "QuantityValue"]] = None - tvdss_of_hcr_temp: Optional[Union[dict, "QuantityValue"]] = None + tot_phosphate: Optional[Union[dict, "TextValue"]] = None + tot_sulfur: Optional[Union[dict, "TextValue"]] = None + train_line: Optional[Union[str, "TRAINLINEENUM"]] = None + train_stat_loc: Optional[Union[str, "TRAINSTATLOCENUM"]] = None + train_stop_loc: Optional[Union[str, "TRAINSTOPLOCENUM"]] = None + turbidity: Optional[Union[dict, "TextValue"]] = None + tvdss_of_hcr_press: Optional[Union[dict, "TextValue"]] = None + tvdss_of_hcr_temp: Optional[Union[dict, "TextValue"]] = None typ_occup_density: Optional[float] = None - ventilation_rate: Optional[Union[dict, "QuantityValue"]] = None - ventilation_type: Optional[Union[dict, "TextValue"]] = None - vfa: Optional[Union[dict, "QuantityValue"]] = None - vfa_fw: Optional[Union[dict, "QuantityValue"]] = None - vis_media: Optional[Union[str, "VisMediaEnum"]] = None + ventilation_rate: Optional[Union[dict, "TextValue"]] = None + ventilation_type: Optional[Union[str, List[str]]] = empty_list() + vfa: Optional[Union[dict, "TextValue"]] = None + vfa_fw: Optional[Union[dict, "TextValue"]] = None + vis_media: Optional[str] = None viscosity: Optional[Union[dict, "TextValue"]] = None volatile_org_comp: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - wall_area: Optional[Union[dict, "QuantityValue"]] = None - wall_const_type: Optional[Union[str, "WallConstTypeEnum"]] = None - wall_finish_mat: Optional[Union[str, "WallFinishMatEnum"]] = None - wall_height: Optional[Union[dict, "QuantityValue"]] = None - wall_loc: Optional[Union[str, "WallLocEnum"]] = None - wall_surf_treatment: Optional[Union[str, "WallSurfTreatmentEnum"]] = None - wall_texture: Optional[Union[str, "WallTextureEnum"]] = None - wall_thermal_mass: Optional[Union[dict, "QuantityValue"]] = None - wall_water_mold: Optional[Union[dict, "TextValue"]] = None - wastewater_type: Optional[Union[dict, "TextValue"]] = None + wall_area: Optional[Union[dict, "TextValue"]] = None + wall_const_type: Optional[Union[str, "WALLCONSTTYPEENUM"]] = None + wall_finish_mat: Optional[Union[str, "WALLFINISHMATENUM"]] = None + wall_height: Optional[Union[dict, "TextValue"]] = None + wall_loc: Optional[Union[str, "SHAREDENUM0"]] = None + wall_surf_treatment: Optional[Union[str, "WALLSURFTREATMENTENUM"]] = None + wall_texture: Optional[Union[str, "SHAREDENUM4"]] = None + wall_thermal_mass: Optional[Union[dict, "TextValue"]] = None + wall_water_mold: Optional[Union[str, "SHAREDENUM1"]] = None + wastewater_type: Optional[str] = None water_cont_soil_meth: Optional[str] = None water_content: Optional[Union[str, List[str]]] = empty_list() - water_current: Optional[Union[dict, "QuantityValue"]] = None - water_cut: Optional[Union[dict, "QuantityValue"]] = None - water_feat_size: Optional[Union[dict, "QuantityValue"]] = None - water_feat_type: Optional[Union[str, "WaterFeatTypeEnum"]] = None - water_prod_rate: Optional[Union[dict, "QuantityValue"]] = None + water_current: Optional[Union[dict, "TextValue"]] = None + water_cut: Optional[Union[dict, "TextValue"]] = None + water_feat_size: Optional[Union[dict, "TextValue"]] = None + water_feat_type: Optional[Union[str, "WATERFEATTYPEENUM"]] = None + water_prod_rate: Optional[Union[dict, "TextValue"]] = None water_temp_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() watering_regm: Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]] = empty_list() - weekday: Optional[Union[str, "WeekdayEnum"]] = None + weekday: Optional[Union[str, "WEEKDAYENUM"]] = None win: Optional[Union[dict, "TextValue"]] = None wind_direction: Optional[Union[dict, "TextValue"]] = None wind_speed: Optional[Union[dict, "QuantityValue"]] = None - window_cond: Optional[Union[str, "WindowCondEnum"]] = None - window_cover: Optional[Union[str, "WindowCoverEnum"]] = None - window_horiz_pos: Optional[Union[str, "WindowHorizPosEnum"]] = None - window_loc: Optional[Union[str, "WindowLocEnum"]] = None - window_mat: Optional[Union[str, "WindowMatEnum"]] = None + window_cond: Optional[Union[str, "SHAREDENUM2"]] = None + window_cover: Optional[Union[str, "WINDOWCOVERENUM"]] = None + window_horiz_pos: Optional[Union[str, "WINDOWHORIZPOSENUM"]] = None + window_loc: Optional[Union[str, "SHAREDENUM0"]] = None + window_mat: Optional[Union[str, "WINDOWMATENUM"]] = None window_open_freq: Optional[Union[dict, "TextValue"]] = None window_size: Optional[Union[dict, "TextValue"]] = None - window_status: Optional[Union[dict, "TextValue"]] = None - window_type: Optional[Union[str, "WindowTypeEnum"]] = None - window_vert_pos: Optional[Union[str, "WindowVertPosEnum"]] = None - window_water_mold: Optional[Union[dict, "TextValue"]] = None - xylene: Optional[Union[dict, "QuantityValue"]] = None + window_status: Optional[Union[str, "WINDOWSTATUSENUM"]] = None + window_type: Optional[Union[str, "WINDOWTYPEENUM"]] = None + window_vert_pos: Optional[Union[str, "WINDOWVERTPOSENUM"]] = None + window_water_mold: Optional[Union[str, "SHAREDENUM1"]] = None + xylene: Optional[Union[dict, "TextValue"]] = None zinc: Optional[Union[dict, "QuantityValue"]] = None add_date: Optional[str] = None community: Optional[str] = None @@ -1666,8 +1663,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.env_medium, ControlledIdentifiedTermValue): self.env_medium = ControlledIdentifiedTermValue(**as_dict(self.env_medium)) - if self.host_disease_stat is not None and not isinstance(self.host_disease_stat, TextValue): - self.host_disease_stat = TextValue(**as_dict(self.host_disease_stat)) + if self.samp_collec_method is not None and not isinstance(self.samp_collec_method, str): + self.samp_collec_method = str(self.samp_collec_method) + + if self.samp_collec_device is not None and not isinstance(self.samp_collec_device, str): + self.samp_collec_device = str(self.samp_collec_device) if not isinstance(self.neon_biosample_identifiers, list): self.neon_biosample_identifiers = [self.neon_biosample_identifiers] if self.neon_biosample_identifiers is not None else [] @@ -1722,20 +1722,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.abs_air_humidity is not None and not isinstance(self.abs_air_humidity, QuantityValue): self.abs_air_humidity = QuantityValue(**as_dict(self.abs_air_humidity)) - if self.add_recov_method is not None and not isinstance(self.add_recov_method, TextValue): - self.add_recov_method = TextValue(**as_dict(self.add_recov_method)) + if self.add_recov_method is not None and not isinstance(self.add_recov_method, str): + self.add_recov_method = str(self.add_recov_method) if self.additional_info is not None and not isinstance(self.additional_info, TextValue): self.additional_info = TextValue(**as_dict(self.additional_info)) - if self.address is not None and not isinstance(self.address, TextValue): - self.address = TextValue(**as_dict(self.address)) + if self.address is not None and not isinstance(self.address, str): + self.address = str(self.address) if self.adj_room is not None and not isinstance(self.adj_room, TextValue): self.adj_room = TextValue(**as_dict(self.adj_room)) - if self.aero_struc is not None and not isinstance(self.aero_struc, TextValue): - self.aero_struc = TextValue(**as_dict(self.aero_struc)) + if self.aero_struc is not None and not isinstance(self.aero_struc, AEROSTRUCENUM): + self.aero_struc = AEROSTRUCENUM(self.aero_struc) if not isinstance(self.agrochem_addition, list): self.agrochem_addition = [self.agrochem_addition] if self.agrochem_addition is not None else [] @@ -1743,35 +1743,35 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.air_PM_concen, list): self.air_PM_concen = [self.air_PM_concen] if self.air_PM_concen is not None else [] - self.air_PM_concen = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.air_PM_concen] + self.air_PM_concen = [v if isinstance(v, str) else str(v) for v in self.air_PM_concen] - if self.air_temp is not None and not isinstance(self.air_temp, QuantityValue): - self.air_temp = QuantityValue(**as_dict(self.air_temp)) + if self.air_temp is not None and not isinstance(self.air_temp, TextValue): + self.air_temp = TextValue(**as_dict(self.air_temp)) if not isinstance(self.air_temp_regm, list): self.air_temp_regm = [self.air_temp_regm] if self.air_temp_regm is not None else [] self.air_temp_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.air_temp_regm] - if self.al_sat is not None and not isinstance(self.al_sat, QuantityValue): - self.al_sat = QuantityValue(**as_dict(self.al_sat)) + if self.al_sat is not None and not isinstance(self.al_sat, TextValue): + self.al_sat = TextValue(**as_dict(self.al_sat)) if self.al_sat_meth is not None and not isinstance(self.al_sat_meth, TextValue): self.al_sat_meth = TextValue(**as_dict(self.al_sat_meth)) - if self.alkalinity is not None and not isinstance(self.alkalinity, QuantityValue): - self.alkalinity = QuantityValue(**as_dict(self.alkalinity)) + if self.alkalinity is not None and not isinstance(self.alkalinity, TextValue): + self.alkalinity = TextValue(**as_dict(self.alkalinity)) if self.alkalinity_method is not None and not isinstance(self.alkalinity_method, TextValue): self.alkalinity_method = TextValue(**as_dict(self.alkalinity_method)) - if self.alkyl_diethers is not None and not isinstance(self.alkyl_diethers, QuantityValue): - self.alkyl_diethers = QuantityValue(**as_dict(self.alkyl_diethers)) + if self.alkyl_diethers is not None and not isinstance(self.alkyl_diethers, TextValue): + self.alkyl_diethers = TextValue(**as_dict(self.alkyl_diethers)) - if self.alt is not None and not isinstance(self.alt, QuantityValue): - self.alt = QuantityValue(**as_dict(self.alt)) + if self.alt is not None and not isinstance(self.alt, TextValue): + self.alt = TextValue(**as_dict(self.alt)) - if self.aminopept_act is not None and not isinstance(self.aminopept_act, QuantityValue): - self.aminopept_act = QuantityValue(**as_dict(self.aminopept_act)) + if self.aminopept_act is not None and not isinstance(self.aminopept_act, TextValue): + self.aminopept_act = TextValue(**as_dict(self.aminopept_act)) if self.ammonium is not None and not isinstance(self.ammonium, QuantityValue): self.ammonium = QuantityValue(**as_dict(self.ammonium)) @@ -1779,27 +1779,27 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.ammonium_nitrogen is not None and not isinstance(self.ammonium_nitrogen, QuantityValue): self.ammonium_nitrogen = QuantityValue(**as_dict(self.ammonium_nitrogen)) - if self.amount_light is not None and not isinstance(self.amount_light, QuantityValue): - self.amount_light = QuantityValue(**as_dict(self.amount_light)) + if self.amount_light is not None and not isinstance(self.amount_light, TextValue): + self.amount_light = TextValue(**as_dict(self.amount_light)) if self.ances_data is not None and not isinstance(self.ances_data, TextValue): self.ances_data = TextValue(**as_dict(self.ances_data)) - if self.annual_precpt is not None and not isinstance(self.annual_precpt, QuantityValue): - self.annual_precpt = QuantityValue(**as_dict(self.annual_precpt)) + if self.annual_precpt is not None and not isinstance(self.annual_precpt, TextValue): + self.annual_precpt = TextValue(**as_dict(self.annual_precpt)) - if self.annual_temp is not None and not isinstance(self.annual_temp, QuantityValue): - self.annual_temp = QuantityValue(**as_dict(self.annual_temp)) + if self.annual_temp is not None and not isinstance(self.annual_temp, TextValue): + self.annual_temp = TextValue(**as_dict(self.annual_temp)) if not isinstance(self.antibiotic_regm, list): self.antibiotic_regm = [self.antibiotic_regm] if self.antibiotic_regm is not None else [] self.antibiotic_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.antibiotic_regm] - if self.api is not None and not isinstance(self.api, QuantityValue): - self.api = QuantityValue(**as_dict(self.api)) + if self.api is not None and not isinstance(self.api, TextValue): + self.api = TextValue(**as_dict(self.api)) - if self.arch_struc is not None and not isinstance(self.arch_struc, ArchStrucEnum): - self.arch_struc = ArchStrucEnum(self.arch_struc) + if self.arch_struc is not None and not isinstance(self.arch_struc, ARCHSTRUCENUM): + self.arch_struc = ARCHSTRUCENUM(self.arch_struc) if self.aromatics_pc is not None and not isinstance(self.aromatics_pc, TextValue): self.aromatics_pc = TextValue(**as_dict(self.aromatics_pc)) @@ -1811,8 +1811,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.atmospheric_data = [self.atmospheric_data] if self.atmospheric_data is not None else [] self.atmospheric_data = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.atmospheric_data] - if self.avg_dew_point is not None and not isinstance(self.avg_dew_point, QuantityValue): - self.avg_dew_point = QuantityValue(**as_dict(self.avg_dew_point)) + if self.avg_dew_point is not None and not isinstance(self.avg_dew_point, TextValue): + self.avg_dew_point = TextValue(**as_dict(self.avg_dew_point)) if self.avg_occup is not None and not isinstance(self.avg_occup, TextValue): self.avg_occup = TextValue(**as_dict(self.avg_occup)) @@ -1820,17 +1820,17 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.avg_temp is not None and not isinstance(self.avg_temp, QuantityValue): self.avg_temp = QuantityValue(**as_dict(self.avg_temp)) - if self.bac_prod is not None and not isinstance(self.bac_prod, QuantityValue): - self.bac_prod = QuantityValue(**as_dict(self.bac_prod)) + if self.bac_prod is not None and not isinstance(self.bac_prod, TextValue): + self.bac_prod = TextValue(**as_dict(self.bac_prod)) - if self.bac_resp is not None and not isinstance(self.bac_resp, QuantityValue): - self.bac_resp = QuantityValue(**as_dict(self.bac_resp)) + if self.bac_resp is not None and not isinstance(self.bac_resp, TextValue): + self.bac_resp = TextValue(**as_dict(self.bac_resp)) - if self.bacteria_carb_prod is not None and not isinstance(self.bacteria_carb_prod, QuantityValue): - self.bacteria_carb_prod = QuantityValue(**as_dict(self.bacteria_carb_prod)) + if self.bacteria_carb_prod is not None and not isinstance(self.bacteria_carb_prod, TextValue): + self.bacteria_carb_prod = TextValue(**as_dict(self.bacteria_carb_prod)) - if self.barometric_press is not None and not isinstance(self.barometric_press, QuantityValue): - self.barometric_press = QuantityValue(**as_dict(self.barometric_press)) + if self.barometric_press is not None and not isinstance(self.barometric_press, TextValue): + self.barometric_press = TextValue(**as_dict(self.barometric_press)) if self.basin is not None and not isinstance(self.basin, TextValue): self.basin = TextValue(**as_dict(self.basin)) @@ -1841,58 +1841,59 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.bedroom_count is not None and not isinstance(self.bedroom_count, TextValue): self.bedroom_count = TextValue(**as_dict(self.bedroom_count)) - if self.benzene is not None and not isinstance(self.benzene, QuantityValue): - self.benzene = QuantityValue(**as_dict(self.benzene)) + if self.benzene is not None and not isinstance(self.benzene, TextValue): + self.benzene = TextValue(**as_dict(self.benzene)) - if self.biochem_oxygen_dem is not None and not isinstance(self.biochem_oxygen_dem, QuantityValue): - self.biochem_oxygen_dem = QuantityValue(**as_dict(self.biochem_oxygen_dem)) + if self.biochem_oxygen_dem is not None and not isinstance(self.biochem_oxygen_dem, TextValue): + self.biochem_oxygen_dem = TextValue(**as_dict(self.biochem_oxygen_dem)) - if self.biocide is not None and not isinstance(self.biocide, TextValue): - self.biocide = TextValue(**as_dict(self.biocide)) + if self.biocide is not None and not isinstance(self.biocide, str): + self.biocide = str(self.biocide) if self.biocide_admin_method is not None and not isinstance(self.biocide_admin_method, TextValue): self.biocide_admin_method = TextValue(**as_dict(self.biocide_admin_method)) - if self.biol_stat is not None and not isinstance(self.biol_stat, BiolStatEnum): - self.biol_stat = BiolStatEnum(self.biol_stat) + if self.biol_stat is not None and not isinstance(self.biol_stat, str): + self.biol_stat = str(self.biol_stat) if not isinstance(self.biomass, list): self.biomass = [self.biomass] if self.biomass is not None else [] self.biomass = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.biomass] - if self.biotic_regm is not None and not isinstance(self.biotic_regm, TextValue): - self.biotic_regm = TextValue(**as_dict(self.biotic_regm)) + if not isinstance(self.biotic_regm, list): + self.biotic_regm = [self.biotic_regm] if self.biotic_regm is not None else [] + self.biotic_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.biotic_regm] - if self.biotic_relationship is not None and not isinstance(self.biotic_relationship, BioticRelationshipEnum): - self.biotic_relationship = BioticRelationshipEnum(self.biotic_relationship) + if self.biotic_relationship is not None and not isinstance(self.biotic_relationship, BIOTICRELATIONSHIPENUM): + self.biotic_relationship = BIOTICRELATIONSHIPENUM(self.biotic_relationship) - if self.bishomohopanol is not None and not isinstance(self.bishomohopanol, QuantityValue): - self.bishomohopanol = QuantityValue(**as_dict(self.bishomohopanol)) + if self.bishomohopanol is not None and not isinstance(self.bishomohopanol, TextValue): + self.bishomohopanol = TextValue(**as_dict(self.bishomohopanol)) - if self.blood_press_diast is not None and not isinstance(self.blood_press_diast, QuantityValue): - self.blood_press_diast = QuantityValue(**as_dict(self.blood_press_diast)) + if self.blood_press_diast is not None and not isinstance(self.blood_press_diast, TextValue): + self.blood_press_diast = TextValue(**as_dict(self.blood_press_diast)) - if self.blood_press_syst is not None and not isinstance(self.blood_press_syst, QuantityValue): - self.blood_press_syst = QuantityValue(**as_dict(self.blood_press_syst)) + if self.blood_press_syst is not None and not isinstance(self.blood_press_syst, TextValue): + self.blood_press_syst = TextValue(**as_dict(self.blood_press_syst)) - if self.bromide is not None and not isinstance(self.bromide, QuantityValue): - self.bromide = QuantityValue(**as_dict(self.bromide)) + if self.bromide is not None and not isinstance(self.bromide, TextValue): + self.bromide = TextValue(**as_dict(self.bromide)) - if self.build_docs is not None and not isinstance(self.build_docs, BuildDocsEnum): - self.build_docs = BuildDocsEnum(self.build_docs) + if self.build_docs is not None and not isinstance(self.build_docs, BUILDDOCSENUM): + self.build_docs = BUILDDOCSENUM(self.build_docs) if not isinstance(self.build_occup_type, list): self.build_occup_type = [self.build_occup_type] if self.build_occup_type is not None else [] - self.build_occup_type = [v if isinstance(v, BuildOccupTypeEnum) else BuildOccupTypeEnum(v) for v in self.build_occup_type] + self.build_occup_type = [v if isinstance(v, BUILDOCCUPTYPEENUM) else BUILDOCCUPTYPEENUM(v) for v in self.build_occup_type] - if self.building_setting is not None and not isinstance(self.building_setting, BuildingSettingEnum): - self.building_setting = BuildingSettingEnum(self.building_setting) + if self.building_setting is not None and not isinstance(self.building_setting, BUILDINGSETTINGENUM): + self.building_setting = BUILDINGSETTINGENUM(self.building_setting) - if self.built_struc_age is not None and not isinstance(self.built_struc_age, QuantityValue): - self.built_struc_age = QuantityValue(**as_dict(self.built_struc_age)) + if self.built_struc_age is not None and not isinstance(self.built_struc_age, TextValue): + self.built_struc_age = TextValue(**as_dict(self.built_struc_age)) - if self.built_struc_set is not None and not isinstance(self.built_struc_set, TextValue): - self.built_struc_set = TextValue(**as_dict(self.built_struc_set)) + if self.built_struc_set is not None and not isinstance(self.built_struc_set, BUILTSTRUCSETENUM): + self.built_struc_set = BUILTSTRUCSETENUM(self.built_struc_set) if self.built_struc_type is not None and not isinstance(self.built_struc_type, TextValue): self.built_struc_type = TextValue(**as_dict(self.built_struc_type)) @@ -1900,38 +1901,38 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.calcium is not None and not isinstance(self.calcium, QuantityValue): self.calcium = QuantityValue(**as_dict(self.calcium)) - if self.carb_dioxide is not None and not isinstance(self.carb_dioxide, QuantityValue): - self.carb_dioxide = QuantityValue(**as_dict(self.carb_dioxide)) + if self.carb_dioxide is not None and not isinstance(self.carb_dioxide, TextValue): + self.carb_dioxide = TextValue(**as_dict(self.carb_dioxide)) - if self.carb_monoxide is not None and not isinstance(self.carb_monoxide, QuantityValue): - self.carb_monoxide = QuantityValue(**as_dict(self.carb_monoxide)) + if self.carb_monoxide is not None and not isinstance(self.carb_monoxide, TextValue): + self.carb_monoxide = TextValue(**as_dict(self.carb_monoxide)) if self.carb_nitro_ratio is not None and not isinstance(self.carb_nitro_ratio, QuantityValue): self.carb_nitro_ratio = QuantityValue(**as_dict(self.carb_nitro_ratio)) - if self.ceil_area is not None and not isinstance(self.ceil_area, QuantityValue): - self.ceil_area = QuantityValue(**as_dict(self.ceil_area)) + if self.ceil_area is not None and not isinstance(self.ceil_area, TextValue): + self.ceil_area = TextValue(**as_dict(self.ceil_area)) - if self.ceil_cond is not None and not isinstance(self.ceil_cond, CeilCondEnum): - self.ceil_cond = CeilCondEnum(self.ceil_cond) + if self.ceil_cond is not None and not isinstance(self.ceil_cond, SHAREDENUM3): + self.ceil_cond = SHAREDENUM3(self.ceil_cond) - if self.ceil_finish_mat is not None and not isinstance(self.ceil_finish_mat, CeilFinishMatEnum): - self.ceil_finish_mat = CeilFinishMatEnum(self.ceil_finish_mat) + if self.ceil_finish_mat is not None and not isinstance(self.ceil_finish_mat, CEILFINISHMATENUM): + self.ceil_finish_mat = CEILFINISHMATENUM(self.ceil_finish_mat) - if self.ceil_struc is not None and not isinstance(self.ceil_struc, TextValue): - self.ceil_struc = TextValue(**as_dict(self.ceil_struc)) + if self.ceil_struc is not None and not isinstance(self.ceil_struc, CEILSTRUCENUM): + self.ceil_struc = CEILSTRUCENUM(self.ceil_struc) - if self.ceil_texture is not None and not isinstance(self.ceil_texture, CeilTextureEnum): - self.ceil_texture = CeilTextureEnum(self.ceil_texture) + if self.ceil_texture is not None and not isinstance(self.ceil_texture, SHAREDENUM4): + self.ceil_texture = SHAREDENUM4(self.ceil_texture) - if self.ceil_thermal_mass is not None and not isinstance(self.ceil_thermal_mass, QuantityValue): - self.ceil_thermal_mass = QuantityValue(**as_dict(self.ceil_thermal_mass)) + if self.ceil_thermal_mass is not None and not isinstance(self.ceil_thermal_mass, TextValue): + self.ceil_thermal_mass = TextValue(**as_dict(self.ceil_thermal_mass)) - if self.ceil_type is not None and not isinstance(self.ceil_type, CeilTypeEnum): - self.ceil_type = CeilTypeEnum(self.ceil_type) + if self.ceil_type is not None and not isinstance(self.ceil_type, CEILTYPEENUM): + self.ceil_type = CEILTYPEENUM(self.ceil_type) - if self.ceil_water_mold is not None and not isinstance(self.ceil_water_mold, TextValue): - self.ceil_water_mold = TextValue(**as_dict(self.ceil_water_mold)) + if self.ceil_water_mold is not None and not isinstance(self.ceil_water_mold, SHAREDENUM1): + self.ceil_water_mold = SHAREDENUM1(self.ceil_water_mold) if not isinstance(self.chem_administration, list): self.chem_administration = [self.chem_administration] if self.chem_administration is not None else [] @@ -1941,14 +1942,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.chem_mutagen = [self.chem_mutagen] if self.chem_mutagen is not None else [] self.chem_mutagen = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.chem_mutagen] - if self.chem_oxygen_dem is not None and not isinstance(self.chem_oxygen_dem, QuantityValue): - self.chem_oxygen_dem = QuantityValue(**as_dict(self.chem_oxygen_dem)) + if self.chem_oxygen_dem is not None and not isinstance(self.chem_oxygen_dem, TextValue): + self.chem_oxygen_dem = TextValue(**as_dict(self.chem_oxygen_dem)) if self.chem_treat_method is not None and not isinstance(self.chem_treat_method, str): self.chem_treat_method = str(self.chem_treat_method) - if self.chem_treatment is not None and not isinstance(self.chem_treatment, TextValue): - self.chem_treatment = TextValue(**as_dict(self.chem_treatment)) + if self.chem_treatment is not None and not isinstance(self.chem_treatment, str): + self.chem_treatment = str(self.chem_treatment) if self.chimera_check is not None and not isinstance(self.chimera_check, TextValue): self.chimera_check = TextValue(**as_dict(self.chimera_check)) @@ -1972,17 +1973,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.cool_syst_id is not None and not isinstance(self.cool_syst_id, TextValue): self.cool_syst_id = TextValue(**as_dict(self.cool_syst_id)) - if self.core_field is not None and not isinstance(self.core_field, str): - self.core_field = str(self.core_field) - - if self.crop_rotation is not None and not isinstance(self.crop_rotation, TextValue): - self.crop_rotation = TextValue(**as_dict(self.crop_rotation)) + if self.crop_rotation is not None and not isinstance(self.crop_rotation, str): + self.crop_rotation = str(self.crop_rotation) - if self.cult_root_med is not None and not isinstance(self.cult_root_med, TextValue): - self.cult_root_med = TextValue(**as_dict(self.cult_root_med)) + if self.cult_root_med is not None and not isinstance(self.cult_root_med, str): + self.cult_root_med = str(self.cult_root_med) - if self.cur_land_use is not None and not isinstance(self.cur_land_use, CurLandUseEnum): - self.cur_land_use = CurLandUseEnum(self.cur_land_use) + if self.cur_land_use is not None and not isinstance(self.cur_land_use, str): + self.cur_land_use = str(self.cur_land_use) if self.cur_vegetation is not None and not isinstance(self.cur_vegetation, TextValue): self.cur_vegetation = TextValue(**as_dict(self.cur_vegetation)) @@ -1993,27 +1991,27 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.date_last_rain is not None and not isinstance(self.date_last_rain, TimestampValue): self.date_last_rain = TimestampValue(**as_dict(self.date_last_rain)) - if self.density is not None and not isinstance(self.density, QuantityValue): - self.density = QuantityValue(**as_dict(self.density)) + if self.density is not None and not isinstance(self.density, TextValue): + self.density = TextValue(**as_dict(self.density)) - if self.depos_env is not None and not isinstance(self.depos_env, DeposEnvEnum): - self.depos_env = DeposEnvEnum(self.depos_env) + if self.depos_env is not None and not isinstance(self.depos_env, DEPOSENVENUM): + self.depos_env = DEPOSENVENUM(self.depos_env) if self.depth is not None and not isinstance(self.depth, QuantityValue): self.depth = QuantityValue(**as_dict(self.depth)) - if self.dew_point is not None and not isinstance(self.dew_point, QuantityValue): - self.dew_point = QuantityValue(**as_dict(self.dew_point)) + if self.dew_point is not None and not isinstance(self.dew_point, TextValue): + self.dew_point = TextValue(**as_dict(self.dew_point)) if not isinstance(self.diether_lipids, list): self.diether_lipids = [self.diether_lipids] if self.diether_lipids is not None else [] self.diether_lipids = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.diether_lipids] - if self.diss_carb_dioxide is not None and not isinstance(self.diss_carb_dioxide, QuantityValue): - self.diss_carb_dioxide = QuantityValue(**as_dict(self.diss_carb_dioxide)) + if self.diss_carb_dioxide is not None and not isinstance(self.diss_carb_dioxide, TextValue): + self.diss_carb_dioxide = TextValue(**as_dict(self.diss_carb_dioxide)) - if self.diss_hydrogen is not None and not isinstance(self.diss_hydrogen, QuantityValue): - self.diss_hydrogen = QuantityValue(**as_dict(self.diss_hydrogen)) + if self.diss_hydrogen is not None and not isinstance(self.diss_hydrogen, TextValue): + self.diss_hydrogen = TextValue(**as_dict(self.diss_hydrogen)) if self.diss_inorg_carb is not None and not isinstance(self.diss_inorg_carb, QuantityValue): self.diss_inorg_carb = QuantityValue(**as_dict(self.diss_inorg_carb)) @@ -2021,8 +2019,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.diss_inorg_nitro is not None and not isinstance(self.diss_inorg_nitro, QuantityValue): self.diss_inorg_nitro = QuantityValue(**as_dict(self.diss_inorg_nitro)) - if self.diss_inorg_phosp is not None and not isinstance(self.diss_inorg_phosp, QuantityValue): - self.diss_inorg_phosp = QuantityValue(**as_dict(self.diss_inorg_phosp)) + if self.diss_inorg_phosp is not None and not isinstance(self.diss_inorg_phosp, TextValue): + self.diss_inorg_phosp = TextValue(**as_dict(self.diss_inorg_phosp)) if self.diss_iron is not None and not isinstance(self.diss_iron, QuantityValue): self.diss_iron = QuantityValue(**as_dict(self.diss_iron)) @@ -2030,59 +2028,59 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.diss_org_carb is not None and not isinstance(self.diss_org_carb, QuantityValue): self.diss_org_carb = QuantityValue(**as_dict(self.diss_org_carb)) - if self.diss_org_nitro is not None and not isinstance(self.diss_org_nitro, QuantityValue): - self.diss_org_nitro = QuantityValue(**as_dict(self.diss_org_nitro)) + if self.diss_org_nitro is not None and not isinstance(self.diss_org_nitro, TextValue): + self.diss_org_nitro = TextValue(**as_dict(self.diss_org_nitro)) if self.diss_oxygen is not None and not isinstance(self.diss_oxygen, QuantityValue): self.diss_oxygen = QuantityValue(**as_dict(self.diss_oxygen)) - if self.diss_oxygen_fluid is not None and not isinstance(self.diss_oxygen_fluid, QuantityValue): - self.diss_oxygen_fluid = QuantityValue(**as_dict(self.diss_oxygen_fluid)) + if self.diss_oxygen_fluid is not None and not isinstance(self.diss_oxygen_fluid, TextValue): + self.diss_oxygen_fluid = TextValue(**as_dict(self.diss_oxygen_fluid)) if self.dna_cont_well is not None and not isinstance(self.dna_cont_well, str): self.dna_cont_well = str(self.dna_cont_well) - if self.door_comp_type is not None and not isinstance(self.door_comp_type, DoorCompTypeEnum): - self.door_comp_type = DoorCompTypeEnum(self.door_comp_type) + if self.door_comp_type is not None and not isinstance(self.door_comp_type, DOORCOMPTYPEENUM): + self.door_comp_type = DOORCOMPTYPEENUM(self.door_comp_type) - if self.door_cond is not None and not isinstance(self.door_cond, DoorCondEnum): - self.door_cond = DoorCondEnum(self.door_cond) + if self.door_cond is not None and not isinstance(self.door_cond, SHAREDENUM2): + self.door_cond = SHAREDENUM2(self.door_cond) - if self.door_direct is not None and not isinstance(self.door_direct, DoorDirectEnum): - self.door_direct = DoorDirectEnum(self.door_direct) + if self.door_direct is not None and not isinstance(self.door_direct, DOORDIRECTENUM): + self.door_direct = DOORDIRECTENUM(self.door_direct) - if self.door_loc is not None and not isinstance(self.door_loc, DoorLocEnum): - self.door_loc = DoorLocEnum(self.door_loc) + if self.door_loc is not None and not isinstance(self.door_loc, SHAREDENUM0): + self.door_loc = SHAREDENUM0(self.door_loc) - if self.door_mat is not None and not isinstance(self.door_mat, DoorMatEnum): - self.door_mat = DoorMatEnum(self.door_mat) + if self.door_mat is not None and not isinstance(self.door_mat, DOORMATENUM): + self.door_mat = DOORMATENUM(self.door_mat) - if self.door_move is not None and not isinstance(self.door_move, DoorMoveEnum): - self.door_move = DoorMoveEnum(self.door_move) + if self.door_move is not None and not isinstance(self.door_move, DOORMOVEENUM): + self.door_move = DOORMOVEENUM(self.door_move) - if self.door_size is not None and not isinstance(self.door_size, QuantityValue): - self.door_size = QuantityValue(**as_dict(self.door_size)) + if self.door_size is not None and not isinstance(self.door_size, TextValue): + self.door_size = TextValue(**as_dict(self.door_size)) - if self.door_type is not None and not isinstance(self.door_type, DoorTypeEnum): - self.door_type = DoorTypeEnum(self.door_type) + if self.door_type is not None and not isinstance(self.door_type, DOORTYPEENUM): + self.door_type = DOORTYPEENUM(self.door_type) - if self.door_type_metal is not None and not isinstance(self.door_type_metal, DoorTypeMetalEnum): - self.door_type_metal = DoorTypeMetalEnum(self.door_type_metal) + if self.door_type_metal is not None and not isinstance(self.door_type_metal, DOORTYPEMETALENUM): + self.door_type_metal = DOORTYPEMETALENUM(self.door_type_metal) - if self.door_type_wood is not None and not isinstance(self.door_type_wood, DoorTypeWoodEnum): - self.door_type_wood = DoorTypeWoodEnum(self.door_type_wood) + if self.door_type_wood is not None and not isinstance(self.door_type_wood, str): + self.door_type_wood = str(self.door_type_wood) - if self.door_water_mold is not None and not isinstance(self.door_water_mold, TextValue): - self.door_water_mold = TextValue(**as_dict(self.door_water_mold)) + if self.door_water_mold is not None and not isinstance(self.door_water_mold, SHAREDENUM1): + self.door_water_mold = SHAREDENUM1(self.door_water_mold) - if self.down_par is not None and not isinstance(self.down_par, QuantityValue): - self.down_par = QuantityValue(**as_dict(self.down_par)) + if self.down_par is not None and not isinstance(self.down_par, TextValue): + self.down_par = TextValue(**as_dict(self.down_par)) - if self.drainage_class is not None and not isinstance(self.drainage_class, DrainageClassEnum): - self.drainage_class = DrainageClassEnum(self.drainage_class) + if self.drainage_class is not None and not isinstance(self.drainage_class, DRAINAGECLASSENUM): + self.drainage_class = DRAINAGECLASSENUM(self.drainage_class) - if self.drawings is not None and not isinstance(self.drawings, DrawingsEnum): - self.drawings = DrawingsEnum(self.drawings) + if self.drawings is not None and not isinstance(self.drawings, DRAWINGSENUM): + self.drawings = DRAWINGSENUM(self.drawings) if self.ecosystem is not None and not isinstance(self.ecosystem, str): self.ecosystem = str(self.ecosystem) @@ -2096,8 +2094,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.ecosystem_type is not None and not isinstance(self.ecosystem_type, str): self.ecosystem_type = str(self.ecosystem_type) - if self.efficiency_percent is not None and not isinstance(self.efficiency_percent, QuantityValue): - self.efficiency_percent = QuantityValue(**as_dict(self.efficiency_percent)) + if self.efficiency_percent is not None and not isinstance(self.efficiency_percent, TextValue): + self.efficiency_percent = TextValue(**as_dict(self.efficiency_percent)) if self.elev is not None and not isinstance(self.elev, float): self.elev = float(self.elev) @@ -2112,17 +2110,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.env_package is not None and not isinstance(self.env_package, TextValue): self.env_package = TextValue(**as_dict(self.env_package)) - if self.environment_field is not None and not isinstance(self.environment_field, str): - self.environment_field = str(self.environment_field) - if self.escalator is not None and not isinstance(self.escalator, TextValue): self.escalator = TextValue(**as_dict(self.escalator)) - if self.ethylbenzene is not None and not isinstance(self.ethylbenzene, QuantityValue): - self.ethylbenzene = QuantityValue(**as_dict(self.ethylbenzene)) + if self.ethylbenzene is not None and not isinstance(self.ethylbenzene, TextValue): + self.ethylbenzene = TextValue(**as_dict(self.ethylbenzene)) - if self.exp_duct is not None and not isinstance(self.exp_duct, QuantityValue): - self.exp_duct = QuantityValue(**as_dict(self.exp_duct)) + if self.exp_duct is not None and not isinstance(self.exp_duct, TextValue): + self.exp_duct = TextValue(**as_dict(self.exp_duct)) if self.exp_pipe is not None and not isinstance(self.exp_pipe, QuantityValue): self.exp_pipe = QuantityValue(**as_dict(self.exp_pipe)) @@ -2133,17 +2128,17 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.ext_door is not None and not isinstance(self.ext_door, TextValue): self.ext_door = TextValue(**as_dict(self.ext_door)) - if self.ext_wall_orient is not None and not isinstance(self.ext_wall_orient, ExtWallOrientEnum): - self.ext_wall_orient = ExtWallOrientEnum(self.ext_wall_orient) + if self.ext_wall_orient is not None and not isinstance(self.ext_wall_orient, SHAREDENUM0): + self.ext_wall_orient = SHAREDENUM0(self.ext_wall_orient) - if self.ext_window_orient is not None and not isinstance(self.ext_window_orient, ExtWindowOrientEnum): - self.ext_window_orient = ExtWindowOrientEnum(self.ext_window_orient) + if self.ext_window_orient is not None and not isinstance(self.ext_window_orient, SHAREDENUM0): + self.ext_window_orient = SHAREDENUM0(self.ext_window_orient) if self.extreme_event is not None and not isinstance(self.extreme_event, str): self.extreme_event = str(self.extreme_event) - if self.fao_class is not None and not isinstance(self.fao_class, FaoClassEnum): - self.fao_class = FaoClassEnum(self.fao_class) + if self.fao_class is not None and not isinstance(self.fao_class, FAOCLASSENUM): + self.fao_class = FAOCLASSENUM(self.fao_class) if not isinstance(self.fertilizer_regm, list): self.fertilizer_regm = [self.fertilizer_regm] if self.fertilizer_regm is not None else [] @@ -2154,43 +2149,43 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.filter_type, list): self.filter_type = [self.filter_type] if self.filter_type is not None else [] - self.filter_type = [v if isinstance(v, FilterTypeEnum) else FilterTypeEnum(v) for v in self.filter_type] + self.filter_type = [v if isinstance(v, FILTERTYPEENUM) else FILTERTYPEENUM(v) for v in self.filter_type] if self.fire is not None and not isinstance(self.fire, str): self.fire = str(self.fire) - if self.fireplace_type is not None and not isinstance(self.fireplace_type, TextValue): - self.fireplace_type = TextValue(**as_dict(self.fireplace_type)) + if self.fireplace_type is not None and not isinstance(self.fireplace_type, FIREPLACETYPEENUM): + self.fireplace_type = FIREPLACETYPEENUM(self.fireplace_type) if self.flooding is not None and not isinstance(self.flooding, str): self.flooding = str(self.flooding) - if self.floor_age is not None and not isinstance(self.floor_age, QuantityValue): - self.floor_age = QuantityValue(**as_dict(self.floor_age)) + if self.floor_age is not None and not isinstance(self.floor_age, TextValue): + self.floor_age = TextValue(**as_dict(self.floor_age)) - if self.floor_area is not None and not isinstance(self.floor_area, QuantityValue): - self.floor_area = QuantityValue(**as_dict(self.floor_area)) + if self.floor_area is not None and not isinstance(self.floor_area, TextValue): + self.floor_area = TextValue(**as_dict(self.floor_area)) - if self.floor_cond is not None and not isinstance(self.floor_cond, FloorCondEnum): - self.floor_cond = FloorCondEnum(self.floor_cond) + if self.floor_cond is not None and not isinstance(self.floor_cond, SHAREDENUM3): + self.floor_cond = SHAREDENUM3(self.floor_cond) if self.floor_count is not None and not isinstance(self.floor_count, TextValue): self.floor_count = TextValue(**as_dict(self.floor_count)) - if self.floor_finish_mat is not None and not isinstance(self.floor_finish_mat, FloorFinishMatEnum): - self.floor_finish_mat = FloorFinishMatEnum(self.floor_finish_mat) + if self.floor_finish_mat is not None and not isinstance(self.floor_finish_mat, str): + self.floor_finish_mat = str(self.floor_finish_mat) - if self.floor_struc is not None and not isinstance(self.floor_struc, FloorStrucEnum): - self.floor_struc = FloorStrucEnum(self.floor_struc) + if self.floor_struc is not None and not isinstance(self.floor_struc, FLOORSTRUCENUM): + self.floor_struc = FLOORSTRUCENUM(self.floor_struc) - if self.floor_thermal_mass is not None and not isinstance(self.floor_thermal_mass, QuantityValue): - self.floor_thermal_mass = QuantityValue(**as_dict(self.floor_thermal_mass)) + if self.floor_thermal_mass is not None and not isinstance(self.floor_thermal_mass, TextValue): + self.floor_thermal_mass = TextValue(**as_dict(self.floor_thermal_mass)) - if self.floor_water_mold is not None and not isinstance(self.floor_water_mold, FloorWaterMoldEnum): - self.floor_water_mold = FloorWaterMoldEnum(self.floor_water_mold) + if self.floor_water_mold is not None and not isinstance(self.floor_water_mold, FLOORWATERMOLDENUM): + self.floor_water_mold = FLOORWATERMOLDENUM(self.floor_water_mold) - if self.fluor is not None and not isinstance(self.fluor, QuantityValue): - self.fluor = QuantityValue(**as_dict(self.fluor)) + if self.fluor is not None and not isinstance(self.fluor, TextValue): + self.fluor = TextValue(**as_dict(self.fluor)) if self.freq_clean is not None and not isinstance(self.freq_clean, QuantityValue): self.freq_clean = QuantityValue(**as_dict(self.freq_clean)) @@ -2202,8 +2197,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.fungicide_regm = [self.fungicide_regm] if self.fungicide_regm is not None else [] self.fungicide_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.fungicide_regm] - if self.furniture is not None and not isinstance(self.furniture, FurnitureEnum): - self.furniture = FurnitureEnum(self.furniture) + if self.furniture is not None and not isinstance(self.furniture, FURNITUREENUM): + self.furniture = FURNITUREENUM(self.furniture) if not isinstance(self.gaseous_environment, list): self.gaseous_environment = [self.gaseous_environment] if self.gaseous_environment is not None else [] @@ -2213,17 +2208,17 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.gaseous_substances = [self.gaseous_substances] if self.gaseous_substances is not None else [] self.gaseous_substances = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.gaseous_substances] - if self.gender_restroom is not None and not isinstance(self.gender_restroom, GenderRestroomEnum): - self.gender_restroom = GenderRestroomEnum(self.gender_restroom) + if self.gender_restroom is not None and not isinstance(self.gender_restroom, GENDERRESTROOMENUM): + self.gender_restroom = GENDERRESTROOMENUM(self.gender_restroom) - if self.genetic_mod is not None and not isinstance(self.genetic_mod, TextValue): - self.genetic_mod = TextValue(**as_dict(self.genetic_mod)) + if self.genetic_mod is not None and not isinstance(self.genetic_mod, str): + self.genetic_mod = str(self.genetic_mod) if self.geo_loc_name is not None and not isinstance(self.geo_loc_name, TextValue): self.geo_loc_name = TextValue(**as_dict(self.geo_loc_name)) - if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, QuantityValue): - self.glucosidase_act = QuantityValue(**as_dict(self.glucosidase_act)) + if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, TextValue): + self.glucosidase_act = TextValue(**as_dict(self.glucosidase_act)) if self.gravidity is not None and not isinstance(self.gravidity, TextValue): self.gravidity = TextValue(**as_dict(self.gravidity)) @@ -2235,8 +2230,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.growth_facil is not None and not isinstance(self.growth_facil, ControlledTermValue): self.growth_facil = ControlledTermValue(**as_dict(self.growth_facil)) - if self.growth_habit is not None and not isinstance(self.growth_habit, GrowthHabitEnum): - self.growth_habit = GrowthHabitEnum(self.growth_habit) + if self.growth_habit is not None and not isinstance(self.growth_habit, GROWTHHABITENUM): + self.growth_habit = GROWTHHABITENUM(self.growth_habit) if not isinstance(self.growth_hormone_regm, list): self.growth_hormone_regm = [self.growth_hormone_regm] if self.growth_hormone_regm is not None else [] @@ -2245,20 +2240,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.hall_count is not None and not isinstance(self.hall_count, TextValue): self.hall_count = TextValue(**as_dict(self.hall_count)) - if self.handidness is not None and not isinstance(self.handidness, HandidnessEnum): - self.handidness = HandidnessEnum(self.handidness) + if self.handidness is not None and not isinstance(self.handidness, HANDIDNESSENUM): + self.handidness = HANDIDNESSENUM(self.handidness) - if self.hc_produced is not None and not isinstance(self.hc_produced, HcProducedEnum): - self.hc_produced = HcProducedEnum(self.hc_produced) + if self.hc_produced is not None and not isinstance(self.hc_produced, HCPRODUCEDENUM): + self.hc_produced = HCPRODUCEDENUM(self.hc_produced) - if self.hcr is not None and not isinstance(self.hcr, HcrEnum): - self.hcr = HcrEnum(self.hcr) + if self.hcr is not None and not isinstance(self.hcr, HCRENUM): + self.hcr = HCRENUM(self.hcr) - if self.hcr_fw_salinity is not None and not isinstance(self.hcr_fw_salinity, QuantityValue): - self.hcr_fw_salinity = QuantityValue(**as_dict(self.hcr_fw_salinity)) + if self.hcr_fw_salinity is not None and not isinstance(self.hcr_fw_salinity, TextValue): + self.hcr_fw_salinity = TextValue(**as_dict(self.hcr_fw_salinity)) - if self.hcr_geol_age is not None and not isinstance(self.hcr_geol_age, HcrGeolAgeEnum): - self.hcr_geol_age = HcrGeolAgeEnum(self.hcr_geol_age) + if self.hcr_geol_age is not None and not isinstance(self.hcr_geol_age, SHAREDENUM5): + self.hcr_geol_age = SHAREDENUM5(self.hcr_geol_age) if self.hcr_pressure is not None and not isinstance(self.hcr_pressure, TextValue): self.hcr_pressure = TextValue(**as_dict(self.hcr_pressure)) @@ -2268,10 +2263,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.heat_cool_type, list): self.heat_cool_type = [self.heat_cool_type] if self.heat_cool_type is not None else [] - self.heat_cool_type = [v if isinstance(v, HeatCoolTypeEnum) else HeatCoolTypeEnum(v) for v in self.heat_cool_type] + self.heat_cool_type = [v if isinstance(v, HEATCOOLTYPEENUM) else HEATCOOLTYPEENUM(v) for v in self.heat_cool_type] - if self.heat_deliv_loc is not None and not isinstance(self.heat_deliv_loc, HeatDelivLocEnum): - self.heat_deliv_loc = HeatDelivLocEnum(self.heat_deliv_loc) + if self.heat_deliv_loc is not None and not isinstance(self.heat_deliv_loc, SHAREDENUM0): + self.heat_deliv_loc = SHAREDENUM0(self.heat_deliv_loc) if self.heat_sys_deliv_meth is not None and not isinstance(self.heat_sys_deliv_meth, str): self.heat_sys_deliv_meth = str(self.heat_sys_deliv_meth) @@ -2287,8 +2282,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.heavy_metals_meth = [self.heavy_metals_meth] if self.heavy_metals_meth is not None else [] self.heavy_metals_meth = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.heavy_metals_meth] - if self.height_carper_fiber is not None and not isinstance(self.height_carper_fiber, QuantityValue): - self.height_carper_fiber = QuantityValue(**as_dict(self.height_carper_fiber)) + if self.height_carper_fiber is not None and not isinstance(self.height_carper_fiber, TextValue): + self.height_carper_fiber = TextValue(**as_dict(self.height_carper_fiber)) if not isinstance(self.herbicide_regm, list): self.herbicide_regm = [self.herbicide_regm] if self.herbicide_regm is not None else [] @@ -2309,8 +2304,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.host_body_site is not None and not isinstance(self.host_body_site, ControlledTermValue): self.host_body_site = ControlledTermValue(**as_dict(self.host_body_site)) - if self.host_body_temp is not None and not isinstance(self.host_body_temp, QuantityValue): - self.host_body_temp = QuantityValue(**as_dict(self.host_body_temp)) + if self.host_body_temp is not None and not isinstance(self.host_body_temp, TextValue): + self.host_body_temp = TextValue(**as_dict(self.host_body_temp)) if self.host_color is not None and not isinstance(self.host_color, TextValue): self.host_color = TextValue(**as_dict(self.host_color)) @@ -2325,10 +2320,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.host_dry_mass is not None and not isinstance(self.host_dry_mass, QuantityValue): self.host_dry_mass = QuantityValue(**as_dict(self.host_dry_mass)) - if not isinstance(self.host_family_relation, list): - self.host_family_relation = [self.host_family_relation] if self.host_family_relation is not None else [] - self.host_family_relation = [v if isinstance(v, str) else str(v) for v in self.host_family_relation] - if self.host_genotype is not None and not isinstance(self.host_genotype, TextValue): self.host_genotype = TextValue(**as_dict(self.host_genotype)) @@ -2340,10 +2331,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.host_last_meal, list): self.host_last_meal = [self.host_last_meal] if self.host_last_meal is not None else [] - self.host_last_meal = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.host_last_meal] + self.host_last_meal = [v if isinstance(v, str) else str(v) for v in self.host_last_meal] - if self.host_length is not None and not isinstance(self.host_length, QuantityValue): - self.host_length = QuantityValue(**as_dict(self.host_length)) + if self.host_length is not None and not isinstance(self.host_length, TextValue): + self.host_length = TextValue(**as_dict(self.host_length)) if self.host_life_stage is not None and not isinstance(self.host_life_stage, TextValue): self.host_life_stage = TextValue(**as_dict(self.host_life_stage)) @@ -2351,8 +2342,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.host_phenotype is not None and not isinstance(self.host_phenotype, ControlledTermValue): self.host_phenotype = ControlledTermValue(**as_dict(self.host_phenotype)) - if self.host_sex is not None and not isinstance(self.host_sex, HostSexEnum): - self.host_sex = HostSexEnum(self.host_sex) + if self.host_sex is not None and not isinstance(self.host_sex, str): + self.host_sex = str(self.host_sex) if self.host_shape is not None and not isinstance(self.host_shape, TextValue): self.host_shape = TextValue(**as_dict(self.host_shape)) @@ -2374,11 +2365,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.host_taxid is not None and not isinstance(self.host_taxid, ControlledIdentifiedTermValue): self.host_taxid = ControlledIdentifiedTermValue(**as_dict(self.host_taxid)) - if self.host_tot_mass is not None and not isinstance(self.host_tot_mass, QuantityValue): - self.host_tot_mass = QuantityValue(**as_dict(self.host_tot_mass)) + if self.host_tot_mass is not None and not isinstance(self.host_tot_mass, TextValue): + self.host_tot_mass = TextValue(**as_dict(self.host_tot_mass)) - if self.host_wet_mass is not None and not isinstance(self.host_wet_mass, QuantityValue): - self.host_wet_mass = QuantityValue(**as_dict(self.host_wet_mass)) + if self.host_wet_mass is not None and not isinstance(self.host_wet_mass, TextValue): + self.host_wet_mass = TextValue(**as_dict(self.host_wet_mass)) if self.humidity is not None and not isinstance(self.humidity, QuantityValue): self.humidity = QuantityValue(**as_dict(self.humidity)) @@ -2387,33 +2378,30 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.humidity_regm = [self.humidity_regm] if self.humidity_regm is not None else [] self.humidity_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.humidity_regm] - if self.indoor_space is not None and not isinstance(self.indoor_space, IndoorSpaceEnum): - self.indoor_space = IndoorSpaceEnum(self.indoor_space) + if self.indoor_space is not None and not isinstance(self.indoor_space, INDOORSPACEENUM): + self.indoor_space = INDOORSPACEENUM(self.indoor_space) - if self.indoor_surf is not None and not isinstance(self.indoor_surf, IndoorSurfEnum): - self.indoor_surf = IndoorSurfEnum(self.indoor_surf) + if self.indoor_surf is not None and not isinstance(self.indoor_surf, INDOORSURFENUM): + self.indoor_surf = INDOORSURFENUM(self.indoor_surf) - if self.indust_eff_percent is not None and not isinstance(self.indust_eff_percent, QuantityValue): - self.indust_eff_percent = QuantityValue(**as_dict(self.indust_eff_percent)) + if self.indust_eff_percent is not None and not isinstance(self.indust_eff_percent, TextValue): + self.indust_eff_percent = TextValue(**as_dict(self.indust_eff_percent)) if not isinstance(self.inorg_particles, list): self.inorg_particles = [self.inorg_particles] if self.inorg_particles is not None else [] self.inorg_particles = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.inorg_particles] - if self.inside_lux is not None and not isinstance(self.inside_lux, QuantityValue): - self.inside_lux = QuantityValue(**as_dict(self.inside_lux)) + if self.inside_lux is not None and not isinstance(self.inside_lux, TextValue): + self.inside_lux = TextValue(**as_dict(self.inside_lux)) - if self.int_wall_cond is not None and not isinstance(self.int_wall_cond, IntWallCondEnum): - self.int_wall_cond = IntWallCondEnum(self.int_wall_cond) - - if self.investigation_field is not None and not isinstance(self.investigation_field, str): - self.investigation_field = str(self.investigation_field) + if self.int_wall_cond is not None and not isinstance(self.int_wall_cond, SHAREDENUM3): + self.int_wall_cond = SHAREDENUM3(self.int_wall_cond) if self.iw_bt_date_well is not None and not isinstance(self.iw_bt_date_well, TimestampValue): self.iw_bt_date_well = TimestampValue(**as_dict(self.iw_bt_date_well)) - if self.iwf is not None and not isinstance(self.iwf, QuantityValue): - self.iwf = QuantityValue(**as_dict(self.iwf)) + if self.iwf is not None and not isinstance(self.iwf, float): + self.iwf = float(self.iwf) if self.last_clean is not None and not isinstance(self.last_clean, TimestampValue): self.last_clean = TimestampValue(**as_dict(self.last_clean)) @@ -2427,30 +2415,30 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.lbceq is not None and not isinstance(self.lbceq, QuantityValue): self.lbceq = QuantityValue(**as_dict(self.lbceq)) - if self.light_intensity is not None and not isinstance(self.light_intensity, QuantityValue): - self.light_intensity = QuantityValue(**as_dict(self.light_intensity)) + if self.light_intensity is not None and not isinstance(self.light_intensity, TextValue): + self.light_intensity = TextValue(**as_dict(self.light_intensity)) if self.light_regm is not None and not isinstance(self.light_regm, TextValue): self.light_regm = TextValue(**as_dict(self.light_regm)) if not isinstance(self.light_type, list): self.light_type = [self.light_type] if self.light_type is not None else [] - self.light_type = [v if isinstance(v, LightTypeEnum) else LightTypeEnum(v) for v in self.light_type] + self.light_type = [v if isinstance(v, LIGHTTYPEENUM) else LIGHTTYPEENUM(v) for v in self.light_type] if self.link_addit_analys is not None and not isinstance(self.link_addit_analys, TextValue): self.link_addit_analys = TextValue(**as_dict(self.link_addit_analys)) - if self.link_class_info is not None and not isinstance(self.link_class_info, TextValue): - self.link_class_info = TextValue(**as_dict(self.link_class_info)) + if self.link_class_info is not None and not isinstance(self.link_class_info, str): + self.link_class_info = str(self.link_class_info) if self.link_climate_info is not None and not isinstance(self.link_climate_info, TextValue): self.link_climate_info = TextValue(**as_dict(self.link_climate_info)) - if self.lithology is not None and not isinstance(self.lithology, LithologyEnum): - self.lithology = LithologyEnum(self.lithology) + if self.lithology is not None and not isinstance(self.lithology, LITHOLOGYENUM): + self.lithology = LITHOLOGYENUM(self.lithology) - if self.local_class is not None and not isinstance(self.local_class, TextValue): - self.local_class = TextValue(**as_dict(self.local_class)) + if self.local_class is not None and not isinstance(self.local_class, str): + self.local_class = str(self.local_class) if self.local_class_meth is not None and not isinstance(self.local_class_meth, TextValue): self.local_class_meth = TextValue(**as_dict(self.local_class_meth)) @@ -2464,27 +2452,27 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.max_occup is not None and not isinstance(self.max_occup, QuantityValue): self.max_occup = QuantityValue(**as_dict(self.max_occup)) - if self.mean_frict_vel is not None and not isinstance(self.mean_frict_vel, QuantityValue): - self.mean_frict_vel = QuantityValue(**as_dict(self.mean_frict_vel)) + if self.mean_frict_vel is not None and not isinstance(self.mean_frict_vel, TextValue): + self.mean_frict_vel = TextValue(**as_dict(self.mean_frict_vel)) - if self.mean_peak_frict_vel is not None and not isinstance(self.mean_peak_frict_vel, QuantityValue): - self.mean_peak_frict_vel = QuantityValue(**as_dict(self.mean_peak_frict_vel)) + if self.mean_peak_frict_vel is not None and not isinstance(self.mean_peak_frict_vel, TextValue): + self.mean_peak_frict_vel = TextValue(**as_dict(self.mean_peak_frict_vel)) - if self.mech_struc is not None and not isinstance(self.mech_struc, MechStrucEnum): - self.mech_struc = MechStrucEnum(self.mech_struc) + if self.mech_struc is not None and not isinstance(self.mech_struc, MECHSTRUCENUM): + self.mech_struc = MECHSTRUCENUM(self.mech_struc) if not isinstance(self.mechanical_damage, list): self.mechanical_damage = [self.mechanical_damage] if self.mechanical_damage is not None else [] - self.mechanical_damage = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.mechanical_damage] + self.mechanical_damage = [v if isinstance(v, str) else str(v) for v in self.mechanical_damage] - if self.methane is not None and not isinstance(self.methane, QuantityValue): - self.methane = QuantityValue(**as_dict(self.methane)) + if self.methane is not None and not isinstance(self.methane, TextValue): + self.methane = TextValue(**as_dict(self.methane)) if self.micro_biomass_meth is not None and not isinstance(self.micro_biomass_meth, str): self.micro_biomass_meth = str(self.micro_biomass_meth) - if self.microbial_biomass is not None and not isinstance(self.microbial_biomass, QuantityValue): - self.microbial_biomass = QuantityValue(**as_dict(self.microbial_biomass)) + if self.microbial_biomass is not None and not isinstance(self.microbial_biomass, TextValue): + self.microbial_biomass = TextValue(**as_dict(self.microbial_biomass)) if not isinstance(self.mineral_nutr_regm, list): self.mineral_nutr_regm = [self.mineral_nutr_regm] if self.mineral_nutr_regm is not None else [] @@ -2504,8 +2492,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.nitrate_nitrogen is not None and not isinstance(self.nitrate_nitrogen, QuantityValue): self.nitrate_nitrogen = QuantityValue(**as_dict(self.nitrate_nitrogen)) - if self.nitrite is not None and not isinstance(self.nitrite, QuantityValue): - self.nitrite = QuantityValue(**as_dict(self.nitrite)) + if self.nitrite is not None and not isinstance(self.nitrite, TextValue): + self.nitrite = TextValue(**as_dict(self.nitrite)) if self.nitrite_nitrogen is not None and not isinstance(self.nitrite_nitrogen, QuantityValue): self.nitrite_nitrogen = QuantityValue(**as_dict(self.nitrite_nitrogen)) @@ -2523,9 +2511,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.nucl_acid_ext is not None and not isinstance(self.nucl_acid_ext, TextValue): self.nucl_acid_ext = TextValue(**as_dict(self.nucl_acid_ext)) - if self.nucleic_acid_sequence_source_field is not None and not isinstance(self.nucleic_acid_sequence_source_field, str): - self.nucleic_acid_sequence_source_field = str(self.nucleic_acid_sequence_source_field) - if self.number_pets is not None and not isinstance(self.number_pets, QuantityValue): self.number_pets = QuantityValue(**as_dict(self.number_pets)) @@ -2538,8 +2523,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.occup_density_samp is not None and not isinstance(self.occup_density_samp, QuantityValue): self.occup_density_samp = QuantityValue(**as_dict(self.occup_density_samp)) - if self.occup_document is not None and not isinstance(self.occup_document, OccupDocumentEnum): - self.occup_document = OccupDocumentEnum(self.occup_document) + if self.occup_document is not None and not isinstance(self.occup_document, OCCUPDOCUMENTENUM): + self.occup_document = OCCUPDOCUMENTENUM(self.occup_document) if self.occup_samp is not None and not isinstance(self.occup_samp, QuantityValue): self.occup_samp = QuantityValue(**as_dict(self.occup_samp)) @@ -2550,11 +2535,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.org_count_qpcr_info is not None and not isinstance(self.org_count_qpcr_info, str): self.org_count_qpcr_info = str(self.org_count_qpcr_info) - if self.org_matter is not None and not isinstance(self.org_matter, QuantityValue): - self.org_matter = QuantityValue(**as_dict(self.org_matter)) + if self.org_matter is not None and not isinstance(self.org_matter, TextValue): + self.org_matter = TextValue(**as_dict(self.org_matter)) - if self.org_nitro is not None and not isinstance(self.org_nitro, QuantityValue): - self.org_nitro = QuantityValue(**as_dict(self.org_nitro)) + if self.org_nitro is not None and not isinstance(self.org_nitro, TextValue): + self.org_nitro = TextValue(**as_dict(self.org_nitro)) if not isinstance(self.org_particles, list): self.org_particles = [self.org_particles] if self.org_particles is not None else [] @@ -2564,30 +2549,30 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.organism_count = [self.organism_count] if self.organism_count is not None else [] self.organism_count = [v if isinstance(v, QuantityValue) else QuantityValue(**as_dict(v)) for v in self.organism_count] - if self.owc_tvdss is not None and not isinstance(self.owc_tvdss, QuantityValue): - self.owc_tvdss = QuantityValue(**as_dict(self.owc_tvdss)) + if self.owc_tvdss is not None and not isinstance(self.owc_tvdss, TextValue): + self.owc_tvdss = TextValue(**as_dict(self.owc_tvdss)) - if self.oxy_stat_samp is not None and not isinstance(self.oxy_stat_samp, OxyStatSampEnum): - self.oxy_stat_samp = OxyStatSampEnum(self.oxy_stat_samp) + if self.oxy_stat_samp is not None and not isinstance(self.oxy_stat_samp, OXYSTATSAMPENUM): + self.oxy_stat_samp = OXYSTATSAMPENUM(self.oxy_stat_samp) - if self.oxygen is not None and not isinstance(self.oxygen, QuantityValue): - self.oxygen = QuantityValue(**as_dict(self.oxygen)) + if self.oxygen is not None and not isinstance(self.oxygen, TextValue): + self.oxygen = TextValue(**as_dict(self.oxygen)) - if self.part_org_carb is not None and not isinstance(self.part_org_carb, QuantityValue): - self.part_org_carb = QuantityValue(**as_dict(self.part_org_carb)) + if self.part_org_carb is not None and not isinstance(self.part_org_carb, TextValue): + self.part_org_carb = TextValue(**as_dict(self.part_org_carb)) - if self.part_org_nitro is not None and not isinstance(self.part_org_nitro, QuantityValue): - self.part_org_nitro = QuantityValue(**as_dict(self.part_org_nitro)) + if self.part_org_nitro is not None and not isinstance(self.part_org_nitro, TextValue): + self.part_org_nitro = TextValue(**as_dict(self.part_org_nitro)) if not isinstance(self.particle_class, list): self.particle_class = [self.particle_class] if self.particle_class is not None else [] self.particle_class = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.particle_class] - if self.pcr_cond is not None and not isinstance(self.pcr_cond, TextValue): - self.pcr_cond = TextValue(**as_dict(self.pcr_cond)) + if self.pcr_cond is not None and not isinstance(self.pcr_cond, str): + self.pcr_cond = str(self.pcr_cond) - if self.pcr_primers is not None and not isinstance(self.pcr_primers, TextValue): - self.pcr_primers = TextValue(**as_dict(self.pcr_primers)) + if self.pcr_primers is not None and not isinstance(self.pcr_primers, str): + self.pcr_primers = str(self.pcr_primers) if self.permeability is not None and not isinstance(self.permeability, TextValue): self.permeability = TextValue(**as_dict(self.permeability)) @@ -2600,8 +2585,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.pesticide_regm = [self.pesticide_regm] if self.pesticide_regm is not None else [] self.pesticide_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.pesticide_regm] - if self.petroleum_hydrocarb is not None and not isinstance(self.petroleum_hydrocarb, QuantityValue): - self.petroleum_hydrocarb = QuantityValue(**as_dict(self.petroleum_hydrocarb)) + if self.petroleum_hydrocarb is not None and not isinstance(self.petroleum_hydrocarb, TextValue): + self.petroleum_hydrocarb = TextValue(**as_dict(self.petroleum_hydrocarb)) if self.ph is not None and not isinstance(self.ph, float): self.ph = float(self.ph) @@ -2617,8 +2602,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.phaeopigments = [self.phaeopigments] if self.phaeopigments is not None else [] self.phaeopigments = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.phaeopigments] - if self.phosphate is not None and not isinstance(self.phosphate, QuantityValue): - self.phosphate = QuantityValue(**as_dict(self.phosphate)) + if self.phosphate is not None and not isinstance(self.phosphate, TextValue): + self.phosphate = TextValue(**as_dict(self.phosphate)) if not isinstance(self.phosplipid_fatt_acid, list): self.phosplipid_fatt_acid = [self.phosplipid_fatt_acid] if self.phosplipid_fatt_acid is not None else [] @@ -2630,11 +2615,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.plant_growth_med is not None and not isinstance(self.plant_growth_med, ControlledTermValue): self.plant_growth_med = ControlledTermValue(**as_dict(self.plant_growth_med)) - if self.plant_product is not None and not isinstance(self.plant_product, TextValue): - self.plant_product = TextValue(**as_dict(self.plant_product)) + if self.plant_product is not None and not isinstance(self.plant_product, str): + self.plant_product = str(self.plant_product) - if self.plant_sex is not None and not isinstance(self.plant_sex, PlantSexEnum): - self.plant_sex = PlantSexEnum(self.plant_sex) + if self.plant_sex is not None and not isinstance(self.plant_sex, PLANTSEXENUM): + self.plant_sex = PLANTSEXENUM(self.plant_sex) if self.plant_struc is not None and not isinstance(self.plant_struc, ControlledTermValue): self.plant_struc = ControlledTermValue(**as_dict(self.plant_struc)) @@ -2643,8 +2628,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.pollutants = [self.pollutants] if self.pollutants is not None else [] self.pollutants = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.pollutants] - if self.pool_dna_extracts is not None and not isinstance(self.pool_dna_extracts, TextValue): - self.pool_dna_extracts = TextValue(**as_dict(self.pool_dna_extracts)) + if self.pool_dna_extracts is not None and not isinstance(self.pool_dna_extracts, str): + self.pool_dna_extracts = str(self.pool_dna_extracts) if self.porosity is not None and not isinstance(self.porosity, TextValue): self.porosity = TextValue(**as_dict(self.porosity)) @@ -2652,41 +2637,41 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.potassium is not None and not isinstance(self.potassium, QuantityValue): self.potassium = QuantityValue(**as_dict(self.potassium)) - if self.pour_point is not None and not isinstance(self.pour_point, QuantityValue): - self.pour_point = QuantityValue(**as_dict(self.pour_point)) + if self.pour_point is not None and not isinstance(self.pour_point, TextValue): + self.pour_point = TextValue(**as_dict(self.pour_point)) - if self.pre_treatment is not None and not isinstance(self.pre_treatment, TextValue): - self.pre_treatment = TextValue(**as_dict(self.pre_treatment)) + if self.pre_treatment is not None and not isinstance(self.pre_treatment, str): + self.pre_treatment = str(self.pre_treatment) if self.pres_animal_insect is not None and not isinstance(self.pres_animal_insect, str): self.pres_animal_insect = str(self.pres_animal_insect) - if self.pressure is not None and not isinstance(self.pressure, QuantityValue): - self.pressure = QuantityValue(**as_dict(self.pressure)) + if self.pressure is not None and not isinstance(self.pressure, TextValue): + self.pressure = TextValue(**as_dict(self.pressure)) if self.prev_land_use_meth is not None and not isinstance(self.prev_land_use_meth, str): self.prev_land_use_meth = str(self.prev_land_use_meth) - if self.previous_land_use is not None and not isinstance(self.previous_land_use, TextValue): - self.previous_land_use = TextValue(**as_dict(self.previous_land_use)) + if self.previous_land_use is not None and not isinstance(self.previous_land_use, str): + self.previous_land_use = str(self.previous_land_use) - if self.primary_prod is not None and not isinstance(self.primary_prod, QuantityValue): - self.primary_prod = QuantityValue(**as_dict(self.primary_prod)) + if self.primary_prod is not None and not isinstance(self.primary_prod, TextValue): + self.primary_prod = TextValue(**as_dict(self.primary_prod)) - if self.primary_treatment is not None and not isinstance(self.primary_treatment, TextValue): - self.primary_treatment = TextValue(**as_dict(self.primary_treatment)) + if self.primary_treatment is not None and not isinstance(self.primary_treatment, str): + self.primary_treatment = str(self.primary_treatment) - if self.prod_rate is not None and not isinstance(self.prod_rate, QuantityValue): - self.prod_rate = QuantityValue(**as_dict(self.prod_rate)) + if self.prod_rate is not None and not isinstance(self.prod_rate, TextValue): + self.prod_rate = TextValue(**as_dict(self.prod_rate)) if self.prod_start_date is not None and not isinstance(self.prod_start_date, TimestampValue): self.prod_start_date = TimestampValue(**as_dict(self.prod_start_date)) - if self.profile_position is not None and not isinstance(self.profile_position, ProfilePositionEnum): - self.profile_position = ProfilePositionEnum(self.profile_position) + if self.profile_position is not None and not isinstance(self.profile_position, PROFILEPOSITIONENUM): + self.profile_position = PROFILEPOSITIONENUM(self.profile_position) - if self.quad_pos is not None and not isinstance(self.quad_pos, QuadPosEnum): - self.quad_pos = QuadPosEnum(self.quad_pos) + if self.quad_pos is not None and not isinstance(self.quad_pos, QUADPOSENUM): + self.quad_pos = QUADPOSENUM(self.quad_pos) if not isinstance(self.radiation_regm, list): self.radiation_regm = [self.radiation_regm] if self.radiation_regm is not None else [] @@ -2696,20 +2681,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.rainfall_regm = [self.rainfall_regm] if self.rainfall_regm is not None else [] self.rainfall_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.rainfall_regm] - if self.reactor_type is not None and not isinstance(self.reactor_type, TextValue): - self.reactor_type = TextValue(**as_dict(self.reactor_type)) + if self.reactor_type is not None and not isinstance(self.reactor_type, str): + self.reactor_type = str(self.reactor_type) - if self.redox_potential is not None and not isinstance(self.redox_potential, QuantityValue): - self.redox_potential = QuantityValue(**as_dict(self.redox_potential)) + if self.redox_potential is not None and not isinstance(self.redox_potential, TextValue): + self.redox_potential = TextValue(**as_dict(self.redox_potential)) - if self.rel_air_humidity is not None and not isinstance(self.rel_air_humidity, QuantityValue): - self.rel_air_humidity = QuantityValue(**as_dict(self.rel_air_humidity)) + if self.rel_air_humidity is not None and not isinstance(self.rel_air_humidity, float): + self.rel_air_humidity = float(self.rel_air_humidity) - if self.rel_humidity_out is not None and not isinstance(self.rel_humidity_out, QuantityValue): - self.rel_humidity_out = QuantityValue(**as_dict(self.rel_humidity_out)) + if self.rel_humidity_out is not None and not isinstance(self.rel_humidity_out, TextValue): + self.rel_humidity_out = TextValue(**as_dict(self.rel_humidity_out)) - if self.rel_samp_loc is not None and not isinstance(self.rel_samp_loc, RelSampLocEnum): - self.rel_samp_loc = RelSampLocEnum(self.rel_samp_loc) + if self.rel_samp_loc is not None and not isinstance(self.rel_samp_loc, RELSAMPLOCENUM): + self.rel_samp_loc = RELSAMPLOCENUM(self.rel_samp_loc) if self.reservoir is not None and not isinstance(self.reservoir, TextValue): self.reservoir = TextValue(**as_dict(self.reservoir)) @@ -2717,17 +2702,17 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.resins_pc is not None and not isinstance(self.resins_pc, TextValue): self.resins_pc = TextValue(**as_dict(self.resins_pc)) - if self.room_air_exch_rate is not None and not isinstance(self.room_air_exch_rate, QuantityValue): - self.room_air_exch_rate = QuantityValue(**as_dict(self.room_air_exch_rate)) + if self.room_air_exch_rate is not None and not isinstance(self.room_air_exch_rate, TextValue): + self.room_air_exch_rate = TextValue(**as_dict(self.room_air_exch_rate)) if self.room_architec_elem is not None and not isinstance(self.room_architec_elem, str): self.room_architec_elem = str(self.room_architec_elem) - if self.room_condt is not None and not isinstance(self.room_condt, RoomCondtEnum): - self.room_condt = RoomCondtEnum(self.room_condt) + if self.room_condt is not None and not isinstance(self.room_condt, ROOMCONDTENUM): + self.room_condt = ROOMCONDTENUM(self.room_condt) - if self.room_connected is not None and not isinstance(self.room_connected, RoomConnectedEnum): - self.room_connected = RoomConnectedEnum(self.room_connected) + if self.room_connected is not None and not isinstance(self.room_connected, ROOMCONNECTEDENUM): + self.room_connected = ROOMCONNECTEDENUM(self.room_connected) if self.room_count is not None and not isinstance(self.room_count, TextValue): self.room_count = TextValue(**as_dict(self.room_count)) @@ -2744,8 +2729,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.room_hallway is not None and not isinstance(self.room_hallway, TextValue): self.room_hallway = TextValue(**as_dict(self.room_hallway)) - if self.room_loc is not None and not isinstance(self.room_loc, RoomLocEnum): - self.room_loc = RoomLocEnum(self.room_loc) + if self.room_loc is not None and not isinstance(self.room_loc, ROOMLOCENUM): + self.room_loc = ROOMLOCENUM(self.room_loc) if self.room_moist_dam_hist is not None and not isinstance(self.room_moist_dam_hist, int): self.room_moist_dam_hist = int(self.room_moist_dam_hist) @@ -2756,11 +2741,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.room_occup is not None and not isinstance(self.room_occup, QuantityValue): self.room_occup = QuantityValue(**as_dict(self.room_occup)) - if self.room_samp_pos is not None and not isinstance(self.room_samp_pos, RoomSampPosEnum): - self.room_samp_pos = RoomSampPosEnum(self.room_samp_pos) + if self.room_samp_pos is not None and not isinstance(self.room_samp_pos, ROOMSAMPPOSENUM): + self.room_samp_pos = ROOMSAMPPOSENUM(self.room_samp_pos) - if self.room_type is not None and not isinstance(self.room_type, RoomTypeEnum): - self.room_type = RoomTypeEnum(self.room_type) + if self.room_type is not None and not isinstance(self.room_type, str): + self.room_type = str(self.room_type) if self.room_vol is not None and not isinstance(self.room_vol, TextValue): self.room_vol = TextValue(**as_dict(self.room_vol)) @@ -2795,33 +2780,24 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.root_med_suppl is not None and not isinstance(self.root_med_suppl, TextValue): self.root_med_suppl = TextValue(**as_dict(self.root_med_suppl)) - if self.salinity is not None and not isinstance(self.salinity, QuantityValue): - self.salinity = QuantityValue(**as_dict(self.salinity)) - - if self.salinity_meth is not None and not isinstance(self.salinity_meth, TextValue): - self.salinity_meth = TextValue(**as_dict(self.salinity_meth)) + if self.salinity is not None and not isinstance(self.salinity, TextValue): + self.salinity = TextValue(**as_dict(self.salinity)) if not isinstance(self.salt_regm, list): self.salt_regm = [self.salt_regm] if self.salt_regm is not None else [] self.salt_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.salt_regm] - if self.samp_capt_status is not None and not isinstance(self.samp_capt_status, SampCaptStatusEnum): - self.samp_capt_status = SampCaptStatusEnum(self.samp_capt_status) - - if self.samp_collec_device is not None and not isinstance(self.samp_collec_device, str): - self.samp_collec_device = str(self.samp_collec_device) - - if self.samp_collec_method is not None and not isinstance(self.samp_collec_method, str): - self.samp_collec_method = str(self.samp_collec_method) + if self.samp_capt_status is not None and not isinstance(self.samp_capt_status, SAMPCAPTSTATUSENUM): + self.samp_capt_status = SAMPCAPTSTATUSENUM(self.samp_capt_status) - if self.samp_collect_point is not None and not isinstance(self.samp_collect_point, SampCollectPointEnum): - self.samp_collect_point = SampCollectPointEnum(self.samp_collect_point) + if self.samp_collect_point is not None and not isinstance(self.samp_collect_point, SAMPCOLLECTPOINTENUM): + self.samp_collect_point = SAMPCOLLECTPOINTENUM(self.samp_collect_point) - if self.samp_dis_stage is not None and not isinstance(self.samp_dis_stage, SampDisStageEnum): - self.samp_dis_stage = SampDisStageEnum(self.samp_dis_stage) + if self.samp_dis_stage is not None and not isinstance(self.samp_dis_stage, SAMPDISSTAGEENUM): + self.samp_dis_stage = SAMPDISSTAGEENUM(self.samp_dis_stage) - if self.samp_floor is not None and not isinstance(self.samp_floor, SampFloorEnum): - self.samp_floor = SampFloorEnum(self.samp_floor) + if self.samp_floor is not None and not isinstance(self.samp_floor, str): + self.samp_floor = str(self.samp_floor) if self.samp_loc_corr_rate is not None and not isinstance(self.samp_loc_corr_rate, TextValue): self.samp_loc_corr_rate = TextValue(**as_dict(self.samp_loc_corr_rate)) @@ -2851,14 +2827,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.samp_store_dur is not None and not isinstance(self.samp_store_dur, TextValue): self.samp_store_dur = TextValue(**as_dict(self.samp_store_dur)) - if self.samp_store_loc is not None and not isinstance(self.samp_store_loc, TextValue): - self.samp_store_loc = TextValue(**as_dict(self.samp_store_loc)) + if self.samp_store_loc is not None and not isinstance(self.samp_store_loc, str): + self.samp_store_loc = str(self.samp_store_loc) if self.samp_store_temp is not None and not isinstance(self.samp_store_temp, QuantityValue): self.samp_store_temp = QuantityValue(**as_dict(self.samp_store_temp)) - if self.samp_subtype is not None and not isinstance(self.samp_subtype, SampSubtypeEnum): - self.samp_subtype = SampSubtypeEnum(self.samp_subtype) + if self.samp_subtype is not None and not isinstance(self.samp_subtype, SAMPSUBTYPEENUM): + self.samp_subtype = SAMPSUBTYPEENUM(self.samp_subtype) if self.samp_taxon_id is not None and not isinstance(self.samp_taxon_id, ControlledIdentifiedTermValue): self.samp_taxon_id = ControlledIdentifiedTermValue(**as_dict(self.samp_taxon_id)) @@ -2875,11 +2851,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.samp_type is not None and not isinstance(self.samp_type, TextValue): self.samp_type = TextValue(**as_dict(self.samp_type)) - if self.samp_vol_we_dna_ext is not None and not isinstance(self.samp_vol_we_dna_ext, QuantityValue): - self.samp_vol_we_dna_ext = QuantityValue(**as_dict(self.samp_vol_we_dna_ext)) + if self.samp_vol_we_dna_ext is not None and not isinstance(self.samp_vol_we_dna_ext, TextValue): + self.samp_vol_we_dna_ext = TextValue(**as_dict(self.samp_vol_we_dna_ext)) - if self.samp_weather is not None and not isinstance(self.samp_weather, SampWeatherEnum): - self.samp_weather = SampWeatherEnum(self.samp_weather) + if self.samp_weather is not None and not isinstance(self.samp_weather, SAMPWEATHERENUM): + self.samp_weather = SAMPWEATHERENUM(self.samp_weather) if self.samp_well_name is not None and not isinstance(self.samp_well_name, TextValue): self.samp_well_name = TextValue(**as_dict(self.samp_well_name)) @@ -2894,86 +2870,80 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.season_environment = [self.season_environment] if self.season_environment is not None else [] self.season_environment = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.season_environment] - if self.season_precpt is not None and not isinstance(self.season_precpt, QuantityValue): - self.season_precpt = QuantityValue(**as_dict(self.season_precpt)) + if self.season_precpt is not None and not isinstance(self.season_precpt, TextValue): + self.season_precpt = TextValue(**as_dict(self.season_precpt)) - if self.season_temp is not None and not isinstance(self.season_temp, QuantityValue): - self.season_temp = QuantityValue(**as_dict(self.season_temp)) + if self.season_temp is not None and not isinstance(self.season_temp, TextValue): + self.season_temp = TextValue(**as_dict(self.season_temp)) - if self.season_use is not None and not isinstance(self.season_use, SeasonUseEnum): - self.season_use = SeasonUseEnum(self.season_use) + if self.season_use is not None and not isinstance(self.season_use, SEASONUSEENUM): + self.season_use = SEASONUSEENUM(self.season_use) - if self.secondary_treatment is not None and not isinstance(self.secondary_treatment, TextValue): - self.secondary_treatment = TextValue(**as_dict(self.secondary_treatment)) + if self.secondary_treatment is not None and not isinstance(self.secondary_treatment, str): + self.secondary_treatment = str(self.secondary_treatment) - if self.sediment_type is not None and not isinstance(self.sediment_type, SedimentTypeEnum): - self.sediment_type = SedimentTypeEnum(self.sediment_type) + if self.sediment_type is not None and not isinstance(self.sediment_type, SEDIMENTTYPEENUM): + self.sediment_type = SEDIMENTTYPEENUM(self.sediment_type) if self.seq_meth is not None and not isinstance(self.seq_meth, TextValue): self.seq_meth = TextValue(**as_dict(self.seq_meth)) - if self.seq_quality_check is not None and not isinstance(self.seq_quality_check, TextValue): - self.seq_quality_check = TextValue(**as_dict(self.seq_quality_check)) - - if self.sequencing_field is not None and not isinstance(self.sequencing_field, str): - self.sequencing_field = str(self.sequencing_field) + if self.seq_quality_check is not None and not isinstance(self.seq_quality_check, SEQQUALITYCHECKENUM): + self.seq_quality_check = SEQQUALITYCHECKENUM(self.seq_quality_check) - if self.sewage_type is not None and not isinstance(self.sewage_type, TextValue): - self.sewage_type = TextValue(**as_dict(self.sewage_type)) + if self.sewage_type is not None and not isinstance(self.sewage_type, str): + self.sewage_type = str(self.sewage_type) if self.shad_dev_water_mold is not None and not isinstance(self.shad_dev_water_mold, str): self.shad_dev_water_mold = str(self.shad_dev_water_mold) - if self.shading_device_cond is not None and not isinstance(self.shading_device_cond, ShadingDeviceCondEnum): - self.shading_device_cond = ShadingDeviceCondEnum(self.shading_device_cond) + if self.shading_device_cond is not None and not isinstance(self.shading_device_cond, SHAREDENUM2): + self.shading_device_cond = SHAREDENUM2(self.shading_device_cond) - if self.shading_device_loc is not None and not isinstance(self.shading_device_loc, TextValue): - self.shading_device_loc = TextValue(**as_dict(self.shading_device_loc)) + if self.shading_device_loc is not None and not isinstance(self.shading_device_loc, SHADINGDEVICELOCENUM): + self.shading_device_loc = SHADINGDEVICELOCENUM(self.shading_device_loc) - if self.shading_device_mat is not None and not isinstance(self.shading_device_mat, TextValue): - self.shading_device_mat = TextValue(**as_dict(self.shading_device_mat)) + if self.shading_device_mat is not None and not isinstance(self.shading_device_mat, str): + self.shading_device_mat = str(self.shading_device_mat) - if self.shading_device_type is not None and not isinstance(self.shading_device_type, ShadingDeviceTypeEnum): - self.shading_device_type = ShadingDeviceTypeEnum(self.shading_device_type) + if self.shading_device_type is not None and not isinstance(self.shading_device_type, SHADINGDEVICETYPEENUM): + self.shading_device_type = SHADINGDEVICETYPEENUM(self.shading_device_type) if self.sieving is not None and not isinstance(self.sieving, TextValue): self.sieving = TextValue(**as_dict(self.sieving)) - if self.silicate is not None and not isinstance(self.silicate, QuantityValue): - self.silicate = QuantityValue(**as_dict(self.silicate)) + if self.silicate is not None and not isinstance(self.silicate, TextValue): + self.silicate = TextValue(**as_dict(self.silicate)) if self.size_frac is not None and not isinstance(self.size_frac, TextValue): self.size_frac = TextValue(**as_dict(self.size_frac)) - if self.size_frac_low is not None and not isinstance(self.size_frac_low, QuantityValue): - self.size_frac_low = QuantityValue(**as_dict(self.size_frac_low)) + if self.size_frac_low is not None and not isinstance(self.size_frac_low, TextValue): + self.size_frac_low = TextValue(**as_dict(self.size_frac_low)) - if self.size_frac_up is not None and not isinstance(self.size_frac_up, QuantityValue): - self.size_frac_up = QuantityValue(**as_dict(self.size_frac_up)) + if self.size_frac_up is not None and not isinstance(self.size_frac_up, TextValue): + self.size_frac_up = TextValue(**as_dict(self.size_frac_up)) - if self.slope_aspect is not None and not isinstance(self.slope_aspect, QuantityValue): - self.slope_aspect = QuantityValue(**as_dict(self.slope_aspect)) + if self.slope_aspect is not None and not isinstance(self.slope_aspect, TextValue): + self.slope_aspect = TextValue(**as_dict(self.slope_aspect)) - if self.slope_gradient is not None and not isinstance(self.slope_gradient, QuantityValue): - self.slope_gradient = QuantityValue(**as_dict(self.slope_gradient)) + if self.slope_gradient is not None and not isinstance(self.slope_gradient, TextValue): + self.slope_gradient = TextValue(**as_dict(self.slope_gradient)) - if self.sludge_retent_time is not None and not isinstance(self.sludge_retent_time, QuantityValue): - self.sludge_retent_time = QuantityValue(**as_dict(self.sludge_retent_time)) + if self.sludge_retent_time is not None and not isinstance(self.sludge_retent_time, TextValue): + self.sludge_retent_time = TextValue(**as_dict(self.sludge_retent_time)) if self.sodium is not None and not isinstance(self.sodium, QuantityValue): self.sodium = QuantityValue(**as_dict(self.sodium)) - if self.soil_horizon is not None and not isinstance(self.soil_horizon, SoilHorizonEnum): - self.soil_horizon = SoilHorizonEnum(self.soil_horizon) - - if self.soil_text_measure is not None and not isinstance(self.soil_text_measure, QuantityValue): - self.soil_text_measure = QuantityValue(**as_dict(self.soil_text_measure)) + if self.soil_horizon is not None and not isinstance(self.soil_horizon, SOILHORIZONENUM): + self.soil_horizon = SOILHORIZONENUM(self.soil_horizon) if self.soil_texture_meth is not None and not isinstance(self.soil_texture_meth, str): self.soil_texture_meth = str(self.soil_texture_meth) - if self.soil_type is not None and not isinstance(self.soil_type, TextValue): - self.soil_type = TextValue(**as_dict(self.soil_type)) + if self.soil_type is not None and not isinstance(self.soil_type, str): + self.soil_type = str(self.soil_type) if self.soil_type_meth is not None and not isinstance(self.soil_type_meth, TextValue): self.soil_type_meth = TextValue(**as_dict(self.soil_type_meth)) @@ -2995,29 +2965,29 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.source_mat_id is not None and not isinstance(self.source_mat_id, TextValue): self.source_mat_id = TextValue(**as_dict(self.source_mat_id)) - if self.space_typ_state is not None and not isinstance(self.space_typ_state, TextValue): - self.space_typ_state = TextValue(**as_dict(self.space_typ_state)) + if self.space_typ_state is not None and not isinstance(self.space_typ_state, SPACETYPSTATEENUM): + self.space_typ_state = SPACETYPSTATEENUM(self.space_typ_state) - if self.specific is not None and not isinstance(self.specific, SpecificEnum): - self.specific = SpecificEnum(self.specific) + if self.specific is not None and not isinstance(self.specific, SPECIFICENUM): + self.specific = SPECIFICENUM(self.specific) if self.specific_ecosystem is not None and not isinstance(self.specific_ecosystem, str): self.specific_ecosystem = str(self.specific_ecosystem) - if self.specific_humidity is not None and not isinstance(self.specific_humidity, QuantityValue): - self.specific_humidity = QuantityValue(**as_dict(self.specific_humidity)) + if self.specific_humidity is not None and not isinstance(self.specific_humidity, TextValue): + self.specific_humidity = TextValue(**as_dict(self.specific_humidity)) - if self.sr_dep_env is not None and not isinstance(self.sr_dep_env, SrDepEnvEnum): - self.sr_dep_env = SrDepEnvEnum(self.sr_dep_env) + if self.sr_dep_env is not None and not isinstance(self.sr_dep_env, SRDEPENVENUM): + self.sr_dep_env = SRDEPENVENUM(self.sr_dep_env) - if self.sr_geol_age is not None and not isinstance(self.sr_geol_age, SrGeolAgeEnum): - self.sr_geol_age = SrGeolAgeEnum(self.sr_geol_age) + if self.sr_geol_age is not None and not isinstance(self.sr_geol_age, SHAREDENUM5): + self.sr_geol_age = SHAREDENUM5(self.sr_geol_age) - if self.sr_kerog_type is not None and not isinstance(self.sr_kerog_type, SrKerogTypeEnum): - self.sr_kerog_type = SrKerogTypeEnum(self.sr_kerog_type) + if self.sr_kerog_type is not None and not isinstance(self.sr_kerog_type, SRKEROGTYPEENUM): + self.sr_kerog_type = SRKEROGTYPEENUM(self.sr_kerog_type) - if self.sr_lithology is not None and not isinstance(self.sr_lithology, SrLithologyEnum): - self.sr_lithology = SrLithologyEnum(self.sr_lithology) + if self.sr_lithology is not None and not isinstance(self.sr_lithology, SRLITHOLOGYENUM): + self.sr_lithology = SRLITHOLOGYENUM(self.sr_lithology) if not isinstance(self.standing_water_regm, list): self.standing_water_regm = [self.standing_water_regm] if self.standing_water_regm is not None else [] @@ -3028,45 +2998,45 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.substructure_type, list): self.substructure_type = [self.substructure_type] if self.substructure_type is not None else [] - self.substructure_type = [v if isinstance(v, SubstructureTypeEnum) else SubstructureTypeEnum(v) for v in self.substructure_type] + self.substructure_type = [v if isinstance(v, SUBSTRUCTURETYPEENUM) else SUBSTRUCTURETYPEENUM(v) for v in self.substructure_type] if self.sulfate is not None and not isinstance(self.sulfate, QuantityValue): self.sulfate = QuantityValue(**as_dict(self.sulfate)) - if self.sulfate_fw is not None and not isinstance(self.sulfate_fw, QuantityValue): - self.sulfate_fw = QuantityValue(**as_dict(self.sulfate_fw)) + if self.sulfate_fw is not None and not isinstance(self.sulfate_fw, TextValue): + self.sulfate_fw = TextValue(**as_dict(self.sulfate_fw)) - if self.sulfide is not None and not isinstance(self.sulfide, QuantityValue): - self.sulfide = QuantityValue(**as_dict(self.sulfide)) + if self.sulfide is not None and not isinstance(self.sulfide, TextValue): + self.sulfide = TextValue(**as_dict(self.sulfide)) if not isinstance(self.surf_air_cont, list): self.surf_air_cont = [self.surf_air_cont] if self.surf_air_cont is not None else [] - self.surf_air_cont = [v if isinstance(v, SurfAirContEnum) else SurfAirContEnum(v) for v in self.surf_air_cont] + self.surf_air_cont = [v if isinstance(v, SURFAIRCONTENUM) else SURFAIRCONTENUM(v) for v in self.surf_air_cont] - if self.surf_humidity is not None and not isinstance(self.surf_humidity, QuantityValue): - self.surf_humidity = QuantityValue(**as_dict(self.surf_humidity)) + if self.surf_humidity is not None and not isinstance(self.surf_humidity, float): + self.surf_humidity = float(self.surf_humidity) - if self.surf_material is not None and not isinstance(self.surf_material, SurfMaterialEnum): - self.surf_material = SurfMaterialEnum(self.surf_material) + if self.surf_material is not None and not isinstance(self.surf_material, SURFMATERIALENUM): + self.surf_material = SURFMATERIALENUM(self.surf_material) - if self.surf_moisture is not None and not isinstance(self.surf_moisture, QuantityValue): - self.surf_moisture = QuantityValue(**as_dict(self.surf_moisture)) + if self.surf_moisture is not None and not isinstance(self.surf_moisture, TextValue): + self.surf_moisture = TextValue(**as_dict(self.surf_moisture)) if self.surf_moisture_ph is not None and not isinstance(self.surf_moisture_ph, float): self.surf_moisture_ph = float(self.surf_moisture_ph) - if self.surf_temp is not None and not isinstance(self.surf_temp, QuantityValue): - self.surf_temp = QuantityValue(**as_dict(self.surf_temp)) + if self.surf_temp is not None and not isinstance(self.surf_temp, TextValue): + self.surf_temp = TextValue(**as_dict(self.surf_temp)) - if self.suspend_part_matter is not None and not isinstance(self.suspend_part_matter, QuantityValue): - self.suspend_part_matter = QuantityValue(**as_dict(self.suspend_part_matter)) + if self.suspend_part_matter is not None and not isinstance(self.suspend_part_matter, TextValue): + self.suspend_part_matter = TextValue(**as_dict(self.suspend_part_matter)) if not isinstance(self.suspend_solids, list): self.suspend_solids = [self.suspend_solids] if self.suspend_solids is not None else [] self.suspend_solids = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.suspend_solids] - if self.tan is not None and not isinstance(self.tan, QuantityValue): - self.tan = QuantityValue(**as_dict(self.tan)) + if self.tan is not None and not isinstance(self.tan, TextValue): + self.tan = TextValue(**as_dict(self.tan)) if self.target_gene is not None and not isinstance(self.target_gene, TextValue): self.target_gene = TextValue(**as_dict(self.target_gene)) @@ -3077,39 +3047,39 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.temp is not None and not isinstance(self.temp, QuantityValue): self.temp = QuantityValue(**as_dict(self.temp)) - if self.temp_out is not None and not isinstance(self.temp_out, QuantityValue): - self.temp_out = QuantityValue(**as_dict(self.temp_out)) + if self.temp_out is not None and not isinstance(self.temp_out, TextValue): + self.temp_out = TextValue(**as_dict(self.temp_out)) - if self.tertiary_treatment is not None and not isinstance(self.tertiary_treatment, TextValue): - self.tertiary_treatment = TextValue(**as_dict(self.tertiary_treatment)) + if self.tertiary_treatment is not None and not isinstance(self.tertiary_treatment, str): + self.tertiary_treatment = str(self.tertiary_treatment) - if self.tidal_stage is not None and not isinstance(self.tidal_stage, TidalStageEnum): - self.tidal_stage = TidalStageEnum(self.tidal_stage) + if self.tidal_stage is not None and not isinstance(self.tidal_stage, TIDALSTAGEENUM): + self.tidal_stage = TIDALSTAGEENUM(self.tidal_stage) if not isinstance(self.tillage, list): self.tillage = [self.tillage] if self.tillage is not None else [] - self.tillage = [v if isinstance(v, TillageEnum) else TillageEnum(v) for v in self.tillage] + self.tillage = [v if isinstance(v, TILLAGEENUM) else TILLAGEENUM(v) for v in self.tillage] if self.tiss_cult_growth_med is not None and not isinstance(self.tiss_cult_growth_med, TextValue): self.tiss_cult_growth_med = TextValue(**as_dict(self.tiss_cult_growth_med)) - if self.toluene is not None and not isinstance(self.toluene, QuantityValue): - self.toluene = QuantityValue(**as_dict(self.toluene)) + if self.toluene is not None and not isinstance(self.toluene, TextValue): + self.toluene = TextValue(**as_dict(self.toluene)) if self.tot_carb is not None and not isinstance(self.tot_carb, QuantityValue): self.tot_carb = QuantityValue(**as_dict(self.tot_carb)) - if self.tot_depth_water_col is not None and not isinstance(self.tot_depth_water_col, QuantityValue): - self.tot_depth_water_col = QuantityValue(**as_dict(self.tot_depth_water_col)) + if self.tot_depth_water_col is not None and not isinstance(self.tot_depth_water_col, TextValue): + self.tot_depth_water_col = TextValue(**as_dict(self.tot_depth_water_col)) - if self.tot_diss_nitro is not None and not isinstance(self.tot_diss_nitro, QuantityValue): - self.tot_diss_nitro = QuantityValue(**as_dict(self.tot_diss_nitro)) + if self.tot_diss_nitro is not None and not isinstance(self.tot_diss_nitro, TextValue): + self.tot_diss_nitro = TextValue(**as_dict(self.tot_diss_nitro)) - if self.tot_inorg_nitro is not None and not isinstance(self.tot_inorg_nitro, QuantityValue): - self.tot_inorg_nitro = QuantityValue(**as_dict(self.tot_inorg_nitro)) + if self.tot_inorg_nitro is not None and not isinstance(self.tot_inorg_nitro, TextValue): + self.tot_inorg_nitro = TextValue(**as_dict(self.tot_inorg_nitro)) - if self.tot_iron is not None and not isinstance(self.tot_iron, QuantityValue): - self.tot_iron = QuantityValue(**as_dict(self.tot_iron)) + if self.tot_iron is not None and not isinstance(self.tot_iron, TextValue): + self.tot_iron = TextValue(**as_dict(self.tot_iron)) if self.tot_nitro is not None and not isinstance(self.tot_nitro, QuantityValue): self.tot_nitro = QuantityValue(**as_dict(self.tot_nitro)) @@ -3126,53 +3096,54 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.tot_org_carb is not None and not isinstance(self.tot_org_carb, QuantityValue): self.tot_org_carb = QuantityValue(**as_dict(self.tot_org_carb)) - if self.tot_part_carb is not None and not isinstance(self.tot_part_carb, QuantityValue): - self.tot_part_carb = QuantityValue(**as_dict(self.tot_part_carb)) + if self.tot_part_carb is not None and not isinstance(self.tot_part_carb, TextValue): + self.tot_part_carb = TextValue(**as_dict(self.tot_part_carb)) if self.tot_phosp is not None and not isinstance(self.tot_phosp, QuantityValue): self.tot_phosp = QuantityValue(**as_dict(self.tot_phosp)) - if self.tot_phosphate is not None and not isinstance(self.tot_phosphate, QuantityValue): - self.tot_phosphate = QuantityValue(**as_dict(self.tot_phosphate)) + if self.tot_phosphate is not None and not isinstance(self.tot_phosphate, TextValue): + self.tot_phosphate = TextValue(**as_dict(self.tot_phosphate)) - if self.tot_sulfur is not None and not isinstance(self.tot_sulfur, QuantityValue): - self.tot_sulfur = QuantityValue(**as_dict(self.tot_sulfur)) + if self.tot_sulfur is not None and not isinstance(self.tot_sulfur, TextValue): + self.tot_sulfur = TextValue(**as_dict(self.tot_sulfur)) - if self.train_line is not None and not isinstance(self.train_line, TrainLineEnum): - self.train_line = TrainLineEnum(self.train_line) + if self.train_line is not None and not isinstance(self.train_line, TRAINLINEENUM): + self.train_line = TRAINLINEENUM(self.train_line) - if self.train_stat_loc is not None and not isinstance(self.train_stat_loc, TrainStatLocEnum): - self.train_stat_loc = TrainStatLocEnum(self.train_stat_loc) + if self.train_stat_loc is not None and not isinstance(self.train_stat_loc, TRAINSTATLOCENUM): + self.train_stat_loc = TRAINSTATLOCENUM(self.train_stat_loc) - if self.train_stop_loc is not None and not isinstance(self.train_stop_loc, TrainStopLocEnum): - self.train_stop_loc = TrainStopLocEnum(self.train_stop_loc) + if self.train_stop_loc is not None and not isinstance(self.train_stop_loc, TRAINSTOPLOCENUM): + self.train_stop_loc = TRAINSTOPLOCENUM(self.train_stop_loc) - if self.turbidity is not None and not isinstance(self.turbidity, QuantityValue): - self.turbidity = QuantityValue(**as_dict(self.turbidity)) + if self.turbidity is not None and not isinstance(self.turbidity, TextValue): + self.turbidity = TextValue(**as_dict(self.turbidity)) - if self.tvdss_of_hcr_press is not None and not isinstance(self.tvdss_of_hcr_press, QuantityValue): - self.tvdss_of_hcr_press = QuantityValue(**as_dict(self.tvdss_of_hcr_press)) + if self.tvdss_of_hcr_press is not None and not isinstance(self.tvdss_of_hcr_press, TextValue): + self.tvdss_of_hcr_press = TextValue(**as_dict(self.tvdss_of_hcr_press)) - if self.tvdss_of_hcr_temp is not None and not isinstance(self.tvdss_of_hcr_temp, QuantityValue): - self.tvdss_of_hcr_temp = QuantityValue(**as_dict(self.tvdss_of_hcr_temp)) + if self.tvdss_of_hcr_temp is not None and not isinstance(self.tvdss_of_hcr_temp, TextValue): + self.tvdss_of_hcr_temp = TextValue(**as_dict(self.tvdss_of_hcr_temp)) if self.typ_occup_density is not None and not isinstance(self.typ_occup_density, float): self.typ_occup_density = float(self.typ_occup_density) - if self.ventilation_rate is not None and not isinstance(self.ventilation_rate, QuantityValue): - self.ventilation_rate = QuantityValue(**as_dict(self.ventilation_rate)) + if self.ventilation_rate is not None and not isinstance(self.ventilation_rate, TextValue): + self.ventilation_rate = TextValue(**as_dict(self.ventilation_rate)) - if self.ventilation_type is not None and not isinstance(self.ventilation_type, TextValue): - self.ventilation_type = TextValue(**as_dict(self.ventilation_type)) + if not isinstance(self.ventilation_type, list): + self.ventilation_type = [self.ventilation_type] if self.ventilation_type is not None else [] + self.ventilation_type = [v if isinstance(v, str) else str(v) for v in self.ventilation_type] - if self.vfa is not None and not isinstance(self.vfa, QuantityValue): - self.vfa = QuantityValue(**as_dict(self.vfa)) + if self.vfa is not None and not isinstance(self.vfa, TextValue): + self.vfa = TextValue(**as_dict(self.vfa)) - if self.vfa_fw is not None and not isinstance(self.vfa_fw, QuantityValue): - self.vfa_fw = QuantityValue(**as_dict(self.vfa_fw)) + if self.vfa_fw is not None and not isinstance(self.vfa_fw, TextValue): + self.vfa_fw = TextValue(**as_dict(self.vfa_fw)) - if self.vis_media is not None and not isinstance(self.vis_media, VisMediaEnum): - self.vis_media = VisMediaEnum(self.vis_media) + if self.vis_media is not None and not isinstance(self.vis_media, str): + self.vis_media = str(self.vis_media) if self.viscosity is not None and not isinstance(self.viscosity, TextValue): self.viscosity = TextValue(**as_dict(self.viscosity)) @@ -3181,35 +3152,35 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.volatile_org_comp = [self.volatile_org_comp] if self.volatile_org_comp is not None else [] self.volatile_org_comp = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.volatile_org_comp] - if self.wall_area is not None and not isinstance(self.wall_area, QuantityValue): - self.wall_area = QuantityValue(**as_dict(self.wall_area)) + if self.wall_area is not None and not isinstance(self.wall_area, TextValue): + self.wall_area = TextValue(**as_dict(self.wall_area)) - if self.wall_const_type is not None and not isinstance(self.wall_const_type, WallConstTypeEnum): - self.wall_const_type = WallConstTypeEnum(self.wall_const_type) + if self.wall_const_type is not None and not isinstance(self.wall_const_type, WALLCONSTTYPEENUM): + self.wall_const_type = WALLCONSTTYPEENUM(self.wall_const_type) - if self.wall_finish_mat is not None and not isinstance(self.wall_finish_mat, WallFinishMatEnum): - self.wall_finish_mat = WallFinishMatEnum(self.wall_finish_mat) + if self.wall_finish_mat is not None and not isinstance(self.wall_finish_mat, WALLFINISHMATENUM): + self.wall_finish_mat = WALLFINISHMATENUM(self.wall_finish_mat) - if self.wall_height is not None and not isinstance(self.wall_height, QuantityValue): - self.wall_height = QuantityValue(**as_dict(self.wall_height)) + if self.wall_height is not None and not isinstance(self.wall_height, TextValue): + self.wall_height = TextValue(**as_dict(self.wall_height)) - if self.wall_loc is not None and not isinstance(self.wall_loc, WallLocEnum): - self.wall_loc = WallLocEnum(self.wall_loc) + if self.wall_loc is not None and not isinstance(self.wall_loc, SHAREDENUM0): + self.wall_loc = SHAREDENUM0(self.wall_loc) - if self.wall_surf_treatment is not None and not isinstance(self.wall_surf_treatment, WallSurfTreatmentEnum): - self.wall_surf_treatment = WallSurfTreatmentEnum(self.wall_surf_treatment) + if self.wall_surf_treatment is not None and not isinstance(self.wall_surf_treatment, WALLSURFTREATMENTENUM): + self.wall_surf_treatment = WALLSURFTREATMENTENUM(self.wall_surf_treatment) - if self.wall_texture is not None and not isinstance(self.wall_texture, WallTextureEnum): - self.wall_texture = WallTextureEnum(self.wall_texture) + if self.wall_texture is not None and not isinstance(self.wall_texture, SHAREDENUM4): + self.wall_texture = SHAREDENUM4(self.wall_texture) - if self.wall_thermal_mass is not None and not isinstance(self.wall_thermal_mass, QuantityValue): - self.wall_thermal_mass = QuantityValue(**as_dict(self.wall_thermal_mass)) + if self.wall_thermal_mass is not None and not isinstance(self.wall_thermal_mass, TextValue): + self.wall_thermal_mass = TextValue(**as_dict(self.wall_thermal_mass)) - if self.wall_water_mold is not None and not isinstance(self.wall_water_mold, TextValue): - self.wall_water_mold = TextValue(**as_dict(self.wall_water_mold)) + if self.wall_water_mold is not None and not isinstance(self.wall_water_mold, SHAREDENUM1): + self.wall_water_mold = SHAREDENUM1(self.wall_water_mold) - if self.wastewater_type is not None and not isinstance(self.wastewater_type, TextValue): - self.wastewater_type = TextValue(**as_dict(self.wastewater_type)) + if self.wastewater_type is not None and not isinstance(self.wastewater_type, str): + self.wastewater_type = str(self.wastewater_type) if self.water_cont_soil_meth is not None and not isinstance(self.water_cont_soil_meth, str): self.water_cont_soil_meth = str(self.water_cont_soil_meth) @@ -3218,20 +3189,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.water_content = [self.water_content] if self.water_content is not None else [] self.water_content = [v if isinstance(v, str) else str(v) for v in self.water_content] - if self.water_current is not None and not isinstance(self.water_current, QuantityValue): - self.water_current = QuantityValue(**as_dict(self.water_current)) + if self.water_current is not None and not isinstance(self.water_current, TextValue): + self.water_current = TextValue(**as_dict(self.water_current)) - if self.water_cut is not None and not isinstance(self.water_cut, QuantityValue): - self.water_cut = QuantityValue(**as_dict(self.water_cut)) + if self.water_cut is not None and not isinstance(self.water_cut, TextValue): + self.water_cut = TextValue(**as_dict(self.water_cut)) - if self.water_feat_size is not None and not isinstance(self.water_feat_size, QuantityValue): - self.water_feat_size = QuantityValue(**as_dict(self.water_feat_size)) + if self.water_feat_size is not None and not isinstance(self.water_feat_size, TextValue): + self.water_feat_size = TextValue(**as_dict(self.water_feat_size)) - if self.water_feat_type is not None and not isinstance(self.water_feat_type, WaterFeatTypeEnum): - self.water_feat_type = WaterFeatTypeEnum(self.water_feat_type) + if self.water_feat_type is not None and not isinstance(self.water_feat_type, WATERFEATTYPEENUM): + self.water_feat_type = WATERFEATTYPEENUM(self.water_feat_type) - if self.water_prod_rate is not None and not isinstance(self.water_prod_rate, QuantityValue): - self.water_prod_rate = QuantityValue(**as_dict(self.water_prod_rate)) + if self.water_prod_rate is not None and not isinstance(self.water_prod_rate, TextValue): + self.water_prod_rate = TextValue(**as_dict(self.water_prod_rate)) if not isinstance(self.water_temp_regm, list): self.water_temp_regm = [self.water_temp_regm] if self.water_temp_regm is not None else [] @@ -3241,8 +3212,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.watering_regm = [self.watering_regm] if self.watering_regm is not None else [] self.watering_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.watering_regm] - if self.weekday is not None and not isinstance(self.weekday, WeekdayEnum): - self.weekday = WeekdayEnum(self.weekday) + if self.weekday is not None and not isinstance(self.weekday, WEEKDAYENUM): + self.weekday = WEEKDAYENUM(self.weekday) if self.win is not None and not isinstance(self.win, TextValue): self.win = TextValue(**as_dict(self.win)) @@ -3253,20 +3224,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.wind_speed is not None and not isinstance(self.wind_speed, QuantityValue): self.wind_speed = QuantityValue(**as_dict(self.wind_speed)) - if self.window_cond is not None and not isinstance(self.window_cond, WindowCondEnum): - self.window_cond = WindowCondEnum(self.window_cond) + if self.window_cond is not None and not isinstance(self.window_cond, SHAREDENUM2): + self.window_cond = SHAREDENUM2(self.window_cond) - if self.window_cover is not None and not isinstance(self.window_cover, WindowCoverEnum): - self.window_cover = WindowCoverEnum(self.window_cover) + if self.window_cover is not None and not isinstance(self.window_cover, WINDOWCOVERENUM): + self.window_cover = WINDOWCOVERENUM(self.window_cover) - if self.window_horiz_pos is not None and not isinstance(self.window_horiz_pos, WindowHorizPosEnum): - self.window_horiz_pos = WindowHorizPosEnum(self.window_horiz_pos) + if self.window_horiz_pos is not None and not isinstance(self.window_horiz_pos, WINDOWHORIZPOSENUM): + self.window_horiz_pos = WINDOWHORIZPOSENUM(self.window_horiz_pos) - if self.window_loc is not None and not isinstance(self.window_loc, WindowLocEnum): - self.window_loc = WindowLocEnum(self.window_loc) + if self.window_loc is not None and not isinstance(self.window_loc, SHAREDENUM0): + self.window_loc = SHAREDENUM0(self.window_loc) - if self.window_mat is not None and not isinstance(self.window_mat, WindowMatEnum): - self.window_mat = WindowMatEnum(self.window_mat) + if self.window_mat is not None and not isinstance(self.window_mat, WINDOWMATENUM): + self.window_mat = WINDOWMATENUM(self.window_mat) if self.window_open_freq is not None and not isinstance(self.window_open_freq, TextValue): self.window_open_freq = TextValue(**as_dict(self.window_open_freq)) @@ -3274,20 +3245,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.window_size is not None and not isinstance(self.window_size, TextValue): self.window_size = TextValue(**as_dict(self.window_size)) - if self.window_status is not None and not isinstance(self.window_status, TextValue): - self.window_status = TextValue(**as_dict(self.window_status)) + if self.window_status is not None and not isinstance(self.window_status, WINDOWSTATUSENUM): + self.window_status = WINDOWSTATUSENUM(self.window_status) - if self.window_type is not None and not isinstance(self.window_type, WindowTypeEnum): - self.window_type = WindowTypeEnum(self.window_type) + if self.window_type is not None and not isinstance(self.window_type, WINDOWTYPEENUM): + self.window_type = WINDOWTYPEENUM(self.window_type) - if self.window_vert_pos is not None and not isinstance(self.window_vert_pos, WindowVertPosEnum): - self.window_vert_pos = WindowVertPosEnum(self.window_vert_pos) + if self.window_vert_pos is not None and not isinstance(self.window_vert_pos, WINDOWVERTPOSENUM): + self.window_vert_pos = WINDOWVERTPOSENUM(self.window_vert_pos) - if self.window_water_mold is not None and not isinstance(self.window_water_mold, TextValue): - self.window_water_mold = TextValue(**as_dict(self.window_water_mold)) + if self.window_water_mold is not None and not isinstance(self.window_water_mold, SHAREDENUM1): + self.window_water_mold = SHAREDENUM1(self.window_water_mold) - if self.xylene is not None and not isinstance(self.xylene, QuantityValue): - self.xylene = QuantityValue(**as_dict(self.xylene)) + if self.xylene is not None and not isinstance(self.xylene, TextValue): + self.xylene = TextValue(**as_dict(self.xylene)) if self.zinc is not None and not isinstance(self.zinc, QuantityValue): self.zinc = QuantityValue(**as_dict(self.zinc)) @@ -3347,11 +3318,12 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.air_temp_regm = [self.air_temp_regm] if self.air_temp_regm is not None else [] self.air_temp_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.air_temp_regm] - if self.biotic_regm is not None and not isinstance(self.biotic_regm, TextValue): - self.biotic_regm = TextValue(**as_dict(self.biotic_regm)) + if not isinstance(self.biotic_regm, list): + self.biotic_regm = [self.biotic_regm] if self.biotic_regm is not None else [] + self.biotic_regm = [v if isinstance(v, TextValue) else TextValue(**as_dict(v)) for v in self.biotic_regm] - if self.biotic_relationship is not None and not isinstance(self.biotic_relationship, BioticRelationshipEnum): - self.biotic_relationship = BioticRelationshipEnum(self.biotic_relationship) + if self.biotic_relationship is not None and not isinstance(self.biotic_relationship, BIOTICRELATIONSHIPENUM): + self.biotic_relationship = BIOTICRELATIONSHIPENUM(self.biotic_relationship) if not isinstance(self.climate_environment, list): self.climate_environment = [self.climate_environment] if self.climate_environment is not None else [] @@ -3374,11 +3346,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.light_regm is not None and not isinstance(self.light_regm, TextValue): self.light_regm = TextValue(**as_dict(self.light_regm)) - if self.phosphate is not None and not isinstance(self.phosphate, QuantityValue): - self.phosphate = QuantityValue(**as_dict(self.phosphate)) - - if self.samp_collec_method is not None and not isinstance(self.samp_collec_method, str): - self.samp_collec_method = str(self.samp_collec_method) + if self.phosphate is not None and not isinstance(self.phosphate, TextValue): + self.phosphate = TextValue(**as_dict(self.phosphate)) if self.samp_size is not None and not isinstance(self.samp_size, QuantityValue): self.samp_size = QuantityValue(**as_dict(self.samp_size)) @@ -3701,9 +3670,9 @@ class FieldResearchSite(Site): geo_loc_name: Optional[Union[dict, "TextValue"]] = None habitat: Optional[str] = None lat_lon: Optional[Union[dict, "GeolocationValue"]] = None - local_class: Optional[Union[dict, "TextValue"]] = None + local_class: Optional[str] = None part_of: Optional[Union[Union[str, FieldResearchSiteId], List[Union[str, FieldResearchSiteId]]]] = empty_list() - soil_type: Optional[Union[dict, "TextValue"]] = None + soil_type: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -3726,15 +3695,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.lat_lon is not None and not isinstance(self.lat_lon, GeolocationValue): self.lat_lon = GeolocationValue(**as_dict(self.lat_lon)) - if self.local_class is not None and not isinstance(self.local_class, TextValue): - self.local_class = TextValue(**as_dict(self.local_class)) + if self.local_class is not None and not isinstance(self.local_class, str): + self.local_class = str(self.local_class) if not isinstance(self.part_of, list): self.part_of = [self.part_of] if self.part_of is not None else [] self.part_of = [v if isinstance(v, FieldResearchSiteId) else FieldResearchSiteId(v) for v in self.part_of] - if self.soil_type is not None and not isinstance(self.soil_type, TextValue): - self.soil_type = TextValue(**as_dict(self.soil_type)) + if self.soil_type is not None and not isinstance(self.soil_type, str): + self.soil_type = str(self.soil_type) super().__post_init__(**kwargs) @@ -4007,6 +3976,8 @@ class LibraryPreparation(BiosampleProcessing): library_preparation_kit: Optional[str] = None library_type: Optional[Union[str, "LibraryTypeEnum"]] = None pcr_cycles: Optional[int] = None + is_stranded: Optional[Union[bool, Bool]] = None + stranded_orientation: Optional[Union[str, "StrandedOrientationEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -4035,6 +4006,12 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.pcr_cycles is not None and not isinstance(self.pcr_cycles, int): self.pcr_cycles = int(self.pcr_cycles) + if self.is_stranded is not None and not isinstance(self.is_stranded, Bool): + self.is_stranded = Bool(self.is_stranded) + + if self.stranded_orientation is not None and not isinstance(self.stranded_orientation, StrandedOrientationEnum): + self.stranded_orientation = StrandedOrientationEnum(self.stranded_orientation) + super().__post_init__(**kwargs) self.designated_class = str(self.class_class_curie) @@ -4273,13 +4250,13 @@ class OmicsProcessing(PlannedProcess): nucl_acid_ext: Optional[Union[dict, "TextValue"]] = None omics_type: Optional[Union[dict, "ControlledTermValue"]] = None part_of: Optional[Union[Union[str, StudyId], List[Union[str, StudyId]]]] = empty_list() - pcr_cond: Optional[Union[dict, "TextValue"]] = None - pcr_primers: Optional[Union[dict, "TextValue"]] = None + pcr_cond: Optional[str] = None + pcr_primers: Optional[str] = None principal_investigator: Optional[Union[dict, "PersonValue"]] = None processing_institution: Optional[Union[str, "ProcessingInstitutionEnum"]] = None - samp_vol_we_dna_ext: Optional[Union[dict, "QuantityValue"]] = None + samp_vol_we_dna_ext: Optional[Union[dict, "TextValue"]] = None seq_meth: Optional[Union[dict, "TextValue"]] = None - seq_quality_check: Optional[Union[dict, "TextValue"]] = None + seq_quality_check: Optional[Union[str, "SEQQUALITYCHECKENUM"]] = None target_gene: Optional[Union[dict, "TextValue"]] = None target_subfragment: Optional[Union[dict, "TextValue"]] = None type: Optional[str] = None @@ -4340,11 +4317,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.part_of = [self.part_of] if self.part_of is not None else [] self.part_of = [v if isinstance(v, StudyId) else StudyId(v) for v in self.part_of] - if self.pcr_cond is not None and not isinstance(self.pcr_cond, TextValue): - self.pcr_cond = TextValue(**as_dict(self.pcr_cond)) + if self.pcr_cond is not None and not isinstance(self.pcr_cond, str): + self.pcr_cond = str(self.pcr_cond) - if self.pcr_primers is not None and not isinstance(self.pcr_primers, TextValue): - self.pcr_primers = TextValue(**as_dict(self.pcr_primers)) + if self.pcr_primers is not None and not isinstance(self.pcr_primers, str): + self.pcr_primers = str(self.pcr_primers) if self.principal_investigator is not None and not isinstance(self.principal_investigator, PersonValue): self.principal_investigator = PersonValue(**as_dict(self.principal_investigator)) @@ -4352,14 +4329,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.processing_institution is not None and not isinstance(self.processing_institution, ProcessingInstitutionEnum): self.processing_institution = ProcessingInstitutionEnum(self.processing_institution) - if self.samp_vol_we_dna_ext is not None and not isinstance(self.samp_vol_we_dna_ext, QuantityValue): - self.samp_vol_we_dna_ext = QuantityValue(**as_dict(self.samp_vol_we_dna_ext)) + if self.samp_vol_we_dna_ext is not None and not isinstance(self.samp_vol_we_dna_ext, TextValue): + self.samp_vol_we_dna_ext = TextValue(**as_dict(self.samp_vol_we_dna_ext)) if self.seq_meth is not None and not isinstance(self.seq_meth, TextValue): self.seq_meth = TextValue(**as_dict(self.seq_meth)) - if self.seq_quality_check is not None and not isinstance(self.seq_quality_check, TextValue): - self.seq_quality_check = TextValue(**as_dict(self.seq_quality_check)) + if self.seq_quality_check is not None and not isinstance(self.seq_quality_check, SEQQUALITYCHECKENUM): + self.seq_quality_check = SEQQUALITYCHECKENUM(self.seq_quality_check) if self.target_gene is not None and not isinstance(self.target_gene, TextValue): self.target_gene = TextValue(**as_dict(self.target_gene)) @@ -5600,18 +5577,18 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class MetatranscriptomeActivity(WorkflowExecutionActivity): +class MetatranscriptomeExpressionAnalysis(WorkflowExecutionActivity): """ - A metatranscriptome activity that e.g. pools assembly and annotation activity. + A workflow process that provides expression values and read counts for gene features predicted on the contigs. """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = NMDC["MetatranscriptomeActivity"] - class_class_curie: ClassVar[str] = "nmdc:MetatranscriptomeActivity" - class_name: ClassVar[str] = "MetatranscriptomeActivity" - class_model_uri: ClassVar[URIRef] = NMDC.MetatranscriptomeActivity + class_class_uri: ClassVar[URIRef] = NMDC["MetatranscriptomeExpressionAnalysis"] + class_class_curie: ClassVar[str] = "nmdc:MetatranscriptomeExpressionAnalysis" + class_name: ClassVar[str] = "MetatranscriptomeExpressionAnalysis" + class_model_uri: ClassVar[URIRef] = NMDC.MetatranscriptomeExpressionAnalysis - id: Union[str, MetatranscriptomeActivityId] = None + id: Union[str, MetatranscriptomeExpressionAnalysisId] = None execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None @@ -5622,8 +5599,8 @@ class MetatranscriptomeActivity(WorkflowExecutionActivity): def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): self.MissingRequiredField("id") - if not isinstance(self.id, MetatranscriptomeActivityId): - self.id = MetatranscriptomeActivityId(self.id) + if not isinstance(self.id, MetatranscriptomeExpressionAnalysisId): + self.id = MetatranscriptomeExpressionAnalysisId(self.id) if self.type is not None and not isinstance(self.type, str): self.type = str(self.type) @@ -5923,6 +5900,26 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): # Enumerations +class StrandedOrientationEnum(EnumDefinitionImpl): + """ + This enumeration specifies information about stranded RNA library preparations. + """ + _defn = EnumDefinition( + name="StrandedOrientationEnum", + description="This enumeration specifies information about stranded RNA library preparations.", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "antisense orientation", + PermissibleValue( + text="antisense orientation", + description="Orientation that is complementary (non-coding) to a sequence of messenger RNA.")) + setattr(cls, "sense orientation", + PermissibleValue( + text="sense orientation", + description="Orientation that corresponds to the coding sequence of messenger RNA.")) + class InstrumentModelEnum(EnumDefinitionImpl): Orbitrap = PermissibleValue(text="Orbitrap") @@ -6517,9 +6514,15 @@ class FailureWhereEnum(EnumDefinitionImpl): MetagenomeAssembly = PermissibleValue( text="MetagenomeAssembly", description="A failure has occurred in metagenome assembly, a workflow process.") - MetatranscriptomeActivity = PermissibleValue( - text="MetatranscriptomeActivity", - description="A failure has occurred in metatranscriptome analysis, a workflow process.") + MetatranscriptomeExpressionAnalysis = PermissibleValue( + text="MetatranscriptomeExpressionAnalysis", + description="A failure has occurred in metatranscriptome expression analysis, a workflow process.") + MetatranscriptomeAnnotation = PermissibleValue( + text="MetatranscriptomeAnnotation", + description="A failure has occurred in metatranscriptome annotation analysis, a workflow process.") + MetatranscriptomeAssembly = PermissibleValue( + text="MetatranscriptomeAssembly", + description="A failure has occurred in metatranscriptome assembly analysis, a workflow process.") MagsAnalysisActivity = PermissibleValue( text="MagsAnalysisActivity", description="""A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).""") @@ -6630,46 +6633,34 @@ def _addvals(cls): setattr(cls, "CEREX System 96 processor", PermissibleValue(text="CEREX System 96 processor")) -class ArchStrucEnum(EnumDefinitionImpl): +class AEROSTRUCENUM(EnumDefinitionImpl): - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") + glider = PermissibleValue(text="glider") + plane = PermissibleValue(text="plane") _defn = EnumDefinition( - name="ArchStrucEnum", + name="AEROSTRUCENUM", ) -class BiolStatEnum(EnumDefinitionImpl): +class ARCHSTRUCENUM(EnumDefinitionImpl): - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") + building = PermissibleValue(text="building") + home = PermissibleValue(text="home") + shed = PermissibleValue(text="shed") _defn = EnumDefinition( - name="BiolStatEnum", + name="ARCHSTRUCENUM", ) - @classmethod - def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural")) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line")) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line")) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection")) - -class BioticRelationshipEnum(EnumDefinitionImpl): +class BIOTICRELATIONSHIPENUM(EnumDefinitionImpl): - parasite = PermissibleValue(text="parasite") - commensal = PermissibleValue(text="commensal") - symbiont = PermissibleValue(text="symbiont") + commensalism = PermissibleValue(text="commensalism") + mutualism = PermissibleValue(text="mutualism") + parasitism = PermissibleValue(text="parasitism") + symbiotic = PermissibleValue(text="symbiotic") _defn = EnumDefinition( - name="BioticRelationshipEnum", + name="BIOTICRELATIONSHIPENUM", ) @classmethod @@ -6677,7 +6668,18 @@ def _addvals(cls): setattr(cls, "free living", PermissibleValue(text="free living")) -class BuildDocsEnum(EnumDefinitionImpl): +class BUILDINGSETTINGENUM(EnumDefinitionImpl): + + exurban = PermissibleValue(text="exurban") + rural = PermissibleValue(text="rural") + suburban = PermissibleValue(text="suburban") + urban = PermissibleValue(text="urban") + + _defn = EnumDefinition( + name="BUILDINGSETTINGENUM", + ) + +class BUILDDOCSENUM(EnumDefinitionImpl): schedule = PermissibleValue(text="schedule") sections = PermissibleValue(text="sections") @@ -6685,7 +6687,7 @@ class BuildDocsEnum(EnumDefinitionImpl): windows = PermissibleValue(text="windows") _defn = EnumDefinition( - name="BuildDocsEnum", + name="BUILDDOCSENUM", ) @classmethod @@ -6709,75 +6711,56 @@ def _addvals(cls): setattr(cls, "ventilation system", PermissibleValue(text="ventilation system")) -class BuildOccupTypeEnum(EnumDefinitionImpl): +class BUILDOCCUPTYPEENUM(EnumDefinitionImpl): - office = PermissibleValue(text="office") + airport = PermissibleValue(text="airport") + commercial = PermissibleValue(text="commercial") market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") + office = PermissibleValue(text="office") residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") + restaurant = PermissibleValue(text="restaurant") + school = PermissibleValue(text="school") _defn = EnumDefinition( - name="BuildOccupTypeEnum", + name="BUILDOCCUPTYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise")) - setattr(cls, "high rise", - PermissibleValue(text="high rise")) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed")) setattr(cls, "health care", PermissibleValue(text="health care")) + setattr(cls, "high rise", + PermissibleValue(text="high rise")) + setattr(cls, "low rise", + PermissibleValue(text="low rise")) setattr(cls, "sports complex", PermissibleValue(text="sports complex")) + setattr(cls, "wood framed", + PermissibleValue(text="wood framed")) -class BuildingSettingEnum(EnumDefinitionImpl): +class BUILTSTRUCSETENUM(EnumDefinitionImpl): - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") rural = PermissibleValue(text="rural") + urban = PermissibleValue(text="urban") _defn = EnumDefinition( - name="BuildingSettingEnum", - ) - -class CeilCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="CeilCondEnum", + name="BUILTSTRUCSETENUM", ) - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - -class CeilFinishMatEnum(EnumDefinitionImpl): +class CEILFINISHMATENUM(EnumDefinitionImpl): - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") + drywall = PermissibleValue(text="drywall") fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + plasterboard = PermissibleValue(text="plasterboard") stucco = PermissibleValue(text="stucco") + tiles = PermissibleValue(text="tiles") wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="CeilFinishMatEnum", + name="CEILFINISHMATENUM", ) @classmethod @@ -6787,49 +6770,30 @@ def _addvals(cls): setattr(cls, "mineral wool/calcium silicate", PermissibleValue(text="mineral wool/calcium silicate")) -class CeilTextureEnum(EnumDefinitionImpl): +class CEILSTRUCENUM(EnumDefinitionImpl): - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") + concrete = PermissibleValue(text="concrete") _defn = EnumDefinition( - name="CeilTextureEnum", + name="CEILSTRUCENUM", ) @classmethod def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) + setattr(cls, "wood frame", + PermissibleValue(text="wood frame")) -class CeilTypeEnum(EnumDefinitionImpl): +class CEILTYPEENUM(EnumDefinitionImpl): cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") coffered = PermissibleValue(text="coffered") + concave = PermissibleValue(text="concave") cove = PermissibleValue(text="cove") + dropped = PermissibleValue(text="dropped") stretched = PermissibleValue(text="stretched") _defn = EnumDefinition( - name="CeilTypeEnum", + name="CEILTYPEENUM", ) @classmethod @@ -6837,117 +6801,55 @@ def _addvals(cls): setattr(cls, "barrel-shaped", PermissibleValue(text="barrel-shaped")) -class CurLandUseEnum(EnumDefinitionImpl): - - badlands = PermissibleValue(text="badlands") - cities = PermissibleValue(text="cities") - conifers = PermissibleValue(text="conifers") - farmstead = PermissibleValue(text="farmstead") - gravel = PermissibleValue(text="gravel") - hardwoods = PermissibleValue(text="hardwoods") - hayland = PermissibleValue(text="hayland") - marshlands = PermissibleValue(text="marshlands") - meadows = PermissibleValue(text="meadows") - mudflats = PermissibleValue(text="mudflats") - pastureland = PermissibleValue(text="pastureland") - rainforest = PermissibleValue(text="rainforest") - rangeland = PermissibleValue(text="rangeland") - rock = PermissibleValue(text="rock") - sand = PermissibleValue(text="sand") - swamp = PermissibleValue(text="swamp") - tropical = PermissibleValue(text="tropical") - tundra = PermissibleValue(text="tundra") - - _defn = EnumDefinition( - name="CurLandUseEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crop trees", - PermissibleValue(text="crop trees")) - setattr(cls, "horticultural plants", - PermissibleValue(text="horticultural plants")) - setattr(cls, "industrial areas", - PermissibleValue(text="industrial areas")) - setattr(cls, "intermixed hardwood and conifers", - PermissibleValue(text="intermixed hardwood and conifers")) - setattr(cls, "mines/quarries", - PermissibleValue(text="mines/quarries")) - setattr(cls, "oil waste areas", - PermissibleValue(text="oil waste areas")) - setattr(cls, "permanent snow or ice", - PermissibleValue(text="permanent snow or ice")) - setattr(cls, "roads/railroads", - PermissibleValue(text="roads/railroads")) - setattr(cls, "row crops", - PermissibleValue(text="row crops")) - setattr(cls, "saline seeps", - PermissibleValue(text="saline seeps")) - setattr(cls, "salt flats", - PermissibleValue(text="salt flats")) - setattr(cls, "shrub crops", - PermissibleValue(text="shrub crops")) - setattr(cls, "shrub land", - PermissibleValue(text="shrub land")) - setattr(cls, "small grains", - PermissibleValue(text="small grains")) - setattr(cls, "successional shrub land", - PermissibleValue(text="successional shrub land")) - setattr(cls, "vegetable crops", - PermissibleValue(text="vegetable crops")) - setattr(cls, "vine crops", - PermissibleValue(text="vine crops")) - -class DeposEnvEnum(EnumDefinitionImpl): +class DEPOSENVENUM(EnumDefinitionImpl): other = PermissibleValue(text="other") _defn = EnumDefinition( - name="DeposEnvEnum", + name="DEPOSENVENUM", ) @classmethod def _addvals(cls): - setattr(cls, "Continental - Alluvial", - PermissibleValue(text="Continental - Alluvial")) setattr(cls, "Continental - Aeolian", PermissibleValue(text="Continental - Aeolian")) + setattr(cls, "Continental - Alluvial", + PermissibleValue(text="Continental - Alluvial")) setattr(cls, "Continental - Fluvial", PermissibleValue(text="Continental - Fluvial")) setattr(cls, "Continental - Lacustrine", PermissibleValue(text="Continental - Lacustrine")) - setattr(cls, "Transitional - Deltaic", - PermissibleValue(text="Transitional - Deltaic")) - setattr(cls, "Transitional - Tidal", - PermissibleValue(text="Transitional - Tidal")) - setattr(cls, "Transitional - Lagoonal", - PermissibleValue(text="Transitional - Lagoonal")) - setattr(cls, "Transitional - Beach", - PermissibleValue(text="Transitional - Beach")) - setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake")) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow")) setattr(cls, "Marine - Deep", PermissibleValue(text="Marine - Deep")) setattr(cls, "Marine - Reef", PermissibleValue(text="Marine - Reef")) + setattr(cls, "Marine - Shallow", + PermissibleValue(text="Marine - Shallow")) setattr(cls, "Other - Evaporite", PermissibleValue(text="Other - Evaporite")) setattr(cls, "Other - Glacial", PermissibleValue(text="Other - Glacial")) setattr(cls, "Other - Volcanic", PermissibleValue(text="Other - Volcanic")) + setattr(cls, "Transitional - Beach", + PermissibleValue(text="Transitional - Beach")) + setattr(cls, "Transitional - Deltaic", + PermissibleValue(text="Transitional - Deltaic")) + setattr(cls, "Transitional - Lagoonal", + PermissibleValue(text="Transitional - Lagoonal")) + setattr(cls, "Transitional - Lake", + PermissibleValue(text="Transitional - Lake")) + setattr(cls, "Transitional - Tidal", + PermissibleValue(text="Transitional - Tidal")) -class DoorCompTypeEnum(EnumDefinitionImpl): +class DOORCOMPTYPEENUM(EnumDefinitionImpl): revolving = PermissibleValue(text="revolving") sliding = PermissibleValue(text="sliding") telescopic = PermissibleValue(text="telescopic") _defn = EnumDefinition( - name="DoorCompTypeEnum", + name="DOORCOMPTYPEENUM", ) @classmethod @@ -6955,45 +6857,17 @@ def _addvals(cls): setattr(cls, "metal covered", PermissibleValue(text="metal covered")) -class DoorCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="DoorCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - -class DoorDirectEnum(EnumDefinitionImpl): +class DOORDIRECTENUM(EnumDefinitionImpl): inward = PermissibleValue(text="inward") outward = PermissibleValue(text="outward") sideways = PermissibleValue(text="sideways") _defn = EnumDefinition( - name="DoorDirectEnum", - ) - -class DoorLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="DoorLocEnum", + name="DOORDIRECTENUM", ) -class DoorMatEnum(EnumDefinitionImpl): +class DOORMATENUM(EnumDefinitionImpl): aluminum = PermissibleValue(text="aluminum") fiberboard = PermissibleValue(text="fiberboard") @@ -7003,7 +6877,7 @@ class DoorMatEnum(EnumDefinitionImpl): wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="DoorMatEnum", + name="DOORMATENUM", ) @classmethod @@ -7017,7 +6891,7 @@ def _addvals(cls): setattr(cls, "wood/plastic composite", PermissibleValue(text="wood/plastic composite")) -class DoorMoveEnum(EnumDefinitionImpl): +class DOORMOVEENUM(EnumDefinitionImpl): collapsible = PermissibleValue(text="collapsible") folding = PermissibleValue(text="folding") @@ -7026,7 +6900,7 @@ class DoorMoveEnum(EnumDefinitionImpl): swinging = PermissibleValue(text="swinging") _defn = EnumDefinition( - name="DoorMoveEnum", + name="DOORMOVEENUM", ) @classmethod @@ -7034,23 +6908,23 @@ def _addvals(cls): setattr(cls, "rolling shutter", PermissibleValue(text="rolling shutter")) -class DoorTypeEnum(EnumDefinitionImpl): +class DOORTYPEENUM(EnumDefinitionImpl): composite = PermissibleValue(text="composite") metal = PermissibleValue(text="metal") wooden = PermissibleValue(text="wooden") _defn = EnumDefinition( - name="DoorTypeEnum", + name="DOORTYPEENUM", ) -class DoorTypeMetalEnum(EnumDefinitionImpl): +class DOORTYPEMETALENUM(EnumDefinitionImpl): collapsible = PermissibleValue(text="collapsible") hollow = PermissibleValue(text="hollow") _defn = EnumDefinition( - name="DoorTypeMetalEnum", + name="DOORTYPEMETALENUM", ) @classmethod @@ -7062,64 +6936,37 @@ def _addvals(cls): setattr(cls, "steel plate", PermissibleValue(text="steel plate")) -class DoorTypeWoodEnum(EnumDefinitionImpl): - - battened = PermissibleValue(text="battened") - flush = PermissibleValue(text="flush") - louvered = PermissibleValue(text="louvered") - - _defn = EnumDefinition( - name="DoorTypeWoodEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "bettened and ledged", - PermissibleValue(text="bettened and ledged")) - setattr(cls, "ledged and braced", - PermissibleValue(text="ledged and braced")) - setattr(cls, "ledged and framed", - PermissibleValue(text="ledged and framed")) - setattr(cls, "ledged, braced and frame", - PermissibleValue(text="ledged, braced and frame")) - setattr(cls, "framed and paneled", - PermissibleValue(text="framed and paneled")) - setattr(cls, "glashed or sash", - PermissibleValue(text="glashed or sash")) - setattr(cls, "wire gauged", - PermissibleValue(text="wire gauged")) - -class DrainageClassEnum(EnumDefinitionImpl): +class DRAINAGECLASSENUM(EnumDefinitionImpl): poorly = PermissibleValue(text="poorly") well = PermissibleValue(text="well") _defn = EnumDefinition( - name="DrainageClassEnum", + name="DRAINAGECLASSENUM", ) @classmethod def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly")) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly")) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well")) setattr(cls, "excessively drained", PermissibleValue(text="excessively drained")) + setattr(cls, "moderately well", + PermissibleValue(text="moderately well")) + setattr(cls, "somewhat poorly", + PermissibleValue(text="somewhat poorly")) + setattr(cls, "very poorly", + PermissibleValue(text="very poorly")) -class DrawingsEnum(EnumDefinitionImpl): +class DRAWINGSENUM(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") bid = PermissibleValue(text="bid") + construction = PermissibleValue(text="construction") design = PermissibleValue(text="design") diagram = PermissibleValue(text="diagram") + operation = PermissibleValue(text="operation") sketch = PermissibleValue(text="sketch") _defn = EnumDefinition( - name="DrawingsEnum", + name="DRAWINGSENUM", ) @classmethod @@ -7129,37 +6976,7 @@ def _addvals(cls): setattr(cls, "building navigation map", PermissibleValue(text="building navigation map")) -class ExtWallOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWallOrientEnum", - ) - -class ExtWindowOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWindowOrientEnum", - ) - -class FaoClassEnum(EnumDefinitionImpl): +class FAOCLASSENUM(EnumDefinitionImpl): Acrisols = PermissibleValue(text="Acrisols") Andosols = PermissibleValue(text="Andosols") @@ -7189,87 +7006,49 @@ class FaoClassEnum(EnumDefinitionImpl): Yermosols = PermissibleValue(text="Yermosols") _defn = EnumDefinition( - name="FaoClassEnum", + name="FAOCLASSENUM", ) -class FilterTypeEnum(EnumDefinitionImpl): +class FILTERTYPEENUM(EnumDefinitionImpl): HEPA = PermissibleValue(text="HEPA") electrostatic = PermissibleValue(text="electrostatic") _defn = EnumDefinition( - name="FilterTypeEnum", + name="FILTERTYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter")) setattr(cls, "chemical air filter", PermissibleValue(text="chemical air filter")) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media")) setattr(cls, "gas-phase or ultraviolet air treatments", PermissibleValue(text="gas-phase or ultraviolet air treatments")) + setattr(cls, "low-MERV pleated media", + PermissibleValue(text="low-MERV pleated media")) + setattr(cls, "particulate air filter", + PermissibleValue(text="particulate air filter")) -class FloorCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") +class FIREPLACETYPEENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="FloorCondEnum", + name="FIREPLACETYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "gas burning", + PermissibleValue(text="gas burning")) + setattr(cls, "wood burning", + PermissibleValue(text="wood burning")) -class FloorFinishMatEnum(EnumDefinitionImpl): - - tile = PermissibleValue(text="tile") - carpet = PermissibleValue(text="carpet") - rug = PermissibleValue(text="rug") - lineoleum = PermissibleValue(text="lineoleum") - stone = PermissibleValue(text="stone") - bamboo = PermissibleValue(text="bamboo") - cork = PermissibleValue(text="cork") - terrazo = PermissibleValue(text="terrazo") - concrete = PermissibleValue(text="concrete") - none = PermissibleValue(text="none") - sealed = PermissibleValue(text="sealed") - paint = PermissibleValue(text="paint") - - _defn = EnumDefinition( - name="FloorFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "wood strip or parquet", - PermissibleValue(text="wood strip or parquet")) - setattr(cls, "laminate wood", - PermissibleValue(text="laminate wood")) - setattr(cls, "vinyl composition tile", - PermissibleValue(text="vinyl composition tile")) - setattr(cls, "sheet vinyl", - PermissibleValue(text="sheet vinyl")) - setattr(cls, "clear finish", - PermissibleValue(text="clear finish")) - setattr(cls, "none or unfinished", - PermissibleValue(text="none or unfinished")) - -class FloorStrucEnum(EnumDefinitionImpl): +class FLOORSTRUCENUM(EnumDefinitionImpl): balcony = PermissibleValue(text="balcony") concrete = PermissibleValue(text="concrete") _defn = EnumDefinition( - name="FloorStrucEnum", + name="FLOORSTRUCENUM", ) @classmethod @@ -7285,64 +7064,64 @@ def _addvals(cls): setattr(cls, "wood-framed", PermissibleValue(text="wood-framed")) -class FloorWaterMoldEnum(EnumDefinitionImpl): +class FLOORWATERMOLDENUM(EnumDefinitionImpl): condensation = PermissibleValue(text="condensation") _defn = EnumDefinition( - name="FloorWaterMoldEnum", + name="FLOORWATERMOLDENUM", ) @classmethod def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor")) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor")) - setattr(cls, "water stains", - PermissibleValue(text="water stains")) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration")) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration")) + setattr(cls, "bulging walls", + PermissibleValue(text="bulging walls")) setattr(cls, "ceiling discoloration", PermissibleValue(text="ceiling discoloration")) + setattr(cls, "floor discoloration", + PermissibleValue(text="floor discoloration")) + setattr(cls, "mold odor", + PermissibleValue(text="mold odor")) setattr(cls, "peeling paint or wallpaper", PermissibleValue(text="peeling paint or wallpaper")) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls")) + setattr(cls, "wall discoloration", + PermissibleValue(text="wall discoloration")) + setattr(cls, "water stains", + PermissibleValue(text="water stains")) + setattr(cls, "wet floor", + PermissibleValue(text="wet floor")) -class FreqCleanEnum(EnumDefinitionImpl): +class FREQCLEANENUM(EnumDefinitionImpl): + Annually = PermissibleValue(text="Annually") Daily = PermissibleValue(text="Daily") - Weekly = PermissibleValue(text="Weekly") Monthly = PermissibleValue(text="Monthly") Quarterly = PermissibleValue(text="Quarterly") - Annually = PermissibleValue(text="Annually") + Weekly = PermissibleValue(text="Weekly") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="FreqCleanEnum", + name="FREQCLEANENUM", ) -class FurnitureEnum(EnumDefinitionImpl): +class FURNITUREENUM(EnumDefinitionImpl): cabinet = PermissibleValue(text="cabinet") chair = PermissibleValue(text="chair") desks = PermissibleValue(text="desks") _defn = EnumDefinition( - name="FurnitureEnum", + name="FURNITUREENUM", ) -class GenderRestroomEnum(EnumDefinitionImpl): +class GENDERRESTROOMENUM(EnumDefinitionImpl): female = PermissibleValue(text="female") male = PermissibleValue(text="male") unisex = PermissibleValue(text="unisex") _defn = EnumDefinition( - name="GenderRestroomEnum", + name="GENDERRESTROOMENUM", ) @classmethod @@ -7354,14 +7133,14 @@ def _addvals(cls): setattr(cls, "male and female", PermissibleValue(text="male and female")) -class GrowthHabitEnum(EnumDefinitionImpl): +class GROWTHHABITENUM(EnumDefinitionImpl): erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") prostrate = PermissibleValue(text="prostrate") + spreading = PermissibleValue(text="spreading") _defn = EnumDefinition( - name="GrowthHabitEnum", + name="GROWTHHABITENUM", ) @classmethod @@ -7369,12 +7148,12 @@ def _addvals(cls): setattr(cls, "semi-erect", PermissibleValue(text="semi-erect")) -class HandidnessEnum(EnumDefinitionImpl): +class HANDIDNESSENUM(EnumDefinitionImpl): ambidexterity = PermissibleValue(text="ambidexterity") _defn = EnumDefinition( - name="HandidnessEnum", + name="HANDIDNESSENUM", ) @classmethod @@ -7386,125 +7165,87 @@ def _addvals(cls): setattr(cls, "right handedness", PermissibleValue(text="right handedness")) -class HcProducedEnum(EnumDefinitionImpl): - - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcProducedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate")) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane")) - -class HcrEnum(EnumDefinitionImpl): +class HCRENUM(EnumDefinitionImpl): Coalbed = PermissibleValue(text="Coalbed") Shale = PermissibleValue(text="Shale") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcrEnum", + name="HCRENUM", ) @classmethod def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir")) setattr(cls, "Gas Reservoir", PermissibleValue(text="Gas Reservoir")) + setattr(cls, "Oil Reservoir", + PermissibleValue(text="Oil Reservoir")) setattr(cls, "Oil Sand", PermissibleValue(text="Oil Sand")) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir")) setattr(cls, "Tight Gas Reservoir", PermissibleValue(text="Tight Gas Reservoir")) + setattr(cls, "Tight Oil Reservoir", + PermissibleValue(text="Tight Oil Reservoir")) -class HcrGeolAgeEnum(EnumDefinitionImpl): +class HCPRODUCEDENUM(EnumDefinitionImpl): - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") + Bitumen = PermissibleValue(text="Bitumen") + Gas = PermissibleValue(text="Gas") + Oil = PermissibleValue(text="Oil") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcrGeolAgeEnum", + name="HCPRODUCEDENUM", ) -class HeatCoolTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "Coalbed Methane", + PermissibleValue(text="Coalbed Methane")) + setattr(cls, "Gas-Condensate", + PermissibleValue(text="Gas-Condensate")) + +class HEATCOOLTYPEENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="HeatCoolTypeEnum", + name="HEATCOOLTYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system")) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump")) setattr(cls, "forced air system", PermissibleValue(text="forced air system")) + setattr(cls, "heat pump", + PermissibleValue(text="heat pump")) + setattr(cls, "radiant system", + PermissibleValue(text="radiant system")) setattr(cls, "steam forced heat", PermissibleValue(text="steam forced heat")) setattr(cls, "wood stove", PermissibleValue(text="wood stove")) -class HeatDelivLocEnum(EnumDefinitionImpl): +class HEATSYSDELIVMETHENUM(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="HeatDelivLocEnum", - ) - -class HostSexEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - hermaphrodite = PermissibleValue(text="hermaphrodite") - male = PermissibleValue(text="male") - neuter = PermissibleValue(text="neuter") + conductive = PermissibleValue(text="conductive") + radiant = PermissibleValue(text="radiant") _defn = EnumDefinition( - name="HostSexEnum", + name="HEATSYSDELIVMETHENUM", ) -class IndoorSpaceEnum(EnumDefinitionImpl): +class INDOORSPACEENUM(EnumDefinitionImpl): - bedroom = PermissibleValue(text="bedroom") - office = PermissibleValue(text="office") bathroom = PermissibleValue(text="bathroom") + bedroom = PermissibleValue(text="bedroom") + elevator = PermissibleValue(text="elevator") foyer = PermissibleValue(text="foyer") - kitchen = PermissibleValue(text="kitchen") hallway = PermissibleValue(text="hallway") - elevator = PermissibleValue(text="elevator") + kitchen = PermissibleValue(text="kitchen") + office = PermissibleValue(text="office") _defn = EnumDefinition( - name="IndoorSpaceEnum", + name="INDOORSPACEENUM", ) @classmethod @@ -7512,17 +7253,17 @@ def _addvals(cls): setattr(cls, "locker room", PermissibleValue(text="locker room")) -class IndoorSurfEnum(EnumDefinitionImpl): +class INDOORSURFENUM(EnumDefinitionImpl): cabinet = PermissibleValue(text="cabinet") ceiling = PermissibleValue(text="ceiling") door = PermissibleValue(text="door") shelving = PermissibleValue(text="shelving") - window = PermissibleValue(text="window") wall = PermissibleValue(text="wall") + window = PermissibleValue(text="window") _defn = EnumDefinition( - name="IndoorSurfEnum", + name="INDOORSURFENUM", ) @classmethod @@ -7532,43 +7273,26 @@ def _addvals(cls): setattr(cls, "vent cover", PermissibleValue(text="vent cover")) -class IntWallCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="IntWallCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - -class LightTypeEnum(EnumDefinitionImpl): +class LIGHTTYPEENUM(EnumDefinitionImpl): none = PermissibleValue(text="none") _defn = EnumDefinition( - name="LightTypeEnum", + name="LIGHTTYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light")) - setattr(cls, "electric light", - PermissibleValue(text="electric light")) setattr(cls, "desk lamp", PermissibleValue(text="desk lamp")) + setattr(cls, "electric light", + PermissibleValue(text="electric light")) setattr(cls, "flourescent lights", PermissibleValue(text="flourescent lights")) + setattr(cls, "natural light", + PermissibleValue(text="natural light")) -class LithologyEnum(EnumDefinitionImpl): +class LITHOLOGYENUM(EnumDefinitionImpl): Basement = PermissibleValue(text="Basement") Chalk = PermissibleValue(text="Chalk") @@ -7585,32 +7309,32 @@ class LithologyEnum(EnumDefinitionImpl): other = PermissibleValue(text="other") _defn = EnumDefinition( - name="LithologyEnum", + name="LITHOLOGYENUM", ) -class MechStrucEnum(EnumDefinitionImpl): +class MECHSTRUCENUM(EnumDefinitionImpl): - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") + boat = PermissibleValue(text="boat") + bus = PermissibleValue(text="bus") + car = PermissibleValue(text="car") carriage = PermissibleValue(text="carriage") + coach = PermissibleValue(text="coach") elevator = PermissibleValue(text="elevator") escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") + subway = PermissibleValue(text="subway") train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") _defn = EnumDefinition( - name="MechStrucEnum", + name="MECHSTRUCENUM", ) -class OccupDocumentEnum(EnumDefinitionImpl): +class OCCUPDOCUMENTENUM(EnumDefinitionImpl): estimate = PermissibleValue(text="estimate") videos = PermissibleValue(text="videos") _defn = EnumDefinition( - name="OccupDocumentEnum", + name="OCCUPDOCUMENTENUM", ) @classmethod @@ -7620,54 +7344,22 @@ def _addvals(cls): setattr(cls, "manual count", PermissibleValue(text="manual count")) -class OrganismCountEnum(EnumDefinitionImpl): - - ATP = PermissibleValue(text="ATP") - MPN = PermissibleValue(text="MPN") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OrganismCountEnum", - ) - -class OxyStatSampEnum(EnumDefinitionImpl): +class OXYSTATSAMPENUM(EnumDefinitionImpl): aerobic = PermissibleValue(text="aerobic") anaerobic = PermissibleValue(text="anaerobic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="OxyStatSampEnum", + name="OXYSTATSAMPENUM", ) -class PlantGrowthMedEnum(EnumDefinitionImpl): - - perlite = PermissibleValue(text="perlite") - pumice = PermissibleValue(text="pumice") - sand = PermissibleValue(text="sand") - soil = PermissibleValue(text="soil") - vermiculite = PermissibleValue(text="vermiculite") - water = PermissibleValue(text="water") - - _defn = EnumDefinition( - name="PlantGrowthMedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "other artificial liquid medium", - PermissibleValue(text="other artificial liquid medium")) - setattr(cls, "other artificial solid medium", - PermissibleValue(text="other artificial solid medium")) - setattr(cls, "peat moss", - PermissibleValue(text="peat moss")) - -class PlantSexEnum(EnumDefinitionImpl): +class PLANTSEXENUM(EnumDefinitionImpl): Androdioecious = PermissibleValue(text="Androdioecious") Androecious = PermissibleValue(text="Androecious") - Androgynous = PermissibleValue(text="Androgynous") Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") + Androgynous = PermissibleValue(text="Androgynous") Andromonoecious = PermissibleValue(text="Andromonoecious") Bisexual = PermissibleValue(text="Bisexual") Dichogamous = PermissibleValue(text="Dichogamous") @@ -7695,73 +7387,73 @@ class PlantSexEnum(EnumDefinitionImpl): Unisexual = PermissibleValue(text="Unisexual") _defn = EnumDefinition( - name="PlantSexEnum", + name="PLANTSEXENUM", ) -class ProfilePositionEnum(EnumDefinitionImpl): +class PROFILEPOSITIONENUM(EnumDefinitionImpl): - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") backslope = PermissibleValue(text="backslope") footslope = PermissibleValue(text="footslope") + shoulder = PermissibleValue(text="shoulder") + summit = PermissibleValue(text="summit") toeslope = PermissibleValue(text="toeslope") _defn = EnumDefinition( - name="ProfilePositionEnum", + name="PROFILEPOSITIONENUM", ) -class QuadPosEnum(EnumDefinitionImpl): +class QUADPOSENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="QuadPosEnum", + name="QUADPOSENUM", ) @classmethod def _addvals(cls): + setattr(cls, "East side", + PermissibleValue(text="East side")) setattr(cls, "North side", PermissibleValue(text="North side")) - setattr(cls, "West side", - PermissibleValue(text="West side")) setattr(cls, "South side", PermissibleValue(text="South side")) - setattr(cls, "East side", - PermissibleValue(text="East side")) + setattr(cls, "West side", + PermissibleValue(text="West side")) -class RelSampLocEnum(EnumDefinitionImpl): +class RELSAMPLOCENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="RelSampLocEnum", + name="RELSAMPLOCENUM", ) @classmethod def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car")) setattr(cls, "center of car", PermissibleValue(text="center of car")) + setattr(cls, "edge of car", + PermissibleValue(text="edge of car")) setattr(cls, "under a seat", PermissibleValue(text="under a seat")) -class RoomCondtEnum(EnumDefinitionImpl): +class ROOMCONDTENUM(EnumDefinitionImpl): - new = PermissibleValue(text="new") damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="RoomCondtEnum", + name="ROOMCONDTENUM", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) setattr(cls, "needs repair", PermissibleValue(text="needs repair")) setattr(cls, "visible signs of mold/mildew", PermissibleValue(text="visible signs of mold/mildew")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class RoomConnectedEnum(EnumDefinitionImpl): +class ROOMCONNECTEDENUM(EnumDefinitionImpl): attic = PermissibleValue(text="attic") bathroom = PermissibleValue(text="bathroom") @@ -7773,7 +7465,7 @@ class RoomConnectedEnum(EnumDefinitionImpl): stairwell = PermissibleValue(text="stairwell") _defn = EnumDefinition( - name="RoomConnectedEnum", + name="ROOMCONNECTEDENUM", ) @classmethod @@ -7785,97 +7477,54 @@ def _addvals(cls): setattr(cls, "mail room", PermissibleValue(text="mail room")) -class RoomLocEnum(EnumDefinitionImpl): +class ROOMLOCENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="RoomLocEnum", + name="ROOMLOCENUM", ) @classmethod def _addvals(cls): setattr(cls, "corner room", PermissibleValue(text="corner room")) - setattr(cls, "interior room", - PermissibleValue(text="interior room")) setattr(cls, "exterior wall", PermissibleValue(text="exterior wall")) + setattr(cls, "interior room", + PermissibleValue(text="interior room")) -class RoomSampPosEnum(EnumDefinitionImpl): +class ROOMSAMPPOSENUM(EnumDefinitionImpl): center = PermissibleValue(text="center") _defn = EnumDefinition( - name="RoomSampPosEnum", + name="ROOMSAMPPOSENUM", ) @classmethod def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner")) - setattr(cls, "south corner", - PermissibleValue(text="south corner")) - setattr(cls, "west corner", - PermissibleValue(text="west corner")) setattr(cls, "east corner", PermissibleValue(text="east corner")) + setattr(cls, "north corner", + PermissibleValue(text="north corner")) setattr(cls, "northeast corner", PermissibleValue(text="northeast corner")) setattr(cls, "northwest corner", PermissibleValue(text="northwest corner")) + setattr(cls, "south corner", + PermissibleValue(text="south corner")) setattr(cls, "southeast corner", PermissibleValue(text="southeast corner")) setattr(cls, "southwest corner", PermissibleValue(text="southwest corner")) + setattr(cls, "west corner", + PermissibleValue(text="west corner")) -class RoomTypeEnum(EnumDefinitionImpl): - - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") - - _defn = EnumDefinition( - name="RoomTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room")) - setattr(cls, "examining room", - PermissibleValue(text="examining room")) - setattr(cls, "mail room", - PermissibleValue(text="mail room")) - setattr(cls, "private office", - PermissibleValue(text="private office")) - setattr(cls, "open office", - PermissibleValue(text="open office")) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom")) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room")) - setattr(cls, "data center", - PermissibleValue(text="data center")) - -class SampCaptStatusEnum(EnumDefinitionImpl): +class SAMPCAPTSTATUSENUM(EnumDefinitionImpl): other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampCaptStatusEnum", + name="SAMPCAPTSTATUSENUM", ) @classmethod @@ -7889,36 +7538,36 @@ def _addvals(cls): setattr(cls, "market sample", PermissibleValue(text="market sample")) -class SampCollectPointEnum(EnumDefinitionImpl): +class SAMPCOLLECTPOINTENUM(EnumDefinitionImpl): + other = PermissibleValue(text="other") + separator = PermissibleValue(text="separator") well = PermissibleValue(text="well") wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") - other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampCollectPointEnum", + name="SAMPCOLLECTPOINTENUM", ) @classmethod def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well")) setattr(cls, "drilling rig", PermissibleValue(text="drilling rig")) setattr(cls, "storage tank", PermissibleValue(text="storage tank")) + setattr(cls, "test well", + PermissibleValue(text="test well")) -class SampDisStageEnum(EnumDefinitionImpl): +class SAMPDISSTAGEENUM(EnumDefinitionImpl): dissemination = PermissibleValue(text="dissemination") infection = PermissibleValue(text="infection") inoculation = PermissibleValue(text="inoculation") - penetration = PermissibleValue(text="penetration") other = PermissibleValue(text="other") + penetration = PermissibleValue(text="penetration") _defn = EnumDefinition( - name="SampDisStageEnum", + name="SAMPDISSTAGEENUM", ) @classmethod @@ -7926,65 +7575,37 @@ def _addvals(cls): setattr(cls, "growth and reproduction", PermissibleValue(text="growth and reproduction")) -class SampFloorEnum(EnumDefinitionImpl): - - basement = PermissibleValue(text="basement") - lobby = PermissibleValue(text="lobby") - - _defn = EnumDefinition( - name="SampFloorEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "1st floor", - PermissibleValue(text="1st floor")) - setattr(cls, "2nd floor", - PermissibleValue(text="2nd floor")) - -class SampMdEnum(EnumDefinitionImpl): - - DF = PermissibleValue(text="DF") - RT = PermissibleValue(text="RT") - KB = PermissibleValue(text="KB") - MSL = PermissibleValue(text="MSL") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampMdEnum", - ) - -class SampSubtypeEnum(EnumDefinitionImpl): +class SAMPSUBTYPEENUM(EnumDefinitionImpl): biofilm = PermissibleValue(text="biofilm") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampSubtypeEnum", + name="SAMPSUBTYPEENUM", ) @classmethod def _addvals(cls): + setattr(cls, "not applicable", + PermissibleValue(text="not applicable")) setattr(cls, "oil phase", PermissibleValue(text="oil phase")) setattr(cls, "water phase", PermissibleValue(text="water phase")) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable")) -class SampWeatherEnum(EnumDefinitionImpl): +class SAMPWEATHERENUM(EnumDefinitionImpl): cloudy = PermissibleValue(text="cloudy") foggy = PermissibleValue(text="foggy") hail = PermissibleValue(text="hail") rain = PermissibleValue(text="rain") - snow = PermissibleValue(text="snow") sleet = PermissibleValue(text="sleet") + snow = PermissibleValue(text="snow") sunny = PermissibleValue(text="sunny") windy = PermissibleValue(text="windy") _defn = EnumDefinition( - name="SampWeatherEnum", + name="SAMPWEATHERENUM", ) @classmethod @@ -7992,18 +7613,18 @@ def _addvals(cls): setattr(cls, "clear sky", PermissibleValue(text="clear sky")) -class SeasonUseEnum(EnumDefinitionImpl): +class SEASONUSEENUM(EnumDefinitionImpl): + Fall = PermissibleValue(text="Fall") Spring = PermissibleValue(text="Spring") Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") Winter = PermissibleValue(text="Winter") _defn = EnumDefinition( - name="SeasonUseEnum", + name="SEASONUSEENUM", ) -class SedimentTypeEnum(EnumDefinitionImpl): +class SEDIMENTTYPEENUM(EnumDefinitionImpl): biogenous = PermissibleValue(text="biogenous") cosmogenous = PermissibleValue(text="cosmogenous") @@ -8011,33 +7632,38 @@ class SedimentTypeEnum(EnumDefinitionImpl): lithogenous = PermissibleValue(text="lithogenous") _defn = EnumDefinition( - name="SedimentTypeEnum", + name="SEDIMENTTYPEENUM", ) -class ShadingDeviceCondEnum(EnumDefinitionImpl): +class SEQQUALITYCHECKENUM(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="ShadingDeviceCondEnum", + name="SEQQUALITYCHECKENUM", ) @classmethod def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) + setattr(cls, "manually edited", + PermissibleValue(text="manually edited")) + +class SHADINGDEVICELOCENUM(EnumDefinitionImpl): -class ShadingDeviceTypeEnum(EnumDefinitionImpl): + exterior = PermissibleValue(text="exterior") + interior = PermissibleValue(text="interior") + + _defn = EnumDefinition( + name="SHADINGDEVICELOCENUM", + ) + +class SHADINGDEVICETYPEENUM(EnumDefinitionImpl): tree = PermissibleValue(text="tree") trellis = PermissibleValue(text="trellis") _defn = EnumDefinition( - name="ShadingDeviceTypeEnum", + name="SHADINGDEVICETYPEENUM", ) @classmethod @@ -8063,61 +7689,101 @@ def _addvals(cls): setattr(cls, "venetian awning", PermissibleValue(text="venetian awning")) -class SoilHorizonEnum(EnumDefinitionImpl): +class SHAREDENUM0(EnumDefinitionImpl): - Permafrost = PermissibleValue(text="Permafrost") + east = PermissibleValue(text="east") + north = PermissibleValue(text="north") + northeast = PermissibleValue(text="northeast") + northwest = PermissibleValue(text="northwest") + south = PermissibleValue(text="south") + southeast = PermissibleValue(text="southeast") + southwest = PermissibleValue(text="southwest") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="SoilHorizonEnum", + name="SHAREDENUM0", + ) + +class SHAREDENUM1(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="SHAREDENUM1", ) @classmethod def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon")) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon")) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon")) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon")) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon")) - setattr(cls, "R layer", - PermissibleValue(text="R layer")) - setattr(cls, "M horizon", - PermissibleValue(text="M horizon")) + setattr(cls, "no presence of mold visible", + PermissibleValue(text="no presence of mold visible")) + setattr(cls, "presence of mold visible", + PermissibleValue(text="presence of mold visible")) -class SpecificEnum(EnumDefinitionImpl): +class SHAREDENUM2(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="SpecificEnum", + name="SHAREDENUM2", ) @classmethod def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class SrDepEnvEnum(EnumDefinitionImpl): +class SHAREDENUM3(EnumDefinitionImpl): - Lacustine = PermissibleValue(text="Lacustine") - Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") - Fluviomarine = PermissibleValue(text="Fluviomarine") - Marine = PermissibleValue(text="Marine") - other = PermissibleValue(text="other") + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="SrDepEnvEnum", + name="SHAREDENUM3", ) -class SrGeolAgeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + +class SHAREDENUM4(EnumDefinitionImpl): + + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") + + _defn = EnumDefinition( + name="SHAREDENUM4", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) + +class SHAREDENUM5(EnumDefinitionImpl): Archean = PermissibleValue(text="Archean") Cambrian = PermissibleValue(text="Cambrian") @@ -8139,15 +7805,82 @@ class SrGeolAgeEnum(EnumDefinitionImpl): other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SrGeolAgeEnum", + name="SHAREDENUM5", + ) + +class SOILHORIZONENUM(EnumDefinitionImpl): + + Permafrost = PermissibleValue(text="Permafrost") + + _defn = EnumDefinition( + name="SOILHORIZONENUM", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "A horizon", + PermissibleValue(text="A horizon")) + setattr(cls, "B horizon", + PermissibleValue(text="B horizon")) + setattr(cls, "C horizon", + PermissibleValue(text="C horizon")) + setattr(cls, "E horizon", + PermissibleValue(text="E horizon")) + setattr(cls, "O horizon", + PermissibleValue(text="O horizon")) + setattr(cls, "R layer", + PermissibleValue(text="R layer")) + setattr(cls, "M horizon", + PermissibleValue(text="M horizon")) + +class SPACETYPSTATEENUM(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="SPACETYPSTATEENUM", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "typically occupied", + PermissibleValue(text="typically occupied")) + setattr(cls, "typically unoccupied", + PermissibleValue(text="typically unoccupied")) + +class SPECIFICENUM(EnumDefinitionImpl): + + bid = PermissibleValue(text="bid") + construction = PermissibleValue(text="construction") + design = PermissibleValue(text="design") + operation = PermissibleValue(text="operation") + photos = PermissibleValue(text="photos") + + _defn = EnumDefinition( + name="SPECIFICENUM", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "as built", + PermissibleValue(text="as built")) + +class SRDEPENVENUM(EnumDefinitionImpl): + + Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") + Fluviomarine = PermissibleValue(text="Fluviomarine") + Lacustine = PermissibleValue(text="Lacustine") + Marine = PermissibleValue(text="Marine") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="SRDEPENVENUM", ) -class SrKerogTypeEnum(EnumDefinitionImpl): +class SRKEROGTYPEENUM(EnumDefinitionImpl): other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SrKerogTypeEnum", + name="SRKEROGTYPEENUM", ) @classmethod @@ -8161,25 +7894,25 @@ def _addvals(cls): setattr(cls, "Type IV", PermissibleValue(text="Type IV")) -class SrLithologyEnum(EnumDefinitionImpl): +class SRLITHOLOGYENUM(EnumDefinitionImpl): - Clastic = PermissibleValue(text="Clastic") + Biosilicieous = PermissibleValue(text="Biosilicieous") Carbonate = PermissibleValue(text="Carbonate") + Clastic = PermissibleValue(text="Clastic") Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SrLithologyEnum", + name="SRLITHOLOGYENUM", ) -class SubstructureTypeEnum(EnumDefinitionImpl): +class SUBSTRUCTURETYPEENUM(EnumDefinitionImpl): - crawlspace = PermissibleValue(text="crawlspace") basement = PermissibleValue(text="basement") + crawlspace = PermissibleValue(text="crawlspace") _defn = EnumDefinition( - name="SubstructureTypeEnum", + name="SUBSTRUCTURETYPEENUM", ) @classmethod @@ -8187,29 +7920,29 @@ def _addvals(cls): setattr(cls, "slab on grade", PermissibleValue(text="slab on grade")) -class SurfAirContEnum(EnumDefinitionImpl): +class SURFAIRCONTENUM(EnumDefinitionImpl): + biocides = PermissibleValue(text="biocides") dust = PermissibleValue(text="dust") - radon = PermissibleValue(text="radon") nutrients = PermissibleValue(text="nutrients") - biocides = PermissibleValue(text="biocides") + radon = PermissibleValue(text="radon") _defn = EnumDefinition( - name="SurfAirContEnum", + name="SURFAIRCONTENUM", ) @classmethod def _addvals(cls): + setattr(cls, "biological contaminants", + PermissibleValue(text="biological contaminants")) setattr(cls, "organic matter", PermissibleValue(text="organic matter")) setattr(cls, "particulate matter", PermissibleValue(text="particulate matter")) setattr(cls, "volatile organic compounds", PermissibleValue(text="volatile organic compounds")) - setattr(cls, "biological contaminants", - PermissibleValue(text="biological contaminants")) -class SurfMaterialEnum(EnumDefinitionImpl): +class SURFMATERIALENUM(EnumDefinitionImpl): adobe = PermissibleValue(text="adobe") carpet = PermissibleValue(text="carpet") @@ -8225,7 +7958,7 @@ class SurfMaterialEnum(EnumDefinitionImpl): wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="SurfMaterialEnum", + name="SURFMATERIALENUM", ) @classmethod @@ -8237,114 +7970,96 @@ def _addvals(cls): setattr(cls, "stainless steel", PermissibleValue(text="stainless steel")) -class TidalStageEnum(EnumDefinitionImpl): +class TIDALSTAGEENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="TidalStageEnum", + name="TIDALSTAGEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide")) setattr(cls, "ebb tide", PermissibleValue(text="ebb tide")) setattr(cls, "flood tide", PermissibleValue(text="flood tide")) setattr(cls, "high tide", PermissibleValue(text="high tide")) + setattr(cls, "low tide", + PermissibleValue(text="low tide")) -class TillageEnum(EnumDefinitionImpl): +class TILLAGEENUM(EnumDefinitionImpl): - drill = PermissibleValue(text="drill") chisel = PermissibleValue(text="chisel") - tined = PermissibleValue(text="tined") + drill = PermissibleValue(text="drill") mouldboard = PermissibleValue(text="mouldboard") + tined = PermissibleValue(text="tined") _defn = EnumDefinition( - name="TillageEnum", + name="TILLAGEENUM", ) @classmethod def _addvals(cls): setattr(cls, "cutting disc", PermissibleValue(text="cutting disc")) + setattr(cls, "disc plough", + PermissibleValue(text="disc plough")) setattr(cls, "ridge till", PermissibleValue(text="ridge till")) setattr(cls, "strip tillage", PermissibleValue(text="strip tillage")) setattr(cls, "zonal tillage", PermissibleValue(text="zonal tillage")) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough")) -class TrainLineEnum(EnumDefinitionImpl): +class TRAINLINEENUM(EnumDefinitionImpl): - red = PermissibleValue(text="red") green = PermissibleValue(text="green") orange = PermissibleValue(text="orange") + red = PermissibleValue(text="red") _defn = EnumDefinition( - name="TrainLineEnum", + name="TRAINLINEENUM", ) -class TrainStatLocEnum(EnumDefinitionImpl): +class TRAINSTATLOCENUM(EnumDefinitionImpl): riverside = PermissibleValue(text="riverside") _defn = EnumDefinition( - name="TrainStatLocEnum", + name="TRAINSTATLOCENUM", ) @classmethod def _addvals(cls): + setattr(cls, "forest hills", + PermissibleValue(text="forest hills")) setattr(cls, "south station above ground", PermissibleValue(text="south station above ground")) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground")) setattr(cls, "south station amtrak", PermissibleValue(text="south station amtrak")) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills")) + setattr(cls, "south station underground", + PermissibleValue(text="south station underground")) -class TrainStopLocEnum(EnumDefinitionImpl): +class TRAINSTOPLOCENUM(EnumDefinitionImpl): + downtown = PermissibleValue(text="downtown") end = PermissibleValue(text="end") mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") _defn = EnumDefinition( - name="TrainStopLocEnum", + name="TRAINSTOPLOCENUM", ) -class VisMediaEnum(EnumDefinitionImpl): - - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") - - _defn = EnumDefinition( - name="VisMediaEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building")) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans")) - -class WallConstTypeEnum(EnumDefinitionImpl): +class WALLCONSTTYPEENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="WallConstTypeEnum", + name="WALLCONSTTYPEENUM", ) @classmethod def _addvals(cls): + setattr(cls, "fire resistive", + PermissibleValue(text="fire resistive")) setattr(cls, "frame construction", PermissibleValue(text="frame construction")) setattr(cls, "joisted masonry", @@ -8355,99 +8070,52 @@ def _addvals(cls): PermissibleValue(text="masonry noncombustible")) setattr(cls, "modified fire resistive", PermissibleValue(text="modified fire resistive")) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive")) -class WallFinishMatEnum(EnumDefinitionImpl): +class WALLFINISHMATENUM(EnumDefinitionImpl): + masonry = PermissibleValue(text="masonry") + metal = PermissibleValue(text="metal") plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") terrazzo = PermissibleValue(text="terrazzo") + tile = PermissibleValue(text="tile") wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") _defn = EnumDefinition( - name="WallFinishMatEnum", + name="WALLFINISHMATENUM", ) @classmethod def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster")) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster")) + setattr(cls, "acoustical treatment", + PermissibleValue(text="acoustical treatment")) setattr(cls, "gypsum board", PermissibleValue(text="gypsum board")) + setattr(cls, "gypsum plaster", + PermissibleValue(text="gypsum plaster")) setattr(cls, "stone facing", PermissibleValue(text="stone facing")) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment")) - -class WallLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WallLocEnum", - ) + setattr(cls, "veneer plaster", + PermissibleValue(text="veneer plaster")) -class WallSurfTreatmentEnum(EnumDefinitionImpl): +class WALLSURFTREATMENTENUM(EnumDefinitionImpl): + fabric = PermissibleValue(text="fabric") painted = PermissibleValue(text="painted") paneling = PermissibleValue(text="paneling") stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") _defn = EnumDefinition( - name="WallSurfTreatmentEnum", + name="WALLSURFTREATMENTENUM", ) @classmethod def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper")) setattr(cls, "no treatment", PermissibleValue(text="no treatment")) + setattr(cls, "wall paper", + PermissibleValue(text="wall paper")) -class WallTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="WallTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "", - PermissibleValue(text="")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) - -class WaterFeatTypeEnum(EnumDefinitionImpl): +class WATERFEATTYPEENUM(EnumDefinitionImpl): fountain = PermissibleValue(text="fountain") pool = PermissibleValue(text="pool") @@ -8455,7 +8123,7 @@ class WaterFeatTypeEnum(EnumDefinitionImpl): waterfall = PermissibleValue(text="waterfall") _defn = EnumDefinition( - name="WaterFeatTypeEnum", + name="WATERFEATTYPEENUM", ) @classmethod @@ -8463,69 +8131,41 @@ def _addvals(cls): setattr(cls, "standing feature", PermissibleValue(text="standing feature")) -class WeekdayEnum(EnumDefinitionImpl): +class WEEKDAYENUM(EnumDefinitionImpl): - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") Friday = PermissibleValue(text="Friday") + Monday = PermissibleValue(text="Monday") Saturday = PermissibleValue(text="Saturday") Sunday = PermissibleValue(text="Sunday") + Thursday = PermissibleValue(text="Thursday") + Tuesday = PermissibleValue(text="Tuesday") + Wednesday = PermissibleValue(text="Wednesday") _defn = EnumDefinition( - name="WeekdayEnum", - ) - -class WindowCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="WindowCondEnum", + name="WEEKDAYENUM", ) - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - -class WindowCoverEnum(EnumDefinitionImpl): +class WINDOWCOVERENUM(EnumDefinitionImpl): blinds = PermissibleValue(text="blinds") curtains = PermissibleValue(text="curtains") none = PermissibleValue(text="none") _defn = EnumDefinition( - name="WindowCoverEnum", + name="WINDOWCOVERENUM", ) -class WindowHorizPosEnum(EnumDefinitionImpl): +class WINDOWHORIZPOSENUM(EnumDefinitionImpl): left = PermissibleValue(text="left") middle = PermissibleValue(text="middle") right = PermissibleValue(text="right") _defn = EnumDefinition( - name="WindowHorizPosEnum", - ) - -class WindowLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WindowLocEnum", + name="WINDOWHORIZPOSENUM", ) -class WindowMatEnum(EnumDefinitionImpl): +class WINDOWMATENUM(EnumDefinitionImpl): clad = PermissibleValue(text="clad") fiberglass = PermissibleValue(text="fiberglass") @@ -8534,36 +8174,107 @@ class WindowMatEnum(EnumDefinitionImpl): wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="WindowMatEnum", + name="WINDOWMATENUM", + ) + +class WINDOWSTATUSENUM(EnumDefinitionImpl): + + closed = PermissibleValue(text="closed") + open = PermissibleValue(text="open") + + _defn = EnumDefinition( + name="WINDOWSTATUSENUM", ) -class WindowTypeEnum(EnumDefinitionImpl): +class WINDOWTYPEENUM(EnumDefinitionImpl): _defn = EnumDefinition( - name="WindowTypeEnum", + name="WINDOWTYPEENUM", ) @classmethod def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window")) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window")) setattr(cls, "fixed window", PermissibleValue(text="fixed window")) + setattr(cls, "horizontal sash window", + PermissibleValue(text="horizontal sash window")) + setattr(cls, "single-hung sash window", + PermissibleValue(text="single-hung sash window")) -class WindowVertPosEnum(EnumDefinitionImpl): +class WINDOWVERTPOSENUM(EnumDefinitionImpl): bottom = PermissibleValue(text="bottom") + high = PermissibleValue(text="high") + low = PermissibleValue(text="low") middle = PermissibleValue(text="middle") top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") _defn = EnumDefinition( - name="WindowVertPosEnum", + name="WINDOWVERTPOSENUM", + ) + +class CurLandUseEnum(EnumDefinitionImpl): + + badlands = PermissibleValue(text="badlands") + cities = PermissibleValue(text="cities") + conifers = PermissibleValue(text="conifers") + farmstead = PermissibleValue(text="farmstead") + gravel = PermissibleValue(text="gravel") + hardwoods = PermissibleValue(text="hardwoods") + hayland = PermissibleValue(text="hayland") + marshlands = PermissibleValue(text="marshlands") + meadows = PermissibleValue(text="meadows") + mudflats = PermissibleValue(text="mudflats") + pastureland = PermissibleValue(text="pastureland") + rainforest = PermissibleValue(text="rainforest") + rangeland = PermissibleValue(text="rangeland") + rock = PermissibleValue(text="rock") + sand = PermissibleValue(text="sand") + swamp = PermissibleValue(text="swamp") + tropical = PermissibleValue(text="tropical") + tundra = PermissibleValue(text="tundra") + + _defn = EnumDefinition( + name="CurLandUseEnum", ) + @classmethod + def _addvals(cls): + setattr(cls, "crop trees", + PermissibleValue(text="crop trees")) + setattr(cls, "horticultural plants", + PermissibleValue(text="horticultural plants")) + setattr(cls, "industrial areas", + PermissibleValue(text="industrial areas")) + setattr(cls, "intermixed hardwood and conifers", + PermissibleValue(text="intermixed hardwood and conifers")) + setattr(cls, "mines/quarries", + PermissibleValue(text="mines/quarries")) + setattr(cls, "oil waste areas", + PermissibleValue(text="oil waste areas")) + setattr(cls, "permanent snow or ice", + PermissibleValue(text="permanent snow or ice")) + setattr(cls, "roads/railroads", + PermissibleValue(text="roads/railroads")) + setattr(cls, "row crops", + PermissibleValue(text="row crops")) + setattr(cls, "saline seeps", + PermissibleValue(text="saline seeps")) + setattr(cls, "salt flats", + PermissibleValue(text="salt flats")) + setattr(cls, "shrub crops", + PermissibleValue(text="shrub crops")) + setattr(cls, "shrub land", + PermissibleValue(text="shrub land")) + setattr(cls, "small grains", + PermissibleValue(text="small grains")) + setattr(cls, "successional shrub land", + PermissibleValue(text="successional shrub land")) + setattr(cls, "vegetable crops", + PermissibleValue(text="vegetable crops")) + setattr(cls, "vine crops", + PermissibleValue(text="vine crops")) + class SampleTypeEnum(EnumDefinitionImpl): soil = PermissibleValue(text="soil") @@ -8747,6 +8458,12 @@ class slots: slots.pcr_cycles = Slot(uri=NMDC.pcr_cycles, name="pcr_cycles", curie=NMDC.curie('pcr_cycles'), model_uri=NMDC.pcr_cycles, domain=None, range=Optional[int]) +slots.is_stranded = Slot(uri=NMDC.is_stranded, name="is_stranded", curie=NMDC.curie('is_stranded'), + model_uri=NMDC.is_stranded, domain=None, range=Optional[Union[bool, Bool]]) + +slots.stranded_orientation = Slot(uri=NMDC.stranded_orientation, name="stranded_orientation", curie=NMDC.curie('stranded_orientation'), + model_uri=NMDC.stranded_orientation, domain=None, range=Optional[Union[str, "StrandedOrientationEnum"]]) + slots.mass = Slot(uri=NMDC.mass, name="mass", curie=NMDC.curie('mass'), model_uri=NMDC.mass, domain=None, range=Optional[Union[dict, QuantityValue]]) @@ -8867,8 +8584,8 @@ class slots: slots.metagenome_sequencing_activity_set = Slot(uri=NMDC.metagenome_sequencing_activity_set, name="metagenome_sequencing_activity_set", curie=NMDC.curie('metagenome_sequencing_activity_set'), model_uri=NMDC.metagenome_sequencing_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetagenomeSequencingActivityId], Union[dict, "MetagenomeSequencingActivity"]], List[Union[dict, "MetagenomeSequencingActivity"]]]]) -slots.metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), - model_uri=NMDC.metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.metatranscriptome_expression_analysis_set = Slot(uri=NMDC.metatranscriptome_expression_analysis_set, name="metatranscriptome_expression_analysis_set", curie=NMDC.curie('metatranscriptome_expression_analysis_set'), + model_uri=NMDC.metatranscriptome_expression_analysis_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeExpressionAnalysisId], Union[dict, "MetatranscriptomeExpressionAnalysis"]], List[Union[dict, "MetatranscriptomeExpressionAnalysis"]]]]) slots.read_qc_analysis_activity_set = Slot(uri=NMDC.read_qc_analysis_activity_set, name="read_qc_analysis_activity_set", curie=NMDC.curie('read_qc_analysis_activity_set'), model_uri=NMDC.read_qc_analysis_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]]) @@ -8894,6 +8611,12 @@ class slots: slots.library_preparation_set = Slot(uri=NMDC.library_preparation_set, name="library_preparation_set", curie=NMDC.curie('library_preparation_set'), model_uri=NMDC.library_preparation_set, domain=Database, range=Optional[Union[Dict[Union[str, LibraryPreparationId], Union[dict, "LibraryPreparation"]], List[Union[dict, "LibraryPreparation"]]]]) +slots.metatranscriptome_assembly_set = Slot(uri=NMDC.metatranscriptome_assembly_set, name="metatranscriptome_assembly_set", curie=NMDC.curie('metatranscriptome_assembly_set'), + model_uri=NMDC.metatranscriptome_assembly_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeAssemblyId], Union[dict, "MetatranscriptomeAssembly"]], List[Union[dict, "MetatranscriptomeAssembly"]]]]) + +slots.metatranscriptome_annotation_set = Slot(uri=NMDC.metatranscriptome_annotation_set, name="metatranscriptome_annotation_set", curie=NMDC.curie('metatranscriptome_annotation_set'), + model_uri=NMDC.metatranscriptome_annotation_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeAnnotationActivityId], Union[dict, "MetatranscriptomeAnnotationActivity"]], List[Union[dict, "MetatranscriptomeAnnotationActivity"]]]]) + slots.omics_type = Slot(uri=NMDC.omics_type, name="omics_type", curie=NMDC.curie('omics_type'), model_uri=NMDC.omics_type, domain=OmicsProcessing, range=Optional[Union[dict, "ControlledTermValue"]]) @@ -9305,109 +9028,131 @@ class slots: model_uri=NMDC.smiles, domain=None, range=Optional[Union[str, List[str]]]) slots.abs_air_humidity = Slot(uri=MIXS['0000122'], name="abs_air_humidity", curie=MIXS.curie('0000122'), - model_uri=NMDC.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.add_recov_method = Slot(uri=MIXS['0001009'], name="add_recov_method", curie=MIXS.curie('0001009'), - model_uri=NMDC.add_recov_method, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.add_recov_method, domain=None, range=Optional[str]) slots.additional_info = Slot(uri=MIXS['0000300'], name="additional_info", curie=MIXS.curie('0000300'), model_uri=NMDC.additional_info, domain=None, range=Optional[Union[dict, TextValue]]) slots.address = Slot(uri=MIXS['0000218'], name="address", curie=MIXS.curie('0000218'), - model_uri=NMDC.address, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.address, domain=None, range=Optional[str]) slots.adj_room = Slot(uri=MIXS['0000219'], name="adj_room", curie=MIXS.curie('0000219'), - model_uri=NMDC.adj_room, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.adj_room, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$')) slots.aero_struc = Slot(uri=MIXS['0000773'], name="aero_struc", curie=MIXS.curie('0000773'), - model_uri=NMDC.aero_struc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.aero_struc, domain=None, range=Optional[Union[str, "AEROSTRUCENUM"]]) slots.agrochem_addition = Slot(uri=MIXS['0000639'], name="agrochem_addition", curie=MIXS.curie('0000639'), model_uri=NMDC.agrochem_addition, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.air_PM_concen = Slot(uri=MIXS['0000108'], name="air_PM_concen", curie=MIXS.curie('0000108'), - model_uri=NMDC.air_PM_concen, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) + model_uri=NMDC.air_PM_concen, domain=None, range=Optional[Union[str, List[str]]]) slots.air_temp = Slot(uri=MIXS['0000124'], name="air_temp", curie=MIXS.curie('0000124'), - model_uri=NMDC.air_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.air_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.air_temp_regm = Slot(uri=MIXS['0000551'], name="air_temp_regm", curie=MIXS.curie('0000551'), model_uri=NMDC.air_temp_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.al_sat = Slot(uri=MIXS['0000607'], name="al_sat", curie=MIXS.curie('0000607'), - model_uri=NMDC.al_sat, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.al_sat, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.al_sat_meth = Slot(uri=MIXS['0000324'], name="al_sat_meth", curie=MIXS.curie('0000324'), - model_uri=NMDC.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.alkalinity = Slot(uri=MIXS['0000421'], name="alkalinity", curie=MIXS.curie('0000421'), - model_uri=NMDC.alkalinity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.alkalinity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.alkalinity_method = Slot(uri=MIXS['0000298'], name="alkalinity_method", curie=MIXS.curie('0000298'), model_uri=NMDC.alkalinity_method, domain=None, range=Optional[Union[dict, TextValue]]) slots.alkyl_diethers = Slot(uri=MIXS['0000490'], name="alkyl_diethers", curie=MIXS.curie('0000490'), - model_uri=NMDC.alkyl_diethers, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.alkyl_diethers, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.alt = Slot(uri=MIXS['0000094'], name="alt", curie=MIXS.curie('0000094'), - model_uri=NMDC.alt, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.alt, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.aminopept_act = Slot(uri=MIXS['0000172'], name="aminopept_act", curie=MIXS.curie('0000172'), - model_uri=NMDC.aminopept_act, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.aminopept_act, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ammonium = Slot(uri=MIXS['0000427'], name="ammonium", curie=MIXS.curie('0000427'), - model_uri=NMDC.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.amount_light = Slot(uri=MIXS['0000140'], name="amount_light", curie=MIXS.curie('0000140'), - model_uri=NMDC.amount_light, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.amount_light, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ances_data = Slot(uri=MIXS['0000247'], name="ances_data", curie=MIXS.curie('0000247'), model_uri=NMDC.ances_data, domain=None, range=Optional[Union[dict, TextValue]]) slots.annual_precpt = Slot(uri=MIXS['0000644'], name="annual_precpt", curie=MIXS.curie('0000644'), - model_uri=NMDC.annual_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.annual_precpt, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.annual_temp = Slot(uri=MIXS['0000642'], name="annual_temp", curie=MIXS.curie('0000642'), - model_uri=NMDC.annual_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.annual_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.antibiotic_regm = Slot(uri=MIXS['0000553'], name="antibiotic_regm", curie=MIXS.curie('0000553'), model_uri=NMDC.antibiotic_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.api = Slot(uri=MIXS['0000157'], name="api", curie=MIXS.curie('0000157'), - model_uri=NMDC.api, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.api, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.arch_struc = Slot(uri=MIXS['0000774'], name="arch_struc", curie=MIXS.curie('0000774'), - model_uri=NMDC.arch_struc, domain=None, range=Optional[Union[str, "ArchStrucEnum"]]) + model_uri=NMDC.arch_struc, domain=None, range=Optional[Union[str, "ARCHSTRUCENUM"]]) slots.aromatics_pc = Slot(uri=MIXS['0000133'], name="aromatics_pc", curie=MIXS.curie('0000133'), - model_uri=NMDC.aromatics_pc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.aromatics_pc, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.asphaltenes_pc = Slot(uri=MIXS['0000135'], name="asphaltenes_pc", curie=MIXS.curie('0000135'), - model_uri=NMDC.asphaltenes_pc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.asphaltenes_pc, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.atmospheric_data = Slot(uri=MIXS['0001097'], name="atmospheric_data", curie=MIXS.curie('0001097'), model_uri=NMDC.atmospheric_data, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.avg_dew_point = Slot(uri=MIXS['0000141'], name="avg_dew_point", curie=MIXS.curie('0000141'), - model_uri=NMDC.avg_dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.avg_dew_point, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.avg_occup = Slot(uri=MIXS['0000775'], name="avg_occup", curie=MIXS.curie('0000775'), model_uri=NMDC.avg_occup, domain=None, range=Optional[Union[dict, TextValue]]) slots.avg_temp = Slot(uri=MIXS['0000142'], name="avg_temp", curie=MIXS.curie('0000142'), - model_uri=NMDC.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.bac_prod = Slot(uri=MIXS['0000683'], name="bac_prod", curie=MIXS.curie('0000683'), - model_uri=NMDC.bac_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.bac_prod, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.bac_resp = Slot(uri=MIXS['0000684'], name="bac_resp", curie=MIXS.curie('0000684'), - model_uri=NMDC.bac_resp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.bac_resp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.bacteria_carb_prod = Slot(uri=MIXS['0000173'], name="bacteria_carb_prod", curie=MIXS.curie('0000173'), - model_uri=NMDC.bacteria_carb_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.bacteria_carb_prod, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.barometric_press = Slot(uri=MIXS['0000096'], name="barometric_press", curie=MIXS.curie('0000096'), - model_uri=NMDC.barometric_press, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.barometric_press, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.basin = Slot(uri=MIXS['0000290'], name="basin", curie=MIXS.curie('0000290'), model_uri=NMDC.basin, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9419,94 +9164,106 @@ class slots: model_uri=NMDC.bedroom_count, domain=None, range=Optional[Union[dict, TextValue]]) slots.benzene = Slot(uri=MIXS['0000153'], name="benzene", curie=MIXS.curie('0000153'), - model_uri=NMDC.benzene, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.benzene, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.biochem_oxygen_dem = Slot(uri=MIXS['0000653'], name="biochem_oxygen_dem", curie=MIXS.curie('0000653'), - model_uri=NMDC.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.biocide = Slot(uri=MIXS['0001011'], name="biocide", curie=MIXS.curie('0001011'), - model_uri=NMDC.biocide, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.biocide, domain=None, range=Optional[str]) slots.biocide_admin_method = Slot(uri=MIXS['0000456'], name="biocide_admin_method", curie=MIXS.curie('0000456'), model_uri=NMDC.biocide_admin_method, domain=None, range=Optional[Union[dict, TextValue]]) slots.biol_stat = Slot(uri=MIXS['0000858'], name="biol_stat", curie=MIXS.curie('0000858'), - model_uri=NMDC.biol_stat, domain=None, range=Optional[Union[str, "BiolStatEnum"]]) + model_uri=NMDC.biol_stat, domain=None, range=Optional[str]) slots.biomass = Slot(uri=MIXS['0000174'], name="biomass", curie=MIXS.curie('0000174'), model_uri=NMDC.biomass, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.biotic_regm = Slot(uri=MIXS['0001038'], name="biotic_regm", curie=MIXS.curie('0001038'), - model_uri=NMDC.biotic_regm, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.biotic_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.biotic_relationship = Slot(uri=MIXS['0000028'], name="biotic_relationship", curie=MIXS.curie('0000028'), - model_uri=NMDC.biotic_relationship, domain=None, range=Optional[Union[str, "BioticRelationshipEnum"]]) + model_uri=NMDC.biotic_relationship, domain=None, range=Optional[Union[str, "BIOTICRELATIONSHIPENUM"]]) slots.bishomohopanol = Slot(uri=MIXS['0000175'], name="bishomohopanol", curie=MIXS.curie('0000175'), - model_uri=NMDC.bishomohopanol, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.bishomohopanol, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.blood_press_diast = Slot(uri=MIXS['0000258'], name="blood_press_diast", curie=MIXS.curie('0000258'), - model_uri=NMDC.blood_press_diast, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.blood_press_diast, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.blood_press_syst = Slot(uri=MIXS['0000259'], name="blood_press_syst", curie=MIXS.curie('0000259'), - model_uri=NMDC.blood_press_syst, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.blood_press_syst, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.bromide = Slot(uri=MIXS['0000176'], name="bromide", curie=MIXS.curie('0000176'), - model_uri=NMDC.bromide, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.bromide, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.build_docs = Slot(uri=MIXS['0000787'], name="build_docs", curie=MIXS.curie('0000787'), - model_uri=NMDC.build_docs, domain=None, range=Optional[Union[str, "BuildDocsEnum"]]) + model_uri=NMDC.build_docs, domain=None, range=Optional[Union[str, "BUILDDOCSENUM"]]) slots.build_occup_type = Slot(uri=MIXS['0000761'], name="build_occup_type", curie=MIXS.curie('0000761'), - model_uri=NMDC.build_occup_type, domain=None, range=Optional[Union[Union[str, "BuildOccupTypeEnum"], List[Union[str, "BuildOccupTypeEnum"]]]]) + model_uri=NMDC.build_occup_type, domain=None, range=Optional[Union[Union[str, "BUILDOCCUPTYPEENUM"], List[Union[str, "BUILDOCCUPTYPEENUM"]]]]) slots.building_setting = Slot(uri=MIXS['0000768'], name="building_setting", curie=MIXS.curie('0000768'), - model_uri=NMDC.building_setting, domain=None, range=Optional[Union[str, "BuildingSettingEnum"]]) + model_uri=NMDC.building_setting, domain=None, range=Optional[Union[str, "BUILDINGSETTINGENUM"]]) slots.built_struc_age = Slot(uri=MIXS['0000145'], name="built_struc_age", curie=MIXS.curie('0000145'), - model_uri=NMDC.built_struc_age, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.built_struc_age, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.built_struc_set = Slot(uri=MIXS['0000778'], name="built_struc_set", curie=MIXS.curie('0000778'), - model_uri=NMDC.built_struc_set, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.built_struc_set, domain=None, range=Optional[Union[str, "BUILTSTRUCSETENUM"]]) slots.built_struc_type = Slot(uri=MIXS['0000721'], name="built_struc_type", curie=MIXS.curie('0000721'), model_uri=NMDC.built_struc_type, domain=None, range=Optional[Union[dict, TextValue]]) slots.calcium = Slot(uri=MIXS['0000432'], name="calcium", curie=MIXS.curie('0000432'), - model_uri=NMDC.calcium, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.calcium, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.carb_dioxide = Slot(uri=MIXS['0000097'], name="carb_dioxide", curie=MIXS.curie('0000097'), - model_uri=NMDC.carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.carb_dioxide, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.carb_monoxide = Slot(uri=MIXS['0000098'], name="carb_monoxide", curie=MIXS.curie('0000098'), - model_uri=NMDC.carb_monoxide, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.carb_monoxide, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.carb_nitro_ratio = Slot(uri=MIXS['0000310'], name="carb_nitro_ratio", curie=MIXS.curie('0000310'), model_uri=NMDC.carb_nitro_ratio, domain=None, range=Optional[Union[dict, QuantityValue]]) slots.ceil_area = Slot(uri=MIXS['0000148'], name="ceil_area", curie=MIXS.curie('0000148'), - model_uri=NMDC.ceil_area, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.ceil_area, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ceil_cond = Slot(uri=MIXS['0000779'], name="ceil_cond", curie=MIXS.curie('0000779'), - model_uri=NMDC.ceil_cond, domain=None, range=Optional[Union[str, "CeilCondEnum"]]) + model_uri=NMDC.ceil_cond, domain=None, range=Optional[Union[str, "SHAREDENUM3"]]) slots.ceil_finish_mat = Slot(uri=MIXS['0000780'], name="ceil_finish_mat", curie=MIXS.curie('0000780'), - model_uri=NMDC.ceil_finish_mat, domain=None, range=Optional[Union[str, "CeilFinishMatEnum"]]) + model_uri=NMDC.ceil_finish_mat, domain=None, range=Optional[Union[str, "CEILFINISHMATENUM"]]) slots.ceil_struc = Slot(uri=MIXS['0000782'], name="ceil_struc", curie=MIXS.curie('0000782'), - model_uri=NMDC.ceil_struc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.ceil_struc, domain=None, range=Optional[Union[str, "CEILSTRUCENUM"]]) slots.ceil_texture = Slot(uri=MIXS['0000783'], name="ceil_texture", curie=MIXS.curie('0000783'), - model_uri=NMDC.ceil_texture, domain=None, range=Optional[Union[str, "CeilTextureEnum"]]) + model_uri=NMDC.ceil_texture, domain=None, range=Optional[Union[str, "SHAREDENUM4"]]) slots.ceil_thermal_mass = Slot(uri=MIXS['0000143'], name="ceil_thermal_mass", curie=MIXS.curie('0000143'), - model_uri=NMDC.ceil_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.ceil_thermal_mass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ceil_type = Slot(uri=MIXS['0000784'], name="ceil_type", curie=MIXS.curie('0000784'), - model_uri=NMDC.ceil_type, domain=None, range=Optional[Union[str, "CeilTypeEnum"]]) + model_uri=NMDC.ceil_type, domain=None, range=Optional[Union[str, "CEILTYPEENUM"]]) slots.ceil_water_mold = Slot(uri=MIXS['0000781'], name="ceil_water_mold", curie=MIXS.curie('0000781'), - model_uri=NMDC.ceil_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.ceil_water_mold, domain=None, range=Optional[Union[str, "SHAREDENUM1"]]) slots.chem_administration = Slot(uri=MIXS['0000751'], name="chem_administration", curie=MIXS.curie('0000751'), model_uri=NMDC.chem_administration, domain=None, range=Optional[Union[Union[dict, ControlledTermValue], List[Union[dict, ControlledTermValue]]]]) @@ -9515,22 +9272,26 @@ class slots: model_uri=NMDC.chem_mutagen, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.chem_oxygen_dem = Slot(uri=MIXS['0000656'], name="chem_oxygen_dem", curie=MIXS.curie('0000656'), - model_uri=NMDC.chem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.chem_oxygen_dem, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.chem_treat_method = Slot(uri=MIXS['0000457'], name="chem_treat_method", curie=MIXS.curie('0000457'), model_uri=NMDC.chem_treat_method, domain=None, range=Optional[str]) slots.chem_treatment = Slot(uri=MIXS['0001012'], name="chem_treatment", curie=MIXS.curie('0001012'), - model_uri=NMDC.chem_treatment, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.chem_treatment, domain=None, range=Optional[str]) slots.chimera_check = Slot(uri=MIXS['0000052'], name="chimera_check", curie=MIXS.curie('0000052'), - model_uri=NMDC.chimera_check, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.chimera_check, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.chloride = Slot(uri=MIXS['0000429'], name="chloride", curie=MIXS.curie('0000429'), - model_uri=NMDC.chloride, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.chloride, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.chlorophyll = Slot(uri=MIXS['0000177'], name="chlorophyll", curie=MIXS.curie('0000177'), - model_uri=NMDC.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.climate_environment = Slot(uri=MIXS['0001040'], name="climate_environment", curie=MIXS.curie('0001040'), model_uri=NMDC.climate_environment, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -9539,121 +9300,140 @@ class slots: model_uri=NMDC.collection_date, domain=None, range=Optional[Union[dict, TimestampValue]]) slots.conduc = Slot(uri=MIXS['0000692'], name="conduc", curie=MIXS.curie('0000692'), - model_uri=NMDC.conduc, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.conduc, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.cool_syst_id = Slot(uri=MIXS['0000785'], name="cool_syst_id", curie=MIXS.curie('0000785'), model_uri=NMDC.cool_syst_id, domain=None, range=Optional[Union[dict, TextValue]]) slots.crop_rotation = Slot(uri=MIXS['0000318'], name="crop_rotation", curie=MIXS.curie('0000318'), - model_uri=NMDC.crop_rotation, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.crop_rotation, domain=None, range=Optional[str]) slots.cult_root_med = Slot(uri=MIXS['0001041'], name="cult_root_med", curie=MIXS.curie('0001041'), - model_uri=NMDC.cult_root_med, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.cult_root_med, domain=None, range=Optional[str]) slots.cur_land_use = Slot(uri=MIXS['0001080'], name="cur_land_use", curie=MIXS.curie('0001080'), - model_uri=NMDC.cur_land_use, domain=None, range=Optional[Union[str, "CurLandUseEnum"]]) + model_uri=NMDC.cur_land_use, domain=None, range=Optional[str]) slots.cur_vegetation = Slot(uri=MIXS['0000312'], name="cur_vegetation", curie=MIXS.curie('0000312'), model_uri=NMDC.cur_vegetation, domain=None, range=Optional[Union[dict, TextValue]]) slots.cur_vegetation_meth = Slot(uri=MIXS['0000314'], name="cur_vegetation_meth", curie=MIXS.curie('0000314'), - model_uri=NMDC.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.date_last_rain = Slot(uri=MIXS['0000786'], name="date_last_rain", curie=MIXS.curie('0000786'), model_uri=NMDC.date_last_rain, domain=None, range=Optional[Union[dict, TimestampValue]]) slots.density = Slot(uri=MIXS['0000435'], name="density", curie=MIXS.curie('0000435'), - model_uri=NMDC.density, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.density, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.depos_env = Slot(uri=MIXS['0000992'], name="depos_env", curie=MIXS.curie('0000992'), - model_uri=NMDC.depos_env, domain=None, range=Optional[Union[str, "DeposEnvEnum"]]) + model_uri=NMDC.depos_env, domain=None, range=Optional[Union[str, "DEPOSENVENUM"]]) slots.depth = Slot(uri=MIXS['0000018'], name="depth", curie=MIXS.curie('0000018'), - model_uri=NMDC.depth, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.depth, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.dew_point = Slot(uri=MIXS['0000129'], name="dew_point", curie=MIXS.curie('0000129'), - model_uri=NMDC.dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.dew_point, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diether_lipids = Slot(uri=MIXS['0000178'], name="diether_lipids", curie=MIXS.curie('0000178'), model_uri=NMDC.diether_lipids, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.diss_carb_dioxide = Slot(uri=MIXS['0000436'], name="diss_carb_dioxide", curie=MIXS.curie('0000436'), - model_uri=NMDC.diss_carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_carb_dioxide, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_hydrogen = Slot(uri=MIXS['0000179'], name="diss_hydrogen", curie=MIXS.curie('0000179'), - model_uri=NMDC.diss_hydrogen, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_hydrogen, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_inorg_carb = Slot(uri=MIXS['0000434'], name="diss_inorg_carb", curie=MIXS.curie('0000434'), - model_uri=NMDC.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_inorg_nitro = Slot(uri=MIXS['0000698'], name="diss_inorg_nitro", curie=MIXS.curie('0000698'), - model_uri=NMDC.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_inorg_phosp = Slot(uri=MIXS['0000106'], name="diss_inorg_phosp", curie=MIXS.curie('0000106'), - model_uri=NMDC.diss_inorg_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_inorg_phosp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_iron = Slot(uri=MIXS['0000139'], name="diss_iron", curie=MIXS.curie('0000139'), - model_uri=NMDC.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_org_carb = Slot(uri=MIXS['0000433'], name="diss_org_carb", curie=MIXS.curie('0000433'), - model_uri=NMDC.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_org_nitro = Slot(uri=MIXS['0000162'], name="diss_org_nitro", curie=MIXS.curie('0000162'), - model_uri=NMDC.diss_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_org_nitro, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_oxygen = Slot(uri=MIXS['0000119'], name="diss_oxygen", curie=MIXS.curie('0000119'), - model_uri=NMDC.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.diss_oxygen_fluid = Slot(uri=MIXS['0000438'], name="diss_oxygen_fluid", curie=MIXS.curie('0000438'), - model_uri=NMDC.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.door_comp_type = Slot(uri=MIXS['0000795'], name="door_comp_type", curie=MIXS.curie('0000795'), - model_uri=NMDC.door_comp_type, domain=None, range=Optional[Union[str, "DoorCompTypeEnum"]]) + model_uri=NMDC.door_comp_type, domain=None, range=Optional[Union[str, "DOORCOMPTYPEENUM"]]) slots.door_cond = Slot(uri=MIXS['0000788'], name="door_cond", curie=MIXS.curie('0000788'), - model_uri=NMDC.door_cond, domain=None, range=Optional[Union[str, "DoorCondEnum"]]) + model_uri=NMDC.door_cond, domain=None, range=Optional[Union[str, "SHAREDENUM2"]]) slots.door_direct = Slot(uri=MIXS['0000789'], name="door_direct", curie=MIXS.curie('0000789'), - model_uri=NMDC.door_direct, domain=None, range=Optional[Union[str, "DoorDirectEnum"]]) + model_uri=NMDC.door_direct, domain=None, range=Optional[Union[str, "DOORDIRECTENUM"]]) slots.door_loc = Slot(uri=MIXS['0000790'], name="door_loc", curie=MIXS.curie('0000790'), - model_uri=NMDC.door_loc, domain=None, range=Optional[Union[str, "DoorLocEnum"]]) + model_uri=NMDC.door_loc, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.door_mat = Slot(uri=MIXS['0000791'], name="door_mat", curie=MIXS.curie('0000791'), - model_uri=NMDC.door_mat, domain=None, range=Optional[Union[str, "DoorMatEnum"]]) + model_uri=NMDC.door_mat, domain=None, range=Optional[Union[str, "DOORMATENUM"]]) slots.door_move = Slot(uri=MIXS['0000792'], name="door_move", curie=MIXS.curie('0000792'), - model_uri=NMDC.door_move, domain=None, range=Optional[Union[str, "DoorMoveEnum"]]) + model_uri=NMDC.door_move, domain=None, range=Optional[Union[str, "DOORMOVEENUM"]]) slots.door_size = Slot(uri=MIXS['0000158'], name="door_size", curie=MIXS.curie('0000158'), - model_uri=NMDC.door_size, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.door_size, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.door_type = Slot(uri=MIXS['0000794'], name="door_type", curie=MIXS.curie('0000794'), - model_uri=NMDC.door_type, domain=None, range=Optional[Union[str, "DoorTypeEnum"]]) + model_uri=NMDC.door_type, domain=None, range=Optional[Union[str, "DOORTYPEENUM"]]) slots.door_type_metal = Slot(uri=MIXS['0000796'], name="door_type_metal", curie=MIXS.curie('0000796'), - model_uri=NMDC.door_type_metal, domain=None, range=Optional[Union[str, "DoorTypeMetalEnum"]]) + model_uri=NMDC.door_type_metal, domain=None, range=Optional[Union[str, "DOORTYPEMETALENUM"]]) slots.door_type_wood = Slot(uri=MIXS['0000797'], name="door_type_wood", curie=MIXS.curie('0000797'), - model_uri=NMDC.door_type_wood, domain=None, range=Optional[Union[str, "DoorTypeWoodEnum"]]) + model_uri=NMDC.door_type_wood, domain=None, range=Optional[str]) slots.door_water_mold = Slot(uri=MIXS['0000793'], name="door_water_mold", curie=MIXS.curie('0000793'), - model_uri=NMDC.door_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.door_water_mold, domain=None, range=Optional[Union[str, "SHAREDENUM1"]]) slots.down_par = Slot(uri=MIXS['0000703'], name="down_par", curie=MIXS.curie('0000703'), - model_uri=NMDC.down_par, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.down_par, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.drainage_class = Slot(uri=MIXS['0001085'], name="drainage_class", curie=MIXS.curie('0001085'), - model_uri=NMDC.drainage_class, domain=None, range=Optional[Union[str, "DrainageClassEnum"]]) + model_uri=NMDC.drainage_class, domain=None, range=Optional[Union[str, "DRAINAGECLASSENUM"]]) slots.drawings = Slot(uri=MIXS['0000798'], name="drawings", curie=MIXS.curie('0000798'), - model_uri=NMDC.drawings, domain=None, range=Optional[Union[str, "DrawingsEnum"]]) + model_uri=NMDC.drawings, domain=None, range=Optional[Union[str, "DRAWINGSENUM"]]) slots.efficiency_percent = Slot(uri=MIXS['0000657'], name="efficiency_percent", curie=MIXS.curie('0000657'), - model_uri=NMDC.efficiency_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.efficiency_percent, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.elev = Slot(uri=MIXS['0000093'], name="elev", curie=MIXS.curie('0000093'), - model_uri=NMDC.elev, domain=None, range=Optional[float]) + model_uri=NMDC.elev, domain=None, range=Optional[float], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.elevator = Slot(uri=MIXS['0000799'], name="elevator", curie=MIXS.curie('0000799'), model_uri=NMDC.elevator, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9662,43 +9442,49 @@ class slots: model_uri=NMDC.emulsions, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.env_broad_scale = Slot(uri=MIXS['0000012'], name="env_broad_scale", curie=MIXS.curie('0000012'), - model_uri=NMDC.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]]) + model_uri=NMDC.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.env_local_scale = Slot(uri=MIXS['0000013'], name="env_local_scale", curie=MIXS.curie('0000013'), model_uri=NMDC.env_local_scale, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]]) slots.env_medium = Slot(uri=MIXS['0000014'], name="env_medium", curie=MIXS.curie('0000014'), - model_uri=NMDC.env_medium, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]]) + model_uri=NMDC.env_medium, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.escalator = Slot(uri=MIXS['0000800'], name="escalator", curie=MIXS.curie('0000800'), model_uri=NMDC.escalator, domain=None, range=Optional[Union[dict, TextValue]]) slots.ethylbenzene = Slot(uri=MIXS['0000155'], name="ethylbenzene", curie=MIXS.curie('0000155'), - model_uri=NMDC.ethylbenzene, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.ethylbenzene, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.exp_duct = Slot(uri=MIXS['0000144'], name="exp_duct", curie=MIXS.curie('0000144'), - model_uri=NMDC.exp_duct, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.exp_duct, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.exp_pipe = Slot(uri=MIXS['0000220'], name="exp_pipe", curie=MIXS.curie('0000220'), - model_uri=NMDC.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.experimental_factor = Slot(uri=MIXS['0000008'], name="experimental_factor", curie=MIXS.curie('0000008'), - model_uri=NMDC.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]]) + model_uri=NMDC.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]], + pattern=re.compile(r'^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$')) slots.ext_door = Slot(uri=MIXS['0000170'], name="ext_door", curie=MIXS.curie('0000170'), model_uri=NMDC.ext_door, domain=None, range=Optional[Union[dict, TextValue]]) slots.ext_wall_orient = Slot(uri=MIXS['0000817'], name="ext_wall_orient", curie=MIXS.curie('0000817'), - model_uri=NMDC.ext_wall_orient, domain=None, range=Optional[Union[str, "ExtWallOrientEnum"]]) + model_uri=NMDC.ext_wall_orient, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.ext_window_orient = Slot(uri=MIXS['0000818'], name="ext_window_orient", curie=MIXS.curie('0000818'), - model_uri=NMDC.ext_window_orient, domain=None, range=Optional[Union[str, "ExtWindowOrientEnum"]]) + model_uri=NMDC.ext_window_orient, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.extreme_event = Slot(uri=MIXS['0000320'], name="extreme_event", curie=MIXS.curie('0000320'), model_uri=NMDC.extreme_event, domain=None, range=Optional[str]) slots.fao_class = Slot(uri=MIXS['0001083'], name="fao_class", curie=MIXS.curie('0001083'), - model_uri=NMDC.fao_class, domain=None, range=Optional[Union[str, "FaoClassEnum"]]) + model_uri=NMDC.fao_class, domain=None, range=Optional[Union[str, "FAOCLASSENUM"]]) slots.fertilizer_regm = Slot(uri=MIXS['0000556'], name="fertilizer_regm", curie=MIXS.curie('0000556'), model_uri=NMDC.fertilizer_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -9707,55 +9493,60 @@ class slots: model_uri=NMDC.field, domain=None, range=Optional[Union[dict, TextValue]]) slots.filter_type = Slot(uri=MIXS['0000765'], name="filter_type", curie=MIXS.curie('0000765'), - model_uri=NMDC.filter_type, domain=None, range=Optional[Union[Union[str, "FilterTypeEnum"], List[Union[str, "FilterTypeEnum"]]]]) + model_uri=NMDC.filter_type, domain=None, range=Optional[Union[Union[str, "FILTERTYPEENUM"], List[Union[str, "FILTERTYPEENUM"]]]]) slots.fire = Slot(uri=MIXS['0001086'], name="fire", curie=MIXS.curie('0001086'), model_uri=NMDC.fire, domain=None, range=Optional[str]) slots.fireplace_type = Slot(uri=MIXS['0000802'], name="fireplace_type", curie=MIXS.curie('0000802'), - model_uri=NMDC.fireplace_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.fireplace_type, domain=None, range=Optional[Union[str, "FIREPLACETYPEENUM"]]) slots.flooding = Slot(uri=MIXS['0000319'], name="flooding", curie=MIXS.curie('0000319'), model_uri=NMDC.flooding, domain=None, range=Optional[str]) slots.floor_age = Slot(uri=MIXS['0000164'], name="floor_age", curie=MIXS.curie('0000164'), - model_uri=NMDC.floor_age, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.floor_age, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.floor_area = Slot(uri=MIXS['0000165'], name="floor_area", curie=MIXS.curie('0000165'), - model_uri=NMDC.floor_area, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.floor_area, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.floor_cond = Slot(uri=MIXS['0000803'], name="floor_cond", curie=MIXS.curie('0000803'), - model_uri=NMDC.floor_cond, domain=None, range=Optional[Union[str, "FloorCondEnum"]]) + model_uri=NMDC.floor_cond, domain=None, range=Optional[Union[str, "SHAREDENUM3"]]) slots.floor_count = Slot(uri=MIXS['0000225'], name="floor_count", curie=MIXS.curie('0000225'), model_uri=NMDC.floor_count, domain=None, range=Optional[Union[dict, TextValue]]) slots.floor_finish_mat = Slot(uri=MIXS['0000804'], name="floor_finish_mat", curie=MIXS.curie('0000804'), - model_uri=NMDC.floor_finish_mat, domain=None, range=Optional[Union[str, "FloorFinishMatEnum"]]) + model_uri=NMDC.floor_finish_mat, domain=None, range=Optional[str]) slots.floor_struc = Slot(uri=MIXS['0000806'], name="floor_struc", curie=MIXS.curie('0000806'), - model_uri=NMDC.floor_struc, domain=None, range=Optional[Union[str, "FloorStrucEnum"]]) + model_uri=NMDC.floor_struc, domain=None, range=Optional[Union[str, "FLOORSTRUCENUM"]]) slots.floor_thermal_mass = Slot(uri=MIXS['0000166'], name="floor_thermal_mass", curie=MIXS.curie('0000166'), - model_uri=NMDC.floor_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.floor_thermal_mass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.floor_water_mold = Slot(uri=MIXS['0000805'], name="floor_water_mold", curie=MIXS.curie('0000805'), - model_uri=NMDC.floor_water_mold, domain=None, range=Optional[Union[str, "FloorWaterMoldEnum"]]) + model_uri=NMDC.floor_water_mold, domain=None, range=Optional[Union[str, "FLOORWATERMOLDENUM"]]) slots.fluor = Slot(uri=MIXS['0000704'], name="fluor", curie=MIXS.curie('0000704'), - model_uri=NMDC.fluor, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.fluor, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.freq_clean = Slot(uri=MIXS['0000226'], name="freq_clean", curie=MIXS.curie('0000226'), model_uri=NMDC.freq_clean, domain=None, range=Optional[Union[dict, QuantityValue]]) slots.freq_cook = Slot(uri=MIXS['0000227'], name="freq_cook", curie=MIXS.curie('0000227'), - model_uri=NMDC.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.fungicide_regm = Slot(uri=MIXS['0000557'], name="fungicide_regm", curie=MIXS.curie('0000557'), model_uri=NMDC.fungicide_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.furniture = Slot(uri=MIXS['0000807'], name="furniture", curie=MIXS.curie('0000807'), - model_uri=NMDC.furniture, domain=None, range=Optional[Union[str, "FurnitureEnum"]]) + model_uri=NMDC.furniture, domain=None, range=Optional[Union[str, "FURNITUREENUM"]]) slots.gaseous_environment = Slot(uri=MIXS['0000558'], name="gaseous_environment", curie=MIXS.curie('0000558'), model_uri=NMDC.gaseous_environment, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -9764,16 +9555,18 @@ class slots: model_uri=NMDC.gaseous_substances, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.gender_restroom = Slot(uri=MIXS['0000808'], name="gender_restroom", curie=MIXS.curie('0000808'), - model_uri=NMDC.gender_restroom, domain=None, range=Optional[Union[str, "GenderRestroomEnum"]]) + model_uri=NMDC.gender_restroom, domain=None, range=Optional[Union[str, "GENDERRESTROOMENUM"]]) slots.genetic_mod = Slot(uri=MIXS['0000859'], name="genetic_mod", curie=MIXS.curie('0000859'), - model_uri=NMDC.genetic_mod, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.genetic_mod, domain=None, range=Optional[str]) slots.geo_loc_name = Slot(uri=MIXS['0000010'], name="geo_loc_name", curie=MIXS.curie('0000010'), - model_uri=NMDC.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.glucosidase_act = Slot(uri=MIXS['0000137'], name="glucosidase_act", curie=MIXS.curie('0000137'), - model_uri=NMDC.glucosidase_act, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.glucosidase_act, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.gravidity = Slot(uri=MIXS['0000875'], name="gravidity", curie=MIXS.curie('0000875'), model_uri=NMDC.gravidity, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9785,7 +9578,7 @@ class slots: model_uri=NMDC.growth_facil, domain=None, range=Optional[Union[dict, ControlledTermValue]]) slots.growth_habit = Slot(uri=MIXS['0001044'], name="growth_habit", curie=MIXS.curie('0001044'), - model_uri=NMDC.growth_habit, domain=None, range=Optional[Union[str, "GrowthHabitEnum"]]) + model_uri=NMDC.growth_habit, domain=None, range=Optional[Union[str, "GROWTHHABITENUM"]]) slots.growth_hormone_regm = Slot(uri=MIXS['0000560'], name="growth_hormone_regm", curie=MIXS.curie('0000560'), model_uri=NMDC.growth_hormone_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -9794,31 +9587,34 @@ class slots: model_uri=NMDC.hall_count, domain=None, range=Optional[Union[dict, TextValue]]) slots.handidness = Slot(uri=MIXS['0000809'], name="handidness", curie=MIXS.curie('0000809'), - model_uri=NMDC.handidness, domain=None, range=Optional[Union[str, "HandidnessEnum"]]) + model_uri=NMDC.handidness, domain=None, range=Optional[Union[str, "HANDIDNESSENUM"]]) slots.hc_produced = Slot(uri=MIXS['0000989'], name="hc_produced", curie=MIXS.curie('0000989'), - model_uri=NMDC.hc_produced, domain=None, range=Optional[Union[str, "HcProducedEnum"]]) + model_uri=NMDC.hc_produced, domain=None, range=Optional[Union[str, "HCPRODUCEDENUM"]]) slots.hcr = Slot(uri=MIXS['0000988'], name="hcr", curie=MIXS.curie('0000988'), - model_uri=NMDC.hcr, domain=None, range=Optional[Union[str, "HcrEnum"]]) + model_uri=NMDC.hcr, domain=None, range=Optional[Union[str, "HCRENUM"]]) slots.hcr_fw_salinity = Slot(uri=MIXS['0000406'], name="hcr_fw_salinity", curie=MIXS.curie('0000406'), - model_uri=NMDC.hcr_fw_salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.hcr_fw_salinity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.hcr_geol_age = Slot(uri=MIXS['0000993'], name="hcr_geol_age", curie=MIXS.curie('0000993'), - model_uri=NMDC.hcr_geol_age, domain=None, range=Optional[Union[str, "HcrGeolAgeEnum"]]) + model_uri=NMDC.hcr_geol_age, domain=None, range=Optional[Union[str, "SHAREDENUM5"]]) slots.hcr_pressure = Slot(uri=MIXS['0000395'], name="hcr_pressure", curie=MIXS.curie('0000395'), - model_uri=NMDC.hcr_pressure, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.hcr_pressure, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.hcr_temp = Slot(uri=MIXS['0000393'], name="hcr_temp", curie=MIXS.curie('0000393'), - model_uri=NMDC.hcr_temp, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.hcr_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.heat_cool_type = Slot(uri=MIXS['0000766'], name="heat_cool_type", curie=MIXS.curie('0000766'), - model_uri=NMDC.heat_cool_type, domain=None, range=Optional[Union[Union[str, "HeatCoolTypeEnum"], List[Union[str, "HeatCoolTypeEnum"]]]]) + model_uri=NMDC.heat_cool_type, domain=None, range=Optional[Union[Union[str, "HEATCOOLTYPEENUM"], List[Union[str, "HEATCOOLTYPEENUM"]]]]) slots.heat_deliv_loc = Slot(uri=MIXS['0000810'], name="heat_deliv_loc", curie=MIXS.curie('0000810'), - model_uri=NMDC.heat_deliv_loc, domain=None, range=Optional[Union[str, "HeatDelivLocEnum"]]) + model_uri=NMDC.heat_deliv_loc, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.heat_sys_deliv_meth = Slot(uri=MIXS['0000812'], name="heat_sys_deliv_meth", curie=MIXS.curie('0000812'), model_uri=NMDC.heat_sys_deliv_meth, domain=None, range=Optional[str]) @@ -9830,19 +9626,23 @@ class slots: model_uri=NMDC.heavy_metals, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.heavy_metals_meth = Slot(uri=MIXS['0000343'], name="heavy_metals_meth", curie=MIXS.curie('0000343'), - model_uri=NMDC.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.height_carper_fiber = Slot(uri=MIXS['0000167'], name="height_carper_fiber", curie=MIXS.curie('0000167'), - model_uri=NMDC.height_carper_fiber, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.height_carper_fiber, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.herbicide_regm = Slot(uri=MIXS['0000561'], name="herbicide_regm", curie=MIXS.curie('0000561'), model_uri=NMDC.herbicide_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.horizon_meth = Slot(uri=MIXS['0000321'], name="horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.host_age = Slot(uri=MIXS['0000255'], name="host_age", curie=MIXS.curie('0000255'), - model_uri=NMDC.host_age, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_age, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_body_habitat = Slot(uri=MIXS['0000866'], name="host_body_habitat", curie=MIXS.curie('0000866'), model_uri=NMDC.host_body_habitat, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9854,7 +9654,8 @@ class slots: model_uri=NMDC.host_body_site, domain=None, range=Optional[Union[dict, ControlledTermValue]]) slots.host_body_temp = Slot(uri=MIXS['0000274'], name="host_body_temp", curie=MIXS.curie('0000274'), - model_uri=NMDC.host_body_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_body_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_color = Slot(uri=MIXS['0000260'], name="host_color", curie=MIXS.curie('0000260'), model_uri=NMDC.host_color, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9865,29 +9666,27 @@ class slots: slots.host_diet = Slot(uri=MIXS['0000869'], name="host_diet", curie=MIXS.curie('0000869'), model_uri=NMDC.host_diet, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) -slots.host_disease_stat = Slot(uri=MIXS['0000031'], name="host_disease_stat", curie=MIXS.curie('0000031'), - model_uri=NMDC.host_disease_stat, domain=None, range=Optional[Union[dict, TextValue]]) - slots.host_dry_mass = Slot(uri=MIXS['0000257'], name="host_dry_mass", curie=MIXS.curie('0000257'), - model_uri=NMDC.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_family_relation = Slot(uri=MIXS['0000872'], name="host_family_relation", curie=MIXS.curie('0000872'), - model_uri=NMDC.host_family_relation, domain=None, range=Optional[Union[str, List[str]]]) + model_uri=NMDC.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_genotype = Slot(uri=MIXS['0000365'], name="host_genotype", curie=MIXS.curie('0000365'), model_uri=NMDC.host_genotype, domain=None, range=Optional[Union[dict, TextValue]]) slots.host_growth_cond = Slot(uri=MIXS['0000871'], name="host_growth_cond", curie=MIXS.curie('0000871'), - model_uri=NMDC.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_height = Slot(uri=MIXS['0000264'], name="host_height", curie=MIXS.curie('0000264'), - model_uri=NMDC.host_height, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_height, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_last_meal = Slot(uri=MIXS['0000870'], name="host_last_meal", curie=MIXS.curie('0000870'), - model_uri=NMDC.host_last_meal, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) + model_uri=NMDC.host_last_meal, domain=None, range=Optional[Union[str, List[str]]]) slots.host_length = Slot(uri=MIXS['0000256'], name="host_length", curie=MIXS.curie('0000256'), - model_uri=NMDC.host_length, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_length, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_life_stage = Slot(uri=MIXS['0000251'], name="host_life_stage", curie=MIXS.curie('0000251'), model_uri=NMDC.host_life_stage, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9896,7 +9695,7 @@ class slots: model_uri=NMDC.host_phenotype, domain=None, range=Optional[Union[dict, ControlledTermValue]]) slots.host_sex = Slot(uri=MIXS['0000811'], name="host_sex", curie=MIXS.curie('0000811'), - model_uri=NMDC.host_sex, domain=None, range=Optional[Union[str, "HostSexEnum"]]) + model_uri=NMDC.host_sex, domain=None, range=Optional[str]) slots.host_shape = Slot(uri=MIXS['0000261'], name="host_shape", curie=MIXS.curie('0000261'), model_uri=NMDC.host_shape, domain=None, range=Optional[Union[dict, TextValue]]) @@ -9917,100 +9716,117 @@ class slots: model_uri=NMDC.host_taxid, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]]) slots.host_tot_mass = Slot(uri=MIXS['0000263'], name="host_tot_mass", curie=MIXS.curie('0000263'), - model_uri=NMDC.host_tot_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_tot_mass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.host_wet_mass = Slot(uri=MIXS['0000567'], name="host_wet_mass", curie=MIXS.curie('0000567'), - model_uri=NMDC.host_wet_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.host_wet_mass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.humidity = Slot(uri=MIXS['0000100'], name="humidity", curie=MIXS.curie('0000100'), - model_uri=NMDC.humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.humidity, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.humidity_regm = Slot(uri=MIXS['0000568'], name="humidity_regm", curie=MIXS.curie('0000568'), model_uri=NMDC.humidity_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.indoor_space = Slot(uri=MIXS['0000763'], name="indoor_space", curie=MIXS.curie('0000763'), - model_uri=NMDC.indoor_space, domain=None, range=Optional[Union[str, "IndoorSpaceEnum"]]) + model_uri=NMDC.indoor_space, domain=None, range=Optional[Union[str, "INDOORSPACEENUM"]]) slots.indoor_surf = Slot(uri=MIXS['0000764'], name="indoor_surf", curie=MIXS.curie('0000764'), - model_uri=NMDC.indoor_surf, domain=None, range=Optional[Union[str, "IndoorSurfEnum"]]) + model_uri=NMDC.indoor_surf, domain=None, range=Optional[Union[str, "INDOORSURFENUM"]]) slots.indust_eff_percent = Slot(uri=MIXS['0000662'], name="indust_eff_percent", curie=MIXS.curie('0000662'), - model_uri=NMDC.indust_eff_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.indust_eff_percent, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.inorg_particles = Slot(uri=MIXS['0000664'], name="inorg_particles", curie=MIXS.curie('0000664'), model_uri=NMDC.inorg_particles, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.inside_lux = Slot(uri=MIXS['0000168'], name="inside_lux", curie=MIXS.curie('0000168'), - model_uri=NMDC.inside_lux, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.inside_lux, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.int_wall_cond = Slot(uri=MIXS['0000813'], name="int_wall_cond", curie=MIXS.curie('0000813'), - model_uri=NMDC.int_wall_cond, domain=None, range=Optional[Union[str, "IntWallCondEnum"]]) + model_uri=NMDC.int_wall_cond, domain=None, range=Optional[Union[str, "SHAREDENUM3"]]) slots.iw_bt_date_well = Slot(uri=MIXS['0001010'], name="iw_bt_date_well", curie=MIXS.curie('0001010'), model_uri=NMDC.iw_bt_date_well, domain=None, range=Optional[Union[dict, TimestampValue]]) slots.iwf = Slot(uri=MIXS['0000455'], name="iwf", curie=MIXS.curie('0000455'), - model_uri=NMDC.iwf, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.iwf, domain=None, range=Optional[float], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.last_clean = Slot(uri=MIXS['0000814'], name="last_clean", curie=MIXS.curie('0000814'), model_uri=NMDC.last_clean, domain=None, range=Optional[Union[dict, TimestampValue]]) slots.lat_lon = Slot(uri=MIXS['0000009'], name="lat_lon", curie=MIXS.curie('0000009'), - model_uri=NMDC.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]]) + model_uri=NMDC.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]], + pattern=re.compile(r'^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$')) slots.light_intensity = Slot(uri=MIXS['0000706'], name="light_intensity", curie=MIXS.curie('0000706'), - model_uri=NMDC.light_intensity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.light_intensity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.light_regm = Slot(uri=MIXS['0000569'], name="light_regm", curie=MIXS.curie('0000569'), model_uri=NMDC.light_regm, domain=None, range=Optional[Union[dict, TextValue]]) slots.light_type = Slot(uri=MIXS['0000769'], name="light_type", curie=MIXS.curie('0000769'), - model_uri=NMDC.light_type, domain=None, range=Optional[Union[Union[str, "LightTypeEnum"], List[Union[str, "LightTypeEnum"]]]]) + model_uri=NMDC.light_type, domain=None, range=Optional[Union[Union[str, "LIGHTTYPEENUM"], List[Union[str, "LIGHTTYPEENUM"]]]]) slots.link_addit_analys = Slot(uri=MIXS['0000340'], name="link_addit_analys", curie=MIXS.curie('0000340'), - model_uri=NMDC.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.link_class_info = Slot(uri=MIXS['0000329'], name="link_class_info", curie=MIXS.curie('0000329'), - model_uri=NMDC.link_class_info, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.link_class_info, domain=None, range=Optional[str]) slots.link_climate_info = Slot(uri=MIXS['0000328'], name="link_climate_info", curie=MIXS.curie('0000328'), - model_uri=NMDC.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.lithology = Slot(uri=MIXS['0000990'], name="lithology", curie=MIXS.curie('0000990'), - model_uri=NMDC.lithology, domain=None, range=Optional[Union[str, "LithologyEnum"]]) + model_uri=NMDC.lithology, domain=None, range=Optional[Union[str, "LITHOLOGYENUM"]]) slots.local_class = Slot(uri=MIXS['0000330'], name="local_class", curie=MIXS.curie('0000330'), - model_uri=NMDC.local_class, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.local_class, domain=None, range=Optional[str]) slots.local_class_meth = Slot(uri=MIXS['0000331'], name="local_class_meth", curie=MIXS.curie('0000331'), - model_uri=NMDC.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.magnesium = Slot(uri=MIXS['0000431'], name="magnesium", curie=MIXS.curie('0000431'), - model_uri=NMDC.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.max_occup = Slot(uri=MIXS['0000229'], name="max_occup", curie=MIXS.curie('0000229'), - model_uri=NMDC.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.mean_frict_vel = Slot(uri=MIXS['0000498'], name="mean_frict_vel", curie=MIXS.curie('0000498'), - model_uri=NMDC.mean_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.mean_frict_vel, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.mean_peak_frict_vel = Slot(uri=MIXS['0000502'], name="mean_peak_frict_vel", curie=MIXS.curie('0000502'), - model_uri=NMDC.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.mech_struc = Slot(uri=MIXS['0000815'], name="mech_struc", curie=MIXS.curie('0000815'), - model_uri=NMDC.mech_struc, domain=None, range=Optional[Union[str, "MechStrucEnum"]]) + model_uri=NMDC.mech_struc, domain=None, range=Optional[Union[str, "MECHSTRUCENUM"]]) slots.mechanical_damage = Slot(uri=MIXS['0001052'], name="mechanical_damage", curie=MIXS.curie('0001052'), - model_uri=NMDC.mechanical_damage, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) + model_uri=NMDC.mechanical_damage, domain=None, range=Optional[Union[str, List[str]]]) slots.methane = Slot(uri=MIXS['0000101'], name="methane", curie=MIXS.curie('0000101'), - model_uri=NMDC.methane, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.methane, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.micro_biomass_meth = Slot(uri=MIXS['0000339'], name="micro_biomass_meth", curie=MIXS.curie('0000339'), model_uri=NMDC.micro_biomass_meth, domain=None, range=Optional[str]) slots.microbial_biomass = Slot(uri=MIXS['0000650'], name="microbial_biomass", curie=MIXS.curie('0000650'), - model_uri=NMDC.microbial_biomass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.microbial_biomass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.mineral_nutr_regm = Slot(uri=MIXS['0000570'], name="mineral_nutr_regm", curie=MIXS.curie('0000570'), model_uri=NMDC.mineral_nutr_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10022,52 +9838,64 @@ class slots: model_uri=NMDC.n_alkanes, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.nitrate = Slot(uri=MIXS['0000425'], name="nitrate", curie=MIXS.curie('0000425'), - model_uri=NMDC.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.nitrite = Slot(uri=MIXS['0000426'], name="nitrite", curie=MIXS.curie('0000426'), - model_uri=NMDC.nitrite, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.nitrite, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.nitro = Slot(uri=MIXS['0000504'], name="nitro", curie=MIXS.curie('0000504'), - model_uri=NMDC.nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.nitro, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.non_min_nutr_regm = Slot(uri=MIXS['0000571'], name="non_min_nutr_regm", curie=MIXS.curie('0000571'), model_uri=NMDC.non_min_nutr_regm, domain=None, range=Optional[Union[str, List[str]]]) slots.nucl_acid_amp = Slot(uri=MIXS['0000038'], name="nucl_acid_amp", curie=MIXS.curie('0000038'), - model_uri=NMDC.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.nucl_acid_ext = Slot(uri=MIXS['0000037'], name="nucl_acid_ext", curie=MIXS.curie('0000037'), - model_uri=NMDC.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.number_pets = Slot(uri=MIXS['0000231'], name="number_pets", curie=MIXS.curie('0000231'), - model_uri=NMDC.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.number_plants = Slot(uri=MIXS['0000230'], name="number_plants", curie=MIXS.curie('0000230'), - model_uri=NMDC.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.number_resident = Slot(uri=MIXS['0000232'], name="number_resident", curie=MIXS.curie('0000232'), - model_uri=NMDC.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.occup_density_samp = Slot(uri=MIXS['0000217'], name="occup_density_samp", curie=MIXS.curie('0000217'), model_uri=NMDC.occup_density_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) slots.occup_document = Slot(uri=MIXS['0000816'], name="occup_document", curie=MIXS.curie('0000816'), - model_uri=NMDC.occup_document, domain=None, range=Optional[Union[str, "OccupDocumentEnum"]]) + model_uri=NMDC.occup_document, domain=None, range=Optional[Union[str, "OCCUPDOCUMENTENUM"]]) slots.occup_samp = Slot(uri=MIXS['0000772'], name="occup_samp", curie=MIXS.curie('0000772'), - model_uri=NMDC.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.org_carb = Slot(uri=MIXS['0000508'], name="org_carb", curie=MIXS.curie('0000508'), - model_uri=NMDC.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.org_count_qpcr_info = Slot(uri=MIXS['0000099'], name="org_count_qpcr_info", curie=MIXS.curie('0000099'), model_uri=NMDC.org_count_qpcr_info, domain=None, range=Optional[str]) slots.org_matter = Slot(uri=MIXS['0000204'], name="org_matter", curie=MIXS.curie('0000204'), - model_uri=NMDC.org_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.org_matter, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.org_nitro = Slot(uri=MIXS['0000205'], name="org_nitro", curie=MIXS.curie('0000205'), - model_uri=NMDC.org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.org_nitro, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.org_particles = Slot(uri=MIXS['0000665'], name="org_particles", curie=MIXS.curie('0000665'), model_uri=NMDC.org_particles, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10076,28 +9904,32 @@ class slots: model_uri=NMDC.organism_count, domain=None, range=Optional[Union[Union[dict, QuantityValue], List[Union[dict, QuantityValue]]]]) slots.owc_tvdss = Slot(uri=MIXS['0000405'], name="owc_tvdss", curie=MIXS.curie('0000405'), - model_uri=NMDC.owc_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.owc_tvdss, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.oxy_stat_samp = Slot(uri=MIXS['0000753'], name="oxy_stat_samp", curie=MIXS.curie('0000753'), - model_uri=NMDC.oxy_stat_samp, domain=None, range=Optional[Union[str, "OxyStatSampEnum"]]) + model_uri=NMDC.oxy_stat_samp, domain=None, range=Optional[Union[str, "OXYSTATSAMPENUM"]]) slots.oxygen = Slot(uri=MIXS['0000104'], name="oxygen", curie=MIXS.curie('0000104'), - model_uri=NMDC.oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.oxygen, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.part_org_carb = Slot(uri=MIXS['0000515'], name="part_org_carb", curie=MIXS.curie('0000515'), - model_uri=NMDC.part_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.part_org_carb, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.part_org_nitro = Slot(uri=MIXS['0000719'], name="part_org_nitro", curie=MIXS.curie('0000719'), - model_uri=NMDC.part_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.part_org_nitro, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.particle_class = Slot(uri=MIXS['0000206'], name="particle_class", curie=MIXS.curie('0000206'), model_uri=NMDC.particle_class, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.pcr_cond = Slot(uri=MIXS['0000049'], name="pcr_cond", curie=MIXS.curie('0000049'), - model_uri=NMDC.pcr_cond, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.pcr_cond, domain=None, range=Optional[str]) slots.pcr_primers = Slot(uri=MIXS['0000046'], name="pcr_primers", curie=MIXS.curie('0000046'), - model_uri=NMDC.pcr_primers, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.pcr_primers, domain=None, range=Optional[str]) slots.permeability = Slot(uri=MIXS['0000404'], name="permeability", curie=MIXS.curie('0000404'), model_uri=NMDC.permeability, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10109,13 +9941,15 @@ class slots: model_uri=NMDC.pesticide_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.petroleum_hydrocarb = Slot(uri=MIXS['0000516'], name="petroleum_hydrocarb", curie=MIXS.curie('0000516'), - model_uri=NMDC.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ph = Slot(uri=MIXS['0001001'], name="ph", curie=MIXS.curie('0001001'), model_uri=NMDC.ph, domain=None, range=Optional[float]) slots.ph_meth = Slot(uri=MIXS['0001106'], name="ph_meth", curie=MIXS.curie('0001106'), - model_uri=NMDC.ph_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.ph_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.ph_regm = Slot(uri=MIXS['0001056'], name="ph_regm", curie=MIXS.curie('0001056'), model_uri=NMDC.ph_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10124,74 +9958,82 @@ class slots: model_uri=NMDC.phaeopigments, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.phosphate = Slot(uri=MIXS['0000505'], name="phosphate", curie=MIXS.curie('0000505'), - model_uri=NMDC.phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.phosphate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.phosplipid_fatt_acid = Slot(uri=MIXS['0000181'], name="phosplipid_fatt_acid", curie=MIXS.curie('0000181'), model_uri=NMDC.phosplipid_fatt_acid, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.photon_flux = Slot(uri=MIXS['0000725'], name="photon_flux", curie=MIXS.curie('0000725'), - model_uri=NMDC.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.plant_growth_med = Slot(uri=MIXS['0001057'], name="plant_growth_med", curie=MIXS.curie('0001057'), model_uri=NMDC.plant_growth_med, domain=None, range=Optional[Union[dict, ControlledTermValue]]) slots.plant_product = Slot(uri=MIXS['0001058'], name="plant_product", curie=MIXS.curie('0001058'), - model_uri=NMDC.plant_product, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.plant_product, domain=None, range=Optional[str]) slots.plant_sex = Slot(uri=MIXS['0001059'], name="plant_sex", curie=MIXS.curie('0001059'), - model_uri=NMDC.plant_sex, domain=None, range=Optional[Union[str, "PlantSexEnum"]]) + model_uri=NMDC.plant_sex, domain=None, range=Optional[Union[str, "PLANTSEXENUM"]]) slots.plant_struc = Slot(uri=MIXS['0001060'], name="plant_struc", curie=MIXS.curie('0001060'), - model_uri=NMDC.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]]) + model_uri=NMDC.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.pollutants = Slot(uri=MIXS['0000107'], name="pollutants", curie=MIXS.curie('0000107'), model_uri=NMDC.pollutants, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.pool_dna_extracts = Slot(uri=MIXS['0000325'], name="pool_dna_extracts", curie=MIXS.curie('0000325'), - model_uri=NMDC.pool_dna_extracts, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.pool_dna_extracts, domain=None, range=Optional[str]) slots.porosity = Slot(uri=MIXS['0000211'], name="porosity", curie=MIXS.curie('0000211'), model_uri=NMDC.porosity, domain=None, range=Optional[Union[dict, TextValue]]) slots.potassium = Slot(uri=MIXS['0000430'], name="potassium", curie=MIXS.curie('0000430'), - model_uri=NMDC.potassium, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.potassium, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.pour_point = Slot(uri=MIXS['0000127'], name="pour_point", curie=MIXS.curie('0000127'), - model_uri=NMDC.pour_point, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.pour_point, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.pre_treatment = Slot(uri=MIXS['0000348'], name="pre_treatment", curie=MIXS.curie('0000348'), - model_uri=NMDC.pre_treatment, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.pre_treatment, domain=None, range=Optional[str]) slots.pres_animal_insect = Slot(uri=MIXS['0000819'], name="pres_animal_insect", curie=MIXS.curie('0000819'), - model_uri=NMDC.pres_animal_insect, domain=None, range=Optional[str], - pattern=re.compile(r'^(cat|dog|rodent|snake|other);\d+$')) + model_uri=NMDC.pres_animal_insect, domain=None, range=Optional[str]) slots.pressure = Slot(uri=MIXS['0000412'], name="pressure", curie=MIXS.curie('0000412'), - model_uri=NMDC.pressure, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.pressure, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.prev_land_use_meth = Slot(uri=MIXS['0000316'], name="prev_land_use_meth", curie=MIXS.curie('0000316'), - model_uri=NMDC.prev_land_use_meth, domain=None, range=Optional[str]) + model_uri=NMDC.prev_land_use_meth, domain=None, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.previous_land_use = Slot(uri=MIXS['0000315'], name="previous_land_use", curie=MIXS.curie('0000315'), - model_uri=NMDC.previous_land_use, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.previous_land_use, domain=None, range=Optional[str]) slots.primary_prod = Slot(uri=MIXS['0000728'], name="primary_prod", curie=MIXS.curie('0000728'), - model_uri=NMDC.primary_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.primary_prod, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.primary_treatment = Slot(uri=MIXS['0000349'], name="primary_treatment", curie=MIXS.curie('0000349'), - model_uri=NMDC.primary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.primary_treatment, domain=None, range=Optional[str]) slots.prod_rate = Slot(uri=MIXS['0000452'], name="prod_rate", curie=MIXS.curie('0000452'), - model_uri=NMDC.prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.prod_rate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.prod_start_date = Slot(uri=MIXS['0001008'], name="prod_start_date", curie=MIXS.curie('0001008'), model_uri=NMDC.prod_start_date, domain=None, range=Optional[Union[dict, TimestampValue]]) slots.profile_position = Slot(uri=MIXS['0001084'], name="profile_position", curie=MIXS.curie('0001084'), - model_uri=NMDC.profile_position, domain=None, range=Optional[Union[str, "ProfilePositionEnum"]]) + model_uri=NMDC.profile_position, domain=None, range=Optional[Union[str, "PROFILEPOSITIONENUM"]]) slots.quad_pos = Slot(uri=MIXS['0000820'], name="quad_pos", curie=MIXS.curie('0000820'), - model_uri=NMDC.quad_pos, domain=None, range=Optional[Union[str, "QuadPosEnum"]]) + model_uri=NMDC.quad_pos, domain=None, range=Optional[Union[str, "QUADPOSENUM"]]) slots.radiation_regm = Slot(uri=MIXS['0000575'], name="radiation_regm", curie=MIXS.curie('0000575'), model_uri=NMDC.radiation_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10200,37 +10042,42 @@ class slots: model_uri=NMDC.rainfall_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.reactor_type = Slot(uri=MIXS['0000350'], name="reactor_type", curie=MIXS.curie('0000350'), - model_uri=NMDC.reactor_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.reactor_type, domain=None, range=Optional[str]) slots.redox_potential = Slot(uri=MIXS['0000182'], name="redox_potential", curie=MIXS.curie('0000182'), - model_uri=NMDC.redox_potential, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.redox_potential, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.rel_air_humidity = Slot(uri=MIXS['0000121'], name="rel_air_humidity", curie=MIXS.curie('0000121'), - model_uri=NMDC.rel_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.rel_air_humidity, domain=None, range=Optional[float], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.rel_humidity_out = Slot(uri=MIXS['0000188'], name="rel_humidity_out", curie=MIXS.curie('0000188'), - model_uri=NMDC.rel_humidity_out, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.rel_humidity_out, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.rel_samp_loc = Slot(uri=MIXS['0000821'], name="rel_samp_loc", curie=MIXS.curie('0000821'), - model_uri=NMDC.rel_samp_loc, domain=None, range=Optional[Union[str, "RelSampLocEnum"]]) + model_uri=NMDC.rel_samp_loc, domain=None, range=Optional[Union[str, "RELSAMPLOCENUM"]]) slots.reservoir = Slot(uri=MIXS['0000303'], name="reservoir", curie=MIXS.curie('0000303'), model_uri=NMDC.reservoir, domain=None, range=Optional[Union[dict, TextValue]]) slots.resins_pc = Slot(uri=MIXS['0000134'], name="resins_pc", curie=MIXS.curie('0000134'), - model_uri=NMDC.resins_pc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.resins_pc, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_air_exch_rate = Slot(uri=MIXS['0000169'], name="room_air_exch_rate", curie=MIXS.curie('0000169'), - model_uri=NMDC.room_air_exch_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.room_air_exch_rate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_architec_elem = Slot(uri=MIXS['0000233'], name="room_architec_elem", curie=MIXS.curie('0000233'), model_uri=NMDC.room_architec_elem, domain=None, range=Optional[str]) slots.room_condt = Slot(uri=MIXS['0000822'], name="room_condt", curie=MIXS.curie('0000822'), - model_uri=NMDC.room_condt, domain=None, range=Optional[Union[str, "RoomCondtEnum"]]) + model_uri=NMDC.room_condt, domain=None, range=Optional[Union[str, "ROOMCONDTENUM"]]) slots.room_connected = Slot(uri=MIXS['0000826'], name="room_connected", curie=MIXS.curie('0000826'), - model_uri=NMDC.room_connected, domain=None, range=Optional[Union[str, "RoomConnectedEnum"]]) + model_uri=NMDC.room_connected, domain=None, range=Optional[Union[str, "ROOMCONNECTEDENUM"]]) slots.room_count = Slot(uri=MIXS['0000234'], name="room_count", curie=MIXS.curie('0000234'), model_uri=NMDC.room_count, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10239,43 +10086,51 @@ class slots: model_uri=NMDC.room_dim, domain=None, range=Optional[Union[dict, TextValue]]) slots.room_door_dist = Slot(uri=MIXS['0000193'], name="room_door_dist", curie=MIXS.curie('0000193'), - model_uri=NMDC.room_door_dist, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_door_dist, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_door_share = Slot(uri=MIXS['0000242'], name="room_door_share", curie=MIXS.curie('0000242'), - model_uri=NMDC.room_door_share, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_door_share, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$')) slots.room_hallway = Slot(uri=MIXS['0000238'], name="room_hallway", curie=MIXS.curie('0000238'), - model_uri=NMDC.room_hallway, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_hallway, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$')) slots.room_loc = Slot(uri=MIXS['0000823'], name="room_loc", curie=MIXS.curie('0000823'), - model_uri=NMDC.room_loc, domain=None, range=Optional[Union[str, "RoomLocEnum"]]) + model_uri=NMDC.room_loc, domain=None, range=Optional[Union[str, "ROOMLOCENUM"]]) slots.room_moist_dam_hist = Slot(uri=MIXS['0000235'], name="room_moist_dam_hist", curie=MIXS.curie('0000235'), model_uri=NMDC.room_moist_dam_hist, domain=None, range=Optional[int]) slots.room_net_area = Slot(uri=MIXS['0000194'], name="room_net_area", curie=MIXS.curie('0000194'), - model_uri=NMDC.room_net_area, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_net_area, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_occup = Slot(uri=MIXS['0000236'], name="room_occup", curie=MIXS.curie('0000236'), - model_uri=NMDC.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_samp_pos = Slot(uri=MIXS['0000824'], name="room_samp_pos", curie=MIXS.curie('0000824'), - model_uri=NMDC.room_samp_pos, domain=None, range=Optional[Union[str, "RoomSampPosEnum"]]) + model_uri=NMDC.room_samp_pos, domain=None, range=Optional[Union[str, "ROOMSAMPPOSENUM"]]) slots.room_type = Slot(uri=MIXS['0000825'], name="room_type", curie=MIXS.curie('0000825'), - model_uri=NMDC.room_type, domain=None, range=Optional[Union[str, "RoomTypeEnum"]]) + model_uri=NMDC.room_type, domain=None, range=Optional[str]) slots.room_vol = Slot(uri=MIXS['0000195'], name="room_vol", curie=MIXS.curie('0000195'), - model_uri=NMDC.room_vol, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_vol, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.room_wall_share = Slot(uri=MIXS['0000243'], name="room_wall_share", curie=MIXS.curie('0000243'), - model_uri=NMDC.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$')) slots.room_window_count = Slot(uri=MIXS['0000237'], name="room_window_count", curie=MIXS.curie('0000237'), model_uri=NMDC.room_window_count, domain=None, range=Optional[int]) slots.root_cond = Slot(uri=MIXS['0001061'], name="root_cond", curie=MIXS.curie('0001061'), - model_uri=NMDC.root_cond, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.root_cond, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.root_med_carbon = Slot(uri=MIXS['0000577'], name="root_med_carbon", curie=MIXS.curie('0000577'), model_uri=NMDC.root_med_carbon, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10299,34 +10154,27 @@ class slots: model_uri=NMDC.root_med_suppl, domain=None, range=Optional[Union[dict, TextValue]]) slots.salinity = Slot(uri=MIXS['0000183'], name="salinity", curie=MIXS.curie('0000183'), - model_uri=NMDC.salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.salinity_meth = Slot(uri=MIXS['0000341'], name="salinity_meth", curie=MIXS.curie('0000341'), - model_uri=NMDC.salinity_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.salinity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.salt_regm = Slot(uri=MIXS['0000582'], name="salt_regm", curie=MIXS.curie('0000582'), model_uri=NMDC.salt_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.samp_capt_status = Slot(uri=MIXS['0000860'], name="samp_capt_status", curie=MIXS.curie('0000860'), - model_uri=NMDC.samp_capt_status, domain=None, range=Optional[Union[str, "SampCaptStatusEnum"]]) - -slots.samp_collec_device = Slot(uri=MIXS['0000002'], name="samp_collec_device", curie=MIXS.curie('0000002'), - model_uri=NMDC.samp_collec_device, domain=None, range=Optional[str]) - -slots.samp_collec_method = Slot(uri=MIXS['0001225'], name="samp_collec_method", curie=MIXS.curie('0001225'), - model_uri=NMDC.samp_collec_method, domain=None, range=Optional[str]) + model_uri=NMDC.samp_capt_status, domain=None, range=Optional[Union[str, "SAMPCAPTSTATUSENUM"]]) slots.samp_collect_point = Slot(uri=MIXS['0001015'], name="samp_collect_point", curie=MIXS.curie('0001015'), - model_uri=NMDC.samp_collect_point, domain=None, range=Optional[Union[str, "SampCollectPointEnum"]]) + model_uri=NMDC.samp_collect_point, domain=None, range=Optional[Union[str, "SAMPCOLLECTPOINTENUM"]]) slots.samp_dis_stage = Slot(uri=MIXS['0000249'], name="samp_dis_stage", curie=MIXS.curie('0000249'), - model_uri=NMDC.samp_dis_stage, domain=None, range=Optional[Union[str, "SampDisStageEnum"]]) + model_uri=NMDC.samp_dis_stage, domain=None, range=Optional[Union[str, "SAMPDISSTAGEENUM"]]) slots.samp_floor = Slot(uri=MIXS['0000828'], name="samp_floor", curie=MIXS.curie('0000828'), - model_uri=NMDC.samp_floor, domain=None, range=Optional[Union[str, "SampFloorEnum"]]) + model_uri=NMDC.samp_floor, domain=None, range=Optional[str]) slots.samp_loc_corr_rate = Slot(uri=MIXS['0000136'], name="samp_loc_corr_rate", curie=MIXS.curie('0000136'), - model_uri=NMDC.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.samp_mat_process = Slot(uri=MIXS['0000016'], name="samp_mat_process", curie=MIXS.curie('0000016'), model_uri=NMDC.samp_mat_process, domain=None, range=Optional[Union[dict, ControlledTermValue]]) @@ -10338,31 +10186,36 @@ class slots: model_uri=NMDC.samp_name, domain=None, range=Optional[str]) slots.samp_preserv = Slot(uri=MIXS['0000463'], name="samp_preserv", curie=MIXS.curie('0000463'), - model_uri=NMDC.samp_preserv, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.samp_preserv, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.samp_room_id = Slot(uri=MIXS['0000244'], name="samp_room_id", curie=MIXS.curie('0000244'), model_uri=NMDC.samp_room_id, domain=None, range=Optional[Union[dict, TextValue]]) slots.samp_size = Slot(uri=MIXS['0000001'], name="samp_size", curie=MIXS.curie('0000001'), - model_uri=NMDC.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.samp_sort_meth = Slot(uri=MIXS['0000216'], name="samp_sort_meth", curie=MIXS.curie('0000216'), model_uri=NMDC.samp_sort_meth, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.samp_store_dur = Slot(uri=MIXS['0000116'], name="samp_store_dur", curie=MIXS.curie('0000116'), - model_uri=NMDC.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$')) slots.samp_store_loc = Slot(uri=MIXS['0000755'], name="samp_store_loc", curie=MIXS.curie('0000755'), - model_uri=NMDC.samp_store_loc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.samp_store_loc, domain=None, range=Optional[str]) slots.samp_store_temp = Slot(uri=MIXS['0000110'], name="samp_store_temp", curie=MIXS.curie('0000110'), - model_uri=NMDC.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.samp_subtype = Slot(uri=MIXS['0000999'], name="samp_subtype", curie=MIXS.curie('0000999'), - model_uri=NMDC.samp_subtype, domain=None, range=Optional[Union[str, "SampSubtypeEnum"]]) + model_uri=NMDC.samp_subtype, domain=None, range=Optional[Union[str, "SAMPSUBTYPEENUM"]]) slots.samp_taxon_id = Slot(uri=MIXS['0001320'], name="samp_taxon_id", curie=MIXS.curie('0001320'), - model_uri=NMDC.samp_taxon_id, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]]) + model_uri=NMDC.samp_taxon_id, domain=None, range=Optional[Union[dict, ControlledIdentifiedTermValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$')) slots.samp_time_out = Slot(uri=MIXS['0000196'], name="samp_time_out", curie=MIXS.curie('0000196'), model_uri=NMDC.samp_time_out, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10374,109 +10227,123 @@ class slots: model_uri=NMDC.samp_tvdss, domain=None, range=Optional[Union[dict, TextValue]]) slots.samp_type = Slot(uri=MIXS['0000998'], name="samp_type", curie=MIXS.curie('0000998'), - model_uri=NMDC.samp_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.samp_type, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.samp_vol_we_dna_ext = Slot(uri=MIXS['0000111'], name="samp_vol_we_dna_ext", curie=MIXS.curie('0000111'), - model_uri=NMDC.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.samp_weather = Slot(uri=MIXS['0000827'], name="samp_weather", curie=MIXS.curie('0000827'), - model_uri=NMDC.samp_weather, domain=None, range=Optional[Union[str, "SampWeatherEnum"]]) + model_uri=NMDC.samp_weather, domain=None, range=Optional[Union[str, "SAMPWEATHERENUM"]]) slots.samp_well_name = Slot(uri=MIXS['0000296'], name="samp_well_name", curie=MIXS.curie('0000296'), model_uri=NMDC.samp_well_name, domain=None, range=Optional[Union[dict, TextValue]]) slots.saturates_pc = Slot(uri=MIXS['0000131'], name="saturates_pc", curie=MIXS.curie('0000131'), - model_uri=NMDC.saturates_pc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.saturates_pc, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.season = Slot(uri=MIXS['0000829'], name="season", curie=MIXS.curie('0000829'), - model_uri=NMDC.season, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.season, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$')) slots.season_environment = Slot(uri=MIXS['0001068'], name="season_environment", curie=MIXS.curie('0001068'), model_uri=NMDC.season_environment, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.season_precpt = Slot(uri=MIXS['0000645'], name="season_precpt", curie=MIXS.curie('0000645'), - model_uri=NMDC.season_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.season_precpt, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.season_temp = Slot(uri=MIXS['0000643'], name="season_temp", curie=MIXS.curie('0000643'), - model_uri=NMDC.season_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.season_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.season_use = Slot(uri=MIXS['0000830'], name="season_use", curie=MIXS.curie('0000830'), - model_uri=NMDC.season_use, domain=None, range=Optional[Union[str, "SeasonUseEnum"]]) + model_uri=NMDC.season_use, domain=None, range=Optional[Union[str, "SEASONUSEENUM"]]) slots.secondary_treatment = Slot(uri=MIXS['0000351'], name="secondary_treatment", curie=MIXS.curie('0000351'), - model_uri=NMDC.secondary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.secondary_treatment, domain=None, range=Optional[str]) slots.sediment_type = Slot(uri=MIXS['0001078'], name="sediment_type", curie=MIXS.curie('0001078'), - model_uri=NMDC.sediment_type, domain=None, range=Optional[Union[str, "SedimentTypeEnum"]]) + model_uri=NMDC.sediment_type, domain=None, range=Optional[Union[str, "SEDIMENTTYPEENUM"]]) slots.seq_meth = Slot(uri=MIXS['0000050'], name="seq_meth", curie=MIXS.curie('0000050'), - model_uri=NMDC.seq_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.seq_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$')) slots.seq_quality_check = Slot(uri=MIXS['0000051'], name="seq_quality_check", curie=MIXS.curie('0000051'), - model_uri=NMDC.seq_quality_check, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.seq_quality_check, domain=None, range=Optional[Union[str, "SEQQUALITYCHECKENUM"]]) slots.sewage_type = Slot(uri=MIXS['0000215'], name="sewage_type", curie=MIXS.curie('0000215'), - model_uri=NMDC.sewage_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.sewage_type, domain=None, range=Optional[str]) slots.shad_dev_water_mold = Slot(uri=MIXS['0000834'], name="shad_dev_water_mold", curie=MIXS.curie('0000834'), model_uri=NMDC.shad_dev_water_mold, domain=None, range=Optional[str]) slots.shading_device_cond = Slot(uri=MIXS['0000831'], name="shading_device_cond", curie=MIXS.curie('0000831'), - model_uri=NMDC.shading_device_cond, domain=None, range=Optional[Union[str, "ShadingDeviceCondEnum"]]) + model_uri=NMDC.shading_device_cond, domain=None, range=Optional[Union[str, "SHAREDENUM2"]]) slots.shading_device_loc = Slot(uri=MIXS['0000832'], name="shading_device_loc", curie=MIXS.curie('0000832'), - model_uri=NMDC.shading_device_loc, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.shading_device_loc, domain=None, range=Optional[Union[str, "SHADINGDEVICELOCENUM"]]) slots.shading_device_mat = Slot(uri=MIXS['0000245'], name="shading_device_mat", curie=MIXS.curie('0000245'), - model_uri=NMDC.shading_device_mat, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.shading_device_mat, domain=None, range=Optional[str]) slots.shading_device_type = Slot(uri=MIXS['0000835'], name="shading_device_type", curie=MIXS.curie('0000835'), - model_uri=NMDC.shading_device_type, domain=None, range=Optional[Union[str, "ShadingDeviceTypeEnum"]]) + model_uri=NMDC.shading_device_type, domain=None, range=Optional[Union[str, "SHADINGDEVICETYPEENUM"]]) slots.sieving = Slot(uri=MIXS['0000322'], name="sieving", curie=MIXS.curie('0000322'), model_uri=NMDC.sieving, domain=None, range=Optional[Union[dict, TextValue]]) slots.silicate = Slot(uri=MIXS['0000184'], name="silicate", curie=MIXS.curie('0000184'), - model_uri=NMDC.silicate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.silicate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.size_frac = Slot(uri=MIXS['0000017'], name="size_frac", curie=MIXS.curie('0000017'), model_uri=NMDC.size_frac, domain=None, range=Optional[Union[dict, TextValue]]) slots.size_frac_low = Slot(uri=MIXS['0000735'], name="size_frac_low", curie=MIXS.curie('0000735'), - model_uri=NMDC.size_frac_low, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.size_frac_low, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.size_frac_up = Slot(uri=MIXS['0000736'], name="size_frac_up", curie=MIXS.curie('0000736'), - model_uri=NMDC.size_frac_up, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.size_frac_up, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.slope_aspect = Slot(uri=MIXS['0000647'], name="slope_aspect", curie=MIXS.curie('0000647'), - model_uri=NMDC.slope_aspect, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.slope_aspect, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.slope_gradient = Slot(uri=MIXS['0000646'], name="slope_gradient", curie=MIXS.curie('0000646'), - model_uri=NMDC.slope_gradient, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.slope_gradient, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.sludge_retent_time = Slot(uri=MIXS['0000669'], name="sludge_retent_time", curie=MIXS.curie('0000669'), - model_uri=NMDC.sludge_retent_time, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.sludge_retent_time, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.sodium = Slot(uri=MIXS['0000428'], name="sodium", curie=MIXS.curie('0000428'), - model_uri=NMDC.sodium, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.sodium, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.soil_horizon = Slot(uri=MIXS['0001082'], name="soil_horizon", curie=MIXS.curie('0001082'), - model_uri=NMDC.soil_horizon, domain=None, range=Optional[Union[str, "SoilHorizonEnum"]]) - -slots.soil_text_measure = Slot(uri=MIXS['0000335'], name="soil_text_measure", curie=MIXS.curie('0000335'), - model_uri=NMDC.soil_text_measure, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.soil_horizon, domain=None, range=Optional[Union[str, "SOILHORIZONENUM"]]) slots.soil_texture_meth = Slot(uri=MIXS['0000336'], name="soil_texture_meth", curie=MIXS.curie('0000336'), - model_uri=NMDC.soil_texture_meth, domain=None, range=Optional[str]) + model_uri=NMDC.soil_texture_meth, domain=None, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.soil_type = Slot(uri=MIXS['0000332'], name="soil_type", curie=MIXS.curie('0000332'), - model_uri=NMDC.soil_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.soil_type, domain=None, range=Optional[str]) slots.soil_type_meth = Slot(uri=MIXS['0000334'], name="soil_type_meth", curie=MIXS.curie('0000334'), - model_uri=NMDC.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.solar_irradiance = Slot(uri=MIXS['0000112'], name="solar_irradiance", curie=MIXS.curie('0000112'), - model_uri=NMDC.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.soluble_inorg_mat = Slot(uri=MIXS['0000672'], name="soluble_inorg_mat", curie=MIXS.curie('0000672'), model_uri=NMDC.soluble_inorg_mat, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10485,31 +10352,33 @@ class slots: model_uri=NMDC.soluble_org_mat, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.soluble_react_phosp = Slot(uri=MIXS['0000738'], name="soluble_react_phosp", curie=MIXS.curie('0000738'), - model_uri=NMDC.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.source_mat_id = Slot(uri=MIXS['0000026'], name="source_mat_id", curie=MIXS.curie('0000026'), model_uri=NMDC.source_mat_id, domain=None, range=Optional[Union[dict, TextValue]]) slots.space_typ_state = Slot(uri=MIXS['0000770'], name="space_typ_state", curie=MIXS.curie('0000770'), - model_uri=NMDC.space_typ_state, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.space_typ_state, domain=None, range=Optional[Union[str, "SPACETYPSTATEENUM"]]) slots.specific = Slot(uri=MIXS['0000836'], name="specific", curie=MIXS.curie('0000836'), - model_uri=NMDC.specific, domain=None, range=Optional[Union[str, "SpecificEnum"]]) + model_uri=NMDC.specific, domain=None, range=Optional[Union[str, "SPECIFICENUM"]]) slots.specific_humidity = Slot(uri=MIXS['0000214'], name="specific_humidity", curie=MIXS.curie('0000214'), - model_uri=NMDC.specific_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.specific_humidity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.sr_dep_env = Slot(uri=MIXS['0000996'], name="sr_dep_env", curie=MIXS.curie('0000996'), - model_uri=NMDC.sr_dep_env, domain=None, range=Optional[Union[str, "SrDepEnvEnum"]]) + model_uri=NMDC.sr_dep_env, domain=None, range=Optional[Union[str, "SRDEPENVENUM"]]) slots.sr_geol_age = Slot(uri=MIXS['0000997'], name="sr_geol_age", curie=MIXS.curie('0000997'), - model_uri=NMDC.sr_geol_age, domain=None, range=Optional[Union[str, "SrGeolAgeEnum"]]) + model_uri=NMDC.sr_geol_age, domain=None, range=Optional[Union[str, "SHAREDENUM5"]]) slots.sr_kerog_type = Slot(uri=MIXS['0000994'], name="sr_kerog_type", curie=MIXS.curie('0000994'), - model_uri=NMDC.sr_kerog_type, domain=None, range=Optional[Union[str, "SrKerogTypeEnum"]]) + model_uri=NMDC.sr_kerog_type, domain=None, range=Optional[Union[str, "SRKEROGTYPEENUM"]]) slots.sr_lithology = Slot(uri=MIXS['0000995'], name="sr_lithology", curie=MIXS.curie('0000995'), - model_uri=NMDC.sr_lithology, domain=None, range=Optional[Union[str, "SrLithologyEnum"]]) + model_uri=NMDC.sr_lithology, domain=None, range=Optional[Union[str, "SRLITHOLOGYENUM"]]) slots.standing_water_regm = Slot(uri=MIXS['0001069'], name="standing_water_regm", curie=MIXS.curie('0001069'), model_uri=NMDC.standing_water_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10518,43 +10387,51 @@ class slots: model_uri=NMDC.store_cond, domain=None, range=Optional[Union[dict, TextValue]]) slots.substructure_type = Slot(uri=MIXS['0000767'], name="substructure_type", curie=MIXS.curie('0000767'), - model_uri=NMDC.substructure_type, domain=None, range=Optional[Union[Union[str, "SubstructureTypeEnum"], List[Union[str, "SubstructureTypeEnum"]]]]) + model_uri=NMDC.substructure_type, domain=None, range=Optional[Union[Union[str, "SUBSTRUCTURETYPEENUM"], List[Union[str, "SUBSTRUCTURETYPEENUM"]]]]) slots.sulfate = Slot(uri=MIXS['0000423'], name="sulfate", curie=MIXS.curie('0000423'), - model_uri=NMDC.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.sulfate_fw = Slot(uri=MIXS['0000407'], name="sulfate_fw", curie=MIXS.curie('0000407'), - model_uri=NMDC.sulfate_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.sulfate_fw, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.sulfide = Slot(uri=MIXS['0000424'], name="sulfide", curie=MIXS.curie('0000424'), - model_uri=NMDC.sulfide, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.sulfide, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.surf_air_cont = Slot(uri=MIXS['0000759'], name="surf_air_cont", curie=MIXS.curie('0000759'), - model_uri=NMDC.surf_air_cont, domain=None, range=Optional[Union[Union[str, "SurfAirContEnum"], List[Union[str, "SurfAirContEnum"]]]]) + model_uri=NMDC.surf_air_cont, domain=None, range=Optional[Union[Union[str, "SURFAIRCONTENUM"], List[Union[str, "SURFAIRCONTENUM"]]]]) slots.surf_humidity = Slot(uri=MIXS['0000123'], name="surf_humidity", curie=MIXS.curie('0000123'), - model_uri=NMDC.surf_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.surf_humidity, domain=None, range=Optional[float], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.surf_material = Slot(uri=MIXS['0000758'], name="surf_material", curie=MIXS.curie('0000758'), - model_uri=NMDC.surf_material, domain=None, range=Optional[Union[str, "SurfMaterialEnum"]]) + model_uri=NMDC.surf_material, domain=None, range=Optional[Union[str, "SURFMATERIALENUM"]]) slots.surf_moisture = Slot(uri=MIXS['0000128'], name="surf_moisture", curie=MIXS.curie('0000128'), - model_uri=NMDC.surf_moisture, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.surf_moisture, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.surf_moisture_ph = Slot(uri=MIXS['0000760'], name="surf_moisture_ph", curie=MIXS.curie('0000760'), model_uri=NMDC.surf_moisture_ph, domain=None, range=Optional[float]) slots.surf_temp = Slot(uri=MIXS['0000125'], name="surf_temp", curie=MIXS.curie('0000125'), - model_uri=NMDC.surf_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.surf_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.suspend_part_matter = Slot(uri=MIXS['0000741'], name="suspend_part_matter", curie=MIXS.curie('0000741'), - model_uri=NMDC.suspend_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.suspend_part_matter, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.suspend_solids = Slot(uri=MIXS['0000150'], name="suspend_solids", curie=MIXS.curie('0000150'), model_uri=NMDC.suspend_solids, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.tan = Slot(uri=MIXS['0000120'], name="tan", curie=MIXS.curie('0000120'), - model_uri=NMDC.tan, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tan, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.target_gene = Slot(uri=MIXS['0000044'], name="target_gene", curie=MIXS.curie('0000044'), model_uri=NMDC.target_gene, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10563,103 +10440,127 @@ class slots: model_uri=NMDC.target_subfragment, domain=None, range=Optional[Union[dict, TextValue]]) slots.temp = Slot(uri=MIXS['0000113'], name="temp", curie=MIXS.curie('0000113'), - model_uri=NMDC.temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.temp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.temp_out = Slot(uri=MIXS['0000197'], name="temp_out", curie=MIXS.curie('0000197'), - model_uri=NMDC.temp_out, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.temp_out, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tertiary_treatment = Slot(uri=MIXS['0000352'], name="tertiary_treatment", curie=MIXS.curie('0000352'), - model_uri=NMDC.tertiary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.tertiary_treatment, domain=None, range=Optional[str]) slots.tidal_stage = Slot(uri=MIXS['0000750'], name="tidal_stage", curie=MIXS.curie('0000750'), - model_uri=NMDC.tidal_stage, domain=None, range=Optional[Union[str, "TidalStageEnum"]]) + model_uri=NMDC.tidal_stage, domain=None, range=Optional[Union[str, "TIDALSTAGEENUM"]]) slots.tillage = Slot(uri=MIXS['0001081'], name="tillage", curie=MIXS.curie('0001081'), - model_uri=NMDC.tillage, domain=None, range=Optional[Union[Union[str, "TillageEnum"], List[Union[str, "TillageEnum"]]]]) + model_uri=NMDC.tillage, domain=None, range=Optional[Union[Union[str, "TILLAGEENUM"], List[Union[str, "TILLAGEENUM"]]]]) slots.tiss_cult_growth_med = Slot(uri=MIXS['0001070'], name="tiss_cult_growth_med", curie=MIXS.curie('0001070'), - model_uri=NMDC.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.toluene = Slot(uri=MIXS['0000154'], name="toluene", curie=MIXS.curie('0000154'), - model_uri=NMDC.toluene, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.toluene, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_carb = Slot(uri=MIXS['0000525'], name="tot_carb", curie=MIXS.curie('0000525'), - model_uri=NMDC.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_depth_water_col = Slot(uri=MIXS['0000634'], name="tot_depth_water_col", curie=MIXS.curie('0000634'), - model_uri=NMDC.tot_depth_water_col, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_depth_water_col, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_diss_nitro = Slot(uri=MIXS['0000744'], name="tot_diss_nitro", curie=MIXS.curie('0000744'), - model_uri=NMDC.tot_diss_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_diss_nitro, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_inorg_nitro = Slot(uri=MIXS['0000745'], name="tot_inorg_nitro", curie=MIXS.curie('0000745'), - model_uri=NMDC.tot_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_inorg_nitro, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_iron = Slot(uri=MIXS['0000105'], name="tot_iron", curie=MIXS.curie('0000105'), - model_uri=NMDC.tot_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_iron, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_nitro = Slot(uri=MIXS['0000102'], name="tot_nitro", curie=MIXS.curie('0000102'), - model_uri=NMDC.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_nitro_cont_meth = Slot(uri=MIXS['0000338'], name="tot_nitro_cont_meth", curie=MIXS.curie('0000338'), - model_uri=NMDC.tot_nitro_cont_meth, domain=None, range=Optional[str]) + model_uri=NMDC.tot_nitro_cont_meth, domain=None, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.tot_nitro_content = Slot(uri=MIXS['0000530'], name="tot_nitro_content", curie=MIXS.curie('0000530'), - model_uri=NMDC.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_org_c_meth = Slot(uri=MIXS['0000337'], name="tot_org_c_meth", curie=MIXS.curie('0000337'), - model_uri=NMDC.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.tot_org_carb = Slot(uri=MIXS['0000533'], name="tot_org_carb", curie=MIXS.curie('0000533'), - model_uri=NMDC.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_part_carb = Slot(uri=MIXS['0000747'], name="tot_part_carb", curie=MIXS.curie('0000747'), - model_uri=NMDC.tot_part_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_part_carb, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_phosp = Slot(uri=MIXS['0000117'], name="tot_phosp", curie=MIXS.curie('0000117'), - model_uri=NMDC.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_phosphate = Slot(uri=MIXS['0000689'], name="tot_phosphate", curie=MIXS.curie('0000689'), - model_uri=NMDC.tot_phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_phosphate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tot_sulfur = Slot(uri=MIXS['0000419'], name="tot_sulfur", curie=MIXS.curie('0000419'), - model_uri=NMDC.tot_sulfur, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tot_sulfur, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.train_line = Slot(uri=MIXS['0000837'], name="train_line", curie=MIXS.curie('0000837'), - model_uri=NMDC.train_line, domain=None, range=Optional[Union[str, "TrainLineEnum"]]) + model_uri=NMDC.train_line, domain=None, range=Optional[Union[str, "TRAINLINEENUM"]]) slots.train_stat_loc = Slot(uri=MIXS['0000838'], name="train_stat_loc", curie=MIXS.curie('0000838'), - model_uri=NMDC.train_stat_loc, domain=None, range=Optional[Union[str, "TrainStatLocEnum"]]) + model_uri=NMDC.train_stat_loc, domain=None, range=Optional[Union[str, "TRAINSTATLOCENUM"]]) slots.train_stop_loc = Slot(uri=MIXS['0000839'], name="train_stop_loc", curie=MIXS.curie('0000839'), - model_uri=NMDC.train_stop_loc, domain=None, range=Optional[Union[str, "TrainStopLocEnum"]]) + model_uri=NMDC.train_stop_loc, domain=None, range=Optional[Union[str, "TRAINSTOPLOCENUM"]]) slots.turbidity = Slot(uri=MIXS['0000191'], name="turbidity", curie=MIXS.curie('0000191'), - model_uri=NMDC.turbidity, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.turbidity, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tvdss_of_hcr_press = Slot(uri=MIXS['0000397'], name="tvdss_of_hcr_press", curie=MIXS.curie('0000397'), - model_uri=NMDC.tvdss_of_hcr_press, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tvdss_of_hcr_press, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.tvdss_of_hcr_temp = Slot(uri=MIXS['0000394'], name="tvdss_of_hcr_temp", curie=MIXS.curie('0000394'), - model_uri=NMDC.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.typ_occup_density = Slot(uri=MIXS['0000771'], name="typ_occup_density", curie=MIXS.curie('0000771'), model_uri=NMDC.typ_occup_density, domain=None, range=Optional[float]) slots.ventilation_rate = Slot(uri=MIXS['0000114'], name="ventilation_rate", curie=MIXS.curie('0000114'), - model_uri=NMDC.ventilation_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.ventilation_rate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.ventilation_type = Slot(uri=MIXS['0000756'], name="ventilation_type", curie=MIXS.curie('0000756'), - model_uri=NMDC.ventilation_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.ventilation_type, domain=None, range=Optional[Union[str, List[str]]]) slots.vfa = Slot(uri=MIXS['0000152'], name="vfa", curie=MIXS.curie('0000152'), - model_uri=NMDC.vfa, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.vfa, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.vfa_fw = Slot(uri=MIXS['0000408'], name="vfa_fw", curie=MIXS.curie('0000408'), - model_uri=NMDC.vfa_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.vfa_fw, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.vis_media = Slot(uri=MIXS['0000840'], name="vis_media", curie=MIXS.curie('0000840'), - model_uri=NMDC.vis_media, domain=None, range=Optional[Union[str, "VisMediaEnum"]]) + model_uri=NMDC.vis_media, domain=None, range=Optional[str]) slots.viscosity = Slot(uri=MIXS['0000126'], name="viscosity", curie=MIXS.curie('0000126'), model_uri=NMDC.viscosity, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10668,55 +10569,63 @@ class slots: model_uri=NMDC.volatile_org_comp, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.wall_area = Slot(uri=MIXS['0000198'], name="wall_area", curie=MIXS.curie('0000198'), - model_uri=NMDC.wall_area, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.wall_area, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.wall_const_type = Slot(uri=MIXS['0000841'], name="wall_const_type", curie=MIXS.curie('0000841'), - model_uri=NMDC.wall_const_type, domain=None, range=Optional[Union[str, "WallConstTypeEnum"]]) + model_uri=NMDC.wall_const_type, domain=None, range=Optional[Union[str, "WALLCONSTTYPEENUM"]]) slots.wall_finish_mat = Slot(uri=MIXS['0000842'], name="wall_finish_mat", curie=MIXS.curie('0000842'), - model_uri=NMDC.wall_finish_mat, domain=None, range=Optional[Union[str, "WallFinishMatEnum"]]) + model_uri=NMDC.wall_finish_mat, domain=None, range=Optional[Union[str, "WALLFINISHMATENUM"]]) slots.wall_height = Slot(uri=MIXS['0000221'], name="wall_height", curie=MIXS.curie('0000221'), - model_uri=NMDC.wall_height, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.wall_height, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.wall_loc = Slot(uri=MIXS['0000843'], name="wall_loc", curie=MIXS.curie('0000843'), - model_uri=NMDC.wall_loc, domain=None, range=Optional[Union[str, "WallLocEnum"]]) + model_uri=NMDC.wall_loc, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.wall_surf_treatment = Slot(uri=MIXS['0000845'], name="wall_surf_treatment", curie=MIXS.curie('0000845'), - model_uri=NMDC.wall_surf_treatment, domain=None, range=Optional[Union[str, "WallSurfTreatmentEnum"]]) + model_uri=NMDC.wall_surf_treatment, domain=None, range=Optional[Union[str, "WALLSURFTREATMENTENUM"]]) slots.wall_texture = Slot(uri=MIXS['0000846'], name="wall_texture", curie=MIXS.curie('0000846'), - model_uri=NMDC.wall_texture, domain=None, range=Optional[Union[str, "WallTextureEnum"]]) + model_uri=NMDC.wall_texture, domain=None, range=Optional[Union[str, "SHAREDENUM4"]]) slots.wall_thermal_mass = Slot(uri=MIXS['0000222'], name="wall_thermal_mass", curie=MIXS.curie('0000222'), - model_uri=NMDC.wall_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.wall_thermal_mass, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.wall_water_mold = Slot(uri=MIXS['0000844'], name="wall_water_mold", curie=MIXS.curie('0000844'), - model_uri=NMDC.wall_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.wall_water_mold, domain=None, range=Optional[Union[str, "SHAREDENUM1"]]) slots.wastewater_type = Slot(uri=MIXS['0000353'], name="wastewater_type", curie=MIXS.curie('0000353'), - model_uri=NMDC.wastewater_type, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.wastewater_type, domain=None, range=Optional[str]) slots.water_cont_soil_meth = Slot(uri=MIXS['0000323'], name="water_cont_soil_meth", curie=MIXS.curie('0000323'), - model_uri=NMDC.water_cont_soil_meth, domain=None, range=Optional[str]) + model_uri=NMDC.water_cont_soil_meth, domain=None, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.water_content = Slot(uri=MIXS['0000185'], name="water_content", curie=MIXS.curie('0000185'), model_uri=NMDC.water_content, domain=None, range=Optional[str]) slots.water_current = Slot(uri=MIXS['0000203'], name="water_current", curie=MIXS.curie('0000203'), - model_uri=NMDC.water_current, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.water_current, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.water_cut = Slot(uri=MIXS['0000454'], name="water_cut", curie=MIXS.curie('0000454'), - model_uri=NMDC.water_cut, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.water_cut, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.water_feat_size = Slot(uri=MIXS['0000223'], name="water_feat_size", curie=MIXS.curie('0000223'), - model_uri=NMDC.water_feat_size, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.water_feat_size, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.water_feat_type = Slot(uri=MIXS['0000847'], name="water_feat_type", curie=MIXS.curie('0000847'), - model_uri=NMDC.water_feat_type, domain=None, range=Optional[Union[str, "WaterFeatTypeEnum"]]) + model_uri=NMDC.water_feat_type, domain=None, range=Optional[Union[str, "WATERFEATTYPEENUM"]]) slots.water_prod_rate = Slot(uri=MIXS['0000453'], name="water_prod_rate", curie=MIXS.curie('0000453'), - model_uri=NMDC.water_prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.water_prod_rate, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.water_temp_regm = Slot(uri=MIXS['0000590'], name="water_temp_regm", curie=MIXS.curie('0000590'), model_uri=NMDC.water_temp_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) @@ -10725,7 +10634,7 @@ class slots: model_uri=NMDC.watering_regm, domain=None, range=Optional[Union[Union[dict, TextValue], List[Union[dict, TextValue]]]]) slots.weekday = Slot(uri=MIXS['0000848'], name="weekday", curie=MIXS.curie('0000848'), - model_uri=NMDC.weekday, domain=None, range=Optional[Union[str, "WeekdayEnum"]]) + model_uri=NMDC.weekday, domain=None, range=Optional[Union[str, "WEEKDAYENUM"]]) slots.win = Slot(uri=MIXS['0000297'], name="win", curie=MIXS.curie('0000297'), model_uri=NMDC.win, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10734,22 +10643,23 @@ class slots: model_uri=NMDC.wind_direction, domain=None, range=Optional[Union[dict, TextValue]]) slots.wind_speed = Slot(uri=MIXS['0000118'], name="wind_speed", curie=MIXS.curie('0000118'), - model_uri=NMDC.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]]) + model_uri=NMDC.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.window_cond = Slot(uri=MIXS['0000849'], name="window_cond", curie=MIXS.curie('0000849'), - model_uri=NMDC.window_cond, domain=None, range=Optional[Union[str, "WindowCondEnum"]]) + model_uri=NMDC.window_cond, domain=None, range=Optional[Union[str, "SHAREDENUM2"]]) slots.window_cover = Slot(uri=MIXS['0000850'], name="window_cover", curie=MIXS.curie('0000850'), - model_uri=NMDC.window_cover, domain=None, range=Optional[Union[str, "WindowCoverEnum"]]) + model_uri=NMDC.window_cover, domain=None, range=Optional[Union[str, "WINDOWCOVERENUM"]]) slots.window_horiz_pos = Slot(uri=MIXS['0000851'], name="window_horiz_pos", curie=MIXS.curie('0000851'), - model_uri=NMDC.window_horiz_pos, domain=None, range=Optional[Union[str, "WindowHorizPosEnum"]]) + model_uri=NMDC.window_horiz_pos, domain=None, range=Optional[Union[str, "WINDOWHORIZPOSENUM"]]) slots.window_loc = Slot(uri=MIXS['0000852'], name="window_loc", curie=MIXS.curie('0000852'), - model_uri=NMDC.window_loc, domain=None, range=Optional[Union[str, "WindowLocEnum"]]) + model_uri=NMDC.window_loc, domain=None, range=Optional[Union[str, "SHAREDENUM0"]]) slots.window_mat = Slot(uri=MIXS['0000853'], name="window_mat", curie=MIXS.curie('0000853'), - model_uri=NMDC.window_mat, domain=None, range=Optional[Union[str, "WindowMatEnum"]]) + model_uri=NMDC.window_mat, domain=None, range=Optional[Union[str, "WINDOWMATENUM"]]) slots.window_open_freq = Slot(uri=MIXS['0000246'], name="window_open_freq", curie=MIXS.curie('0000246'), model_uri=NMDC.window_open_freq, domain=None, range=Optional[Union[dict, TextValue]]) @@ -10758,34 +10668,26 @@ class slots: model_uri=NMDC.window_size, domain=None, range=Optional[Union[dict, TextValue]]) slots.window_status = Slot(uri=MIXS['0000855'], name="window_status", curie=MIXS.curie('0000855'), - model_uri=NMDC.window_status, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.window_status, domain=None, range=Optional[Union[str, "WINDOWSTATUSENUM"]]) slots.window_type = Slot(uri=MIXS['0000856'], name="window_type", curie=MIXS.curie('0000856'), - model_uri=NMDC.window_type, domain=None, range=Optional[Union[str, "WindowTypeEnum"]]) + model_uri=NMDC.window_type, domain=None, range=Optional[Union[str, "WINDOWTYPEENUM"]]) slots.window_vert_pos = Slot(uri=MIXS['0000857'], name="window_vert_pos", curie=MIXS.curie('0000857'), - model_uri=NMDC.window_vert_pos, domain=None, range=Optional[Union[str, "WindowVertPosEnum"]]) + model_uri=NMDC.window_vert_pos, domain=None, range=Optional[Union[str, "WINDOWVERTPOSENUM"]]) slots.window_water_mold = Slot(uri=MIXS['0000854'], name="window_water_mold", curie=MIXS.curie('0000854'), - model_uri=NMDC.window_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) + model_uri=NMDC.window_water_mold, domain=None, range=Optional[Union[str, "SHAREDENUM1"]]) slots.xylene = Slot(uri=MIXS['0000156'], name="xylene", curie=MIXS.curie('0000156'), - model_uri=NMDC.xylene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.core_field = Slot(uri=MIXS.core_field, name="core field", curie=MIXS.curie('core_field'), - model_uri=NMDC.core_field, domain=None, range=Optional[str]) - -slots.environment_field = Slot(uri=MIXS.environment_field, name="environment field", curie=MIXS.curie('environment_field'), - model_uri=NMDC.environment_field, domain=None, range=Optional[str]) - -slots.investigation_field = Slot(uri=MIXS.investigation_field, name="investigation field", curie=MIXS.curie('investigation_field'), - model_uri=NMDC.investigation_field, domain=None, range=Optional[str]) + model_uri=NMDC.xylene, domain=None, range=Optional[Union[dict, TextValue]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) -slots.nucleic_acid_sequence_source_field = Slot(uri=MIXS.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=MIXS.curie('nucleic_acid_sequence_source_field'), - model_uri=NMDC.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) +slots.samp_collec_method = Slot(uri=MIXS['0001225'], name="samp_collec_method", curie=MIXS.curie('0001225'), + model_uri=NMDC.samp_collec_method, domain=None, range=Optional[str]) -slots.sequencing_field = Slot(uri=MIXS.sequencing_field, name="sequencing field", curie=MIXS.curie('sequencing_field'), - model_uri=NMDC.sequencing_field, domain=None, range=Optional[str]) +slots.samp_collec_device = Slot(uri=MIXS.samp_collec_device, name="samp_collec_device", curie=MIXS.curie('samp_collec_device'), + model_uri=NMDC.samp_collec_device, domain=None, range=Optional[str]) slots.emsl_store_temp = Slot(uri=NMDC.emsl_store_temp, name="emsl_store_temp", curie=NMDC.curie('emsl_store_temp'), model_uri=NMDC.emsl_store_temp, domain=None, range=Optional[str]) @@ -11390,7 +11292,8 @@ class slots: model_uri=NMDC.Biosample_collected_from, domain=Biosample, range=Optional[Union[str, FieldResearchSiteId]]) slots.Biosample_elev = Slot(uri=MIXS['0000093'], name="Biosample_elev", curie=MIXS.curie('0000093'), - model_uri=NMDC.Biosample_elev, domain=Biosample, range=Optional[float]) + model_uri=NMDC.Biosample_elev, domain=Biosample, range=Optional[float], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], @@ -11405,16 +11308,19 @@ class slots: pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) slots.Biosample_lat_lon = Slot(uri=MIXS['0000009'], name="Biosample_lat_lon", curie=MIXS.curie('0000009'), - model_uri=NMDC.Biosample_lat_lon, domain=Biosample, range=Optional[Union[dict, "GeolocationValue"]]) + model_uri=NMDC.Biosample_lat_lon, domain=Biosample, range=Optional[Union[dict, "GeolocationValue"]], + pattern=re.compile(r'^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$')) slots.Biosample_env_broad_scale = Slot(uri=MIXS['0000012'], name="Biosample_env_broad_scale", curie=MIXS.curie('0000012'), - model_uri=NMDC.Biosample_env_broad_scale, domain=Biosample, range=Union[dict, "ControlledIdentifiedTermValue"]) + model_uri=NMDC.Biosample_env_broad_scale, domain=Biosample, range=Union[dict, "ControlledIdentifiedTermValue"], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.Biosample_env_local_scale = Slot(uri=MIXS['0000013'], name="Biosample_env_local_scale", curie=MIXS.curie('0000013'), model_uri=NMDC.Biosample_env_local_scale, domain=Biosample, range=Union[dict, "ControlledIdentifiedTermValue"]) slots.Biosample_env_medium = Slot(uri=MIXS['0000014'], name="Biosample_env_medium", curie=MIXS.curie('0000014'), - model_uri=NMDC.Biosample_env_medium, domain=Biosample, range=Union[dict, "ControlledIdentifiedTermValue"]) + model_uri=NMDC.Biosample_env_medium, domain=Biosample, range=Union[dict, "ControlledIdentifiedTermValue"], + pattern=re.compile(r'^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$')) slots.Biosample_part_of = Slot(uri=DCTERMS.isPartOf, name="Biosample_part_of", curie=DCTERMS.curie('isPartOf'), model_uri=NMDC.Biosample_part_of, domain=Biosample, range=Union[Union[str, StudyId], List[Union[str, StudyId]]]) @@ -11430,61 +11336,73 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Biosample_slope_aspect = Slot(uri=MIXS['0000647'], name="Biosample_slope_aspect", curie=MIXS.curie('0000647'), - model_uri=NMDC.Biosample_slope_aspect, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_slope_aspect, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_slope_gradient = Slot(uri=MIXS['0000646'], name="Biosample_slope_gradient", curie=MIXS.curie('0000646'), - model_uri=NMDC.Biosample_slope_gradient, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_slope_gradient, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_al_sat = Slot(uri=MIXS['0000607'], name="Biosample_al_sat", curie=MIXS.curie('0000607'), - model_uri=NMDC.Biosample_al_sat, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_al_sat, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_al_sat_meth = Slot(uri=MIXS['0000324'], name="Biosample_al_sat_meth", curie=MIXS.curie('0000324'), - model_uri=NMDC.Biosample_al_sat_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) + model_uri=NMDC.Biosample_al_sat_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_annual_precpt = Slot(uri=MIXS['0000644'], name="Biosample_annual_precpt", curie=MIXS.curie('0000644'), - model_uri=NMDC.Biosample_annual_precpt, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_annual_precpt, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_cur_vegetation = Slot(uri=MIXS['0000312'], name="Biosample_cur_vegetation", curie=MIXS.curie('0000312'), model_uri=NMDC.Biosample_cur_vegetation, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) slots.Biosample_cur_vegetation_meth = Slot(uri=MIXS['0000314'], name="Biosample_cur_vegetation_meth", curie=MIXS.curie('0000314'), - model_uri=NMDC.Biosample_cur_vegetation_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) + model_uri=NMDC.Biosample_cur_vegetation_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_heavy_metals = Slot(uri=MIXS['0000652'], name="Biosample_heavy_metals", curie=MIXS.curie('0000652'), model_uri=NMDC.Biosample_heavy_metals, domain=Biosample, range=Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]]) slots.Biosample_heavy_metals_meth = Slot(uri=MIXS['0000343'], name="Biosample_heavy_metals_meth", curie=MIXS.curie('0000343'), - model_uri=NMDC.Biosample_heavy_metals_meth, domain=Biosample, range=Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]]) + model_uri=NMDC.Biosample_heavy_metals_meth, domain=Biosample, range=Optional[Union[Union[dict, "TextValue"], List[Union[dict, "TextValue"]]]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_season_precpt = Slot(uri=MIXS['0000645'], name="Biosample_season_precpt", curie=MIXS.curie('0000645'), - model_uri=NMDC.Biosample_season_precpt, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_season_precpt, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_water_cont_soil_meth = Slot(uri=MIXS['0000323'], name="Biosample_water_cont_soil_meth", curie=MIXS.curie('0000323'), - model_uri=NMDC.Biosample_water_cont_soil_meth, domain=Biosample, range=Optional[str]) + model_uri=NMDC.Biosample_water_cont_soil_meth, domain=Biosample, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_water_content = Slot(uri=MIXS['0000185'], name="Biosample_water_content", curie=MIXS.curie('0000185'), model_uri=NMDC.Biosample_water_content, domain=Biosample, range=Optional[Union[str, List[str]]]) slots.Biosample_ph_meth = Slot(uri=MIXS['0001106'], name="Biosample_ph_meth", curie=MIXS.curie('0001106'), - model_uri=NMDC.Biosample_ph_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) + model_uri=NMDC.Biosample_ph_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_tot_carb = Slot(uri=MIXS['0000525'], name="Biosample_tot_carb", curie=MIXS.curie('0000525'), - model_uri=NMDC.Biosample_tot_carb, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_tot_carb, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_tot_nitro_cont_meth = Slot(uri=MIXS['0000338'], name="Biosample_tot_nitro_cont_meth", curie=MIXS.curie('0000338'), - model_uri=NMDC.Biosample_tot_nitro_cont_meth, domain=Biosample, range=Optional[str]) + model_uri=NMDC.Biosample_tot_nitro_cont_meth, domain=Biosample, range=Optional[str], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_tot_nitro_content = Slot(uri=MIXS['0000530'], name="Biosample_tot_nitro_content", curie=MIXS.curie('0000530'), - model_uri=NMDC.Biosample_tot_nitro_content, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) + model_uri=NMDC.Biosample_tot_nitro_content, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_tot_org_c_meth = Slot(uri=MIXS['0000337'], name="Biosample_tot_org_c_meth", curie=MIXS.curie('0000337'), - model_uri=NMDC.Biosample_tot_org_c_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) + model_uri=NMDC.Biosample_tot_org_c_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]], + pattern=re.compile(r'^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$')) slots.Biosample_tot_org_carb = Slot(uri=MIXS['0000533'], name="Biosample_tot_org_carb", curie=MIXS.curie('0000533'), - model_uri=NMDC.Biosample_tot_org_carb, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]]) - -slots.Biosample_salinity_meth = Slot(uri=MIXS['0000341'], name="Biosample_salinity_meth", curie=MIXS.curie('0000341'), - model_uri=NMDC.Biosample_salinity_meth, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) + model_uri=NMDC.Biosample_tot_org_carb, domain=Biosample, range=Optional[Union[dict, "QuantityValue"]], + pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$')) slots.Biosample_sieving = Slot(uri=MIXS['0000322'], name="Biosample_sieving", curie=MIXS.curie('0000322'), model_uri=NMDC.Biosample_sieving, domain=Biosample, range=Optional[Union[dict, "TextValue"]]) @@ -11725,8 +11643,8 @@ class slots: model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) -slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], +slots.MetatranscriptomeExpressionAnalysis_id = Slot(uri=NMDC.id, name="MetatranscriptomeExpressionAnalysis_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeExpressionAnalysis_id, domain=MetatranscriptomeExpressionAnalysis, range=Union[str, MetatranscriptomeExpressionAnalysisId], pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json deleted file mode 100644 index da3fd61650..0000000000 --- a/nmdc_schema/nmdc.schema.json +++ /dev/null @@ -1,9511 +0,0 @@ -{ - "$defs": { - "AnalysisTypeEnum": { - "description": "", - "enum": [ - "metabolomics", - "metagenomics", - "metagenomics_long_read", - "metaproteomics", - "metatranscriptomics", - "natural organic matter", - "bulk chemistry" - ], - "title": "AnalysisTypeEnum", - "type": "string" - }, - "AnalyticalSample": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AnalyticalSample", - "type": "object" - }, - "ArchStrucEnum": { - "description": "", - "enum": [ - "building", - "shed", - "home" - ], - "title": "ArchStrucEnum", - "type": "string" - }, - "AttributeValue": { - "additionalProperties": false, - "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "AttributeValue", - "type": "object" - }, - "BiolStatEnum": { - "description": "", - "enum": [ - "wild", - "natural", - "semi-natural", - "inbred line", - "breeder's line", - "hybrid", - "clonal selection", - "mutant" - ], - "title": "BiolStatEnum", - "type": "string" - }, - "Biosample": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "dna_cont_well": { - "pattern": ".+" - } - }, - "required": [ - "dna_cont_well" - ] - }, - "then": { - "properties": { - "dna_cont_type": { - "const": "plate" - } - }, - "required": [ - "dna_cont_type" - ] - } - }, - { - "if": { - "properties": { - "dna_cont_type": { - "const": "plate" - } - }, - "required": [ - "dna_cont_type" - ] - }, - "then": { - "properties": { - "dna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" - } - }, - "required": [ - "dna_cont_well" - ] - } - }, - { - "if": { - "properties": { - "rna_cont_well": { - "pattern": ".+" - } - }, - "required": [ - "rna_cont_well" - ] - }, - "then": { - "properties": { - "rna_cont_type": { - "const": "plate" - } - }, - "required": [ - "rna_cont_type" - ] - } - }, - { - "if": { - "properties": { - "rna_cont_type": { - "const": "plate" - } - }, - "required": [ - "rna_cont_type" - ] - }, - "then": { - "properties": { - "rna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" - } - }, - "required": [ - "rna_cont_well" - ] - } - } - ], - "description": "Biological source material which can be characterized by an experiment.", - "properties": { - "abs_air_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture" - }, - "add_date": { - "description": "The date on which the information was added to the database.", - "type": "string" - }, - "add_recov_method": { - "$ref": "#/$defs/TextValue", - "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "additional_info": { - "$ref": "#/$defs/TextValue", - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary" - }, - "address": { - "$ref": "#/$defs/TextValue", - "description": "The street name and building number where the sampling occurred." - }, - "adj_room": { - "$ref": "#/$defs/TextValue", - "description": "List of rooms (room number, room name) immediately adjacent to the sampling room" - }, - "aero_struc": { - "$ref": "#/$defs/TextValue", - "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together" - }, - "agrochem_addition": { - "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "air_PM_concen": { - "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "air_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the air at the time of sampling" - }, - "air_temp_regm": { - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "al_sat": { - "$ref": "#/$defs/QuantityValue", - "description": "The relative abundance of aluminum in the sample" - }, - "al_sat_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining Aluminum saturation" - }, - "alkalinity": { - "$ref": "#/$defs/QuantityValue", - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" - }, - "alkalinity_method": { - "$ref": "#/$defs/TextValue", - "description": "Method used for alkalinity measurement" - }, - "alkyl_diethers": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of alkyl diethers" - }, - "alt": { - "$ref": "#/$defs/QuantityValue", - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" - }, - "alternative_identifiers": { - "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "aminopept_act": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of aminopeptidase activity" - }, - "ammonium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ammonium in the sample" - }, - "ammonium_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ammonium nitrogen in the sample" - }, - "amount_light": { - "$ref": "#/$defs/QuantityValue", - "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area" - }, - "analysis_type": { - "description": "Select all the data types associated or available for this biosample", - "items": { - "$ref": "#/$defs/AnalysisTypeEnum" - }, - "type": "array" - }, - "ances_data": { - "$ref": "#/$defs/TextValue", - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)" - }, - "annual_precpt": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." - }, - "annual_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Mean annual temperature" - }, - "antibiotic_regm": { - "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "api": { - "$ref": "#/$defs/QuantityValue", - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)" - }, - "arch_struc": { - "$ref": "#/$defs/ArchStrucEnum", - "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction" - }, - "aromatics_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "asphaltenes_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "atmospheric_data": { - "description": "Measurement of atmospheric data; can include multiple data", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "avg_dew_point": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day" - }, - "avg_occup": { - "$ref": "#/$defs/TextValue", - "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room." - }, - "avg_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day" - }, - "bac_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Bacterial production in the water column measured by isotope uptake" - }, - "bac_resp": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of bacterial respiration in the water column" - }, - "bacteria_carb_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of bacterial carbon production" - }, - "barometric_press": { - "$ref": "#/$defs/QuantityValue", - "description": "Force per unit area exerted against a surface by the weight of air above that surface" - }, - "basin": { - "$ref": "#/$defs/TextValue", - "description": "Name of the basin (e.g. Campos)" - }, - "bathroom_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of bathrooms in the building" - }, - "bedroom_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of bedrooms in the building" - }, - "benzene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of benzene in the sample" - }, - "biochem_oxygen_dem": { - "$ref": "#/$defs/QuantityValue", - "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period" - }, - "biocide": { - "$ref": "#/$defs/TextValue", - "description": "List of biocides (commercial name of product and supplier) and date of administration" - }, - "biocide_admin_method": { - "$ref": "#/$defs/TextValue", - "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)" - }, - "biol_stat": { - "$ref": "#/$defs/BiolStatEnum", - "description": "The level of genome modification." - }, - "biomass": { - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "biosample_categories": { - "items": { - "$ref": "#/$defs/BiosampleCategoryEnum" - }, - "type": "array" - }, - "biotic_regm": { - "$ref": "#/$defs/TextValue", - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." - }, - "biotic_relationship": { - "$ref": "#/$defs/BioticRelationshipEnum", - "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" - }, - "bishomohopanol": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of bishomohopanol" - }, - "blood_press_diast": { - "$ref": "#/$defs/QuantityValue", - "description": "Resting diastolic blood pressure, measured as mm mercury" - }, - "blood_press_syst": { - "$ref": "#/$defs/QuantityValue", - "description": "Resting systolic blood pressure, measured as mm mercury" - }, - "bromide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of bromide" - }, - "build_docs": { - "$ref": "#/$defs/BuildDocsEnum", - "description": "The building design, construction and operation documents" - }, - "build_occup_type": { - "description": "The primary function for which a building or discrete part of a building is intended to be used", - "items": { - "$ref": "#/$defs/BuildOccupTypeEnum" - }, - "type": "array" - }, - "building_setting": { - "$ref": "#/$defs/BuildingSettingEnum", - "description": "A location (geography) where a building is set" - }, - "built_struc_age": { - "$ref": "#/$defs/QuantityValue", - "description": "The age of the built structure since construction" - }, - "built_struc_set": { - "$ref": "#/$defs/TextValue", - "description": "The characterization of the location of the built structure as high or low human density" - }, - "built_struc_type": { - "$ref": "#/$defs/TextValue", - "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads" - }, - "bulk_elect_conductivity": { - "$ref": "#/$defs/QuantityValue", - "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water." - }, - "calcium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of calcium in the sample" - }, - "carb_dioxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling" - }, - "carb_monoxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Carbon monoxide (gas) amount or concentration at the time of sampling" - }, - "carb_nitro_ratio": { - "$ref": "#/$defs/QuantityValue", - "description": "Ratio of amount or concentrations of carbon to nitrogen" - }, - "ceil_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The area of the ceiling space within the room" - }, - "ceil_cond": { - "$ref": "#/$defs/CeilCondEnum", - "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "ceil_finish_mat": { - "$ref": "#/$defs/CeilFinishMatEnum", - "description": "The type of material used to finish a ceiling" - }, - "ceil_struc": { - "$ref": "#/$defs/TextValue", - "description": "The construction format of the ceiling" - }, - "ceil_texture": { - "$ref": "#/$defs/CeilTextureEnum", - "description": "The feel, appearance, or consistency of a ceiling surface" - }, - "ceil_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow" - }, - "ceil_type": { - "$ref": "#/$defs/CeilTypeEnum", - "description": "The type of ceiling according to the ceiling's appearance or construction" - }, - "ceil_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on the ceiling" - }, - "chem_administration": { - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ] - }, - "type": "array" - }, - "chem_mutagen": { - "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "chem_oxygen_dem": { - "$ref": "#/$defs/QuantityValue", - "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite" - }, - "chem_treat_method": { - "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", - "type": "string" - }, - "chem_treatment": { - "$ref": "#/$defs/TextValue", - "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included" - }, - "chimera_check": { - "$ref": "#/$defs/TextValue", - "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." - }, - "chloride": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of chloride in the sample" - }, - "chlorophyll": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of chlorophyll" - }, - "climate_environment": { - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "collected_from": { - "description": "The Site from which a Biosample was collected", - "type": "string" - }, - "collection_date": { - "$ref": "#/$defs/TimestampValue", - "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" - }, - "collection_date_inc": { - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "type": "string" - }, - "collection_time": { - "description": "The time of sampling, either as an instance (single point) or interval.", - "type": "string" - }, - "collection_time_inc": { - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "type": "string" - }, - "community": { - "type": "string" - }, - "conduc": { - "$ref": "#/$defs/QuantityValue", - "description": "Electrical conductivity of water" - }, - "cool_syst_id": { - "$ref": "#/$defs/TextValue", - "description": "The cooling system identifier" - }, - "core_field": { - "description": "basic fields", - "type": "string" - }, - "crop_rotation": { - "$ref": "#/$defs/TextValue", - "description": "Whether or not crop is rotated, and if yes, rotation schedule" - }, - "cult_root_med": { - "$ref": "#/$defs/TextValue", - "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors." - }, - "cur_land_use": { - "$ref": "#/$defs/CurLandUseEnum", - "description": "Present state of sample site" - }, - "cur_vegetation": { - "$ref": "#/$defs/TextValue", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" - }, - "cur_vegetation_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in vegetation classification" - }, - "date_last_rain": { - "$ref": "#/$defs/TimestampValue", - "description": "The date of the last time it rained" - }, - "density": { - "$ref": "#/$defs/QuantityValue", - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" - }, - "depos_env": { - "$ref": "#/$defs/DeposEnvEnum", - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "depth": { - "$ref": "#/$defs/QuantityValue", - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "dew_point": { - "$ref": "#/$defs/QuantityValue", - "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water." - }, - "diether_lipids": { - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "diss_carb_dioxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" - }, - "diss_hydrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved hydrogen" - }, - "diss_inorg_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" - }, - "diss_inorg_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved inorganic nitrogen" - }, - "diss_inorg_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved inorganic phosphorus in the sample" - }, - "diss_iron": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved iron in the sample" - }, - "diss_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" - }, - "diss_org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" - }, - "diss_oxygen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved oxygen" - }, - "diss_oxygen_fluid": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic)." - }, - "dna_absorb1": { - "description": "260/280 measurement of DNA sample purity", - "type": "number" - }, - "dna_absorb2": { - "description": "260/230 measurement of DNA sample purity", - "type": "number" - }, - "dna_collect_site": { - "description": "Provide information on the site your DNA sample was collected from", - "type": "string" - }, - "dna_concentration": { - "maximum": 2000, - "minimum": 0, - "type": "number" - }, - "dna_cont_type": { - "$ref": "#/$defs/JgiContTypeEnum", - "description": "Tube or plate (96-well)" - }, - "dna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", - "type": "string" - }, - "dna_container_id": { - "type": "string" - }, - "dna_dnase": { - "$ref": "#/$defs/YesNoEnum" - }, - "dna_isolate_meth": { - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "type": "string" - }, - "dna_organisms": { - "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", - "type": "string" - }, - "dna_project_contact": { - "type": "string" - }, - "dna_samp_id": { - "type": "string" - }, - "dna_sample_format": { - "$ref": "#/$defs/DNASampleFormatEnum", - "description": "Solution in which the DNA sample has been suspended" - }, - "dna_sample_name": { - "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "type": "string" - }, - "dna_seq_project": { - "type": "string" - }, - "dna_seq_project_name": { - "type": "string" - }, - "dna_seq_project_pi": { - "type": "string" - }, - "dna_volume": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "dnase_rna": { - "$ref": "#/$defs/YesNoEnum" - }, - "door_comp_type": { - "$ref": "#/$defs/DoorCompTypeEnum", - "description": "The composite type of the door" - }, - "door_cond": { - "$ref": "#/$defs/DoorCondEnum", - "description": "The phsical condition of the door" - }, - "door_direct": { - "$ref": "#/$defs/DoorDirectEnum", - "description": "The direction the door opens" - }, - "door_loc": { - "$ref": "#/$defs/DoorLocEnum", - "description": "The relative location of the door in the room" - }, - "door_mat": { - "$ref": "#/$defs/DoorMatEnum", - "description": "The material the door is composed of" - }, - "door_move": { - "$ref": "#/$defs/DoorMoveEnum", - "description": "The type of movement of the door" - }, - "door_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The size of the door" - }, - "door_type": { - "$ref": "#/$defs/DoorTypeEnum", - "description": "The type of door material" - }, - "door_type_metal": { - "$ref": "#/$defs/DoorTypeMetalEnum", - "description": "The type of metal door" - }, - "door_type_wood": { - "$ref": "#/$defs/DoorTypeWoodEnum", - "description": "The type of wood door" - }, - "door_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on a door" - }, - "down_par": { - "$ref": "#/$defs/QuantityValue", - "description": "Visible waveband radiance and irradiance measurements in the water column" - }, - "drainage_class": { - "$ref": "#/$defs/DrainageClassEnum", - "description": "Drainage classification from a standard system such as the USDA system" - }, - "drawings": { - "$ref": "#/$defs/DrawingsEnum", - "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents" - }, - "ecosystem": { - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_category": { - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_subtype": { - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_type": { - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "type": "string" - }, - "efficiency_percent": { - "$ref": "#/$defs/QuantityValue", - "description": "Percentage of volatile solids removed from the anaerobic digestor" - }, - "elev": { - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "type": "number" - }, - "elevator": { - "$ref": "#/$defs/TextValue", - "description": "The number of elevators within the built structure" - }, - "embargoed": { - "description": "If true, the data are embargoed and not available for public access.", - "type": "boolean" - }, - "emsl_biosample_identifiers": { - "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "emulsions": { - "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "env_broad_scale": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS" - }, - "env_local_scale": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS." - }, - "env_medium": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)." - }, - "env_package": { - "$ref": "#/$defs/TextValue", - "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" - }, - "environment_field": { - "description": "field describing environmental aspect of a sample", - "type": "string" - }, - "escalator": { - "$ref": "#/$defs/TextValue", - "description": "The number of escalators within the built structure" - }, - "ethylbenzene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ethylbenzene in the sample" - }, - "exp_duct": { - "$ref": "#/$defs/QuantityValue", - "description": "The amount of exposed ductwork in the room" - }, - "exp_pipe": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of exposed pipes in the room" - }, - "experimental_factor": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI" - }, - "experimental_factor_other": { - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "type": "string" - }, - "ext_door": { - "$ref": "#/$defs/TextValue", - "description": "The number of exterior doors in the built structure" - }, - "ext_wall_orient": { - "$ref": "#/$defs/ExtWallOrientEnum", - "description": "The orientation of the exterior wall" - }, - "ext_window_orient": { - "$ref": "#/$defs/ExtWindowOrientEnum", - "description": "The compass direction the exterior window of the room is facing" - }, - "extreme_event": { - "description": "Unusual physical events that may have affected microbial populations", - "type": "string" - }, - "fao_class": { - "$ref": "#/$defs/FaoClassEnum", - "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" - }, - "fertilizer_regm": { - "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "field": { - "$ref": "#/$defs/TextValue", - "description": "Name of the hydrocarbon field (e.g. Albacora)" - }, - "filter_method": { - "description": "Type of filter used or how the sample was filtered", - "type": "string" - }, - "filter_type": { - "description": "A device which removes solid particulates or airborne molecular contaminants", - "items": { - "$ref": "#/$defs/FilterTypeEnum" - }, - "type": "array" - }, - "fire": { - "description": "Historical and/or physical evidence of fire", - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$", - "type": "string" - }, - "fireplace_type": { - "$ref": "#/$defs/TextValue", - "description": "A firebox with chimney" - }, - "flooding": { - "description": "Historical and/or physical evidence of flooding", - "type": "string" - }, - "floor_age": { - "$ref": "#/$defs/QuantityValue", - "description": "The time period since installment of the carpet or flooring" - }, - "floor_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The area of the floor space within the room" - }, - "floor_cond": { - "$ref": "#/$defs/FloorCondEnum", - "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "floor_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of floors in the building, including basements and mechanical penthouse" - }, - "floor_finish_mat": { - "$ref": "#/$defs/FloorFinishMatEnum", - "description": "The floor covering type; the finished surface that is walked on" - }, - "floor_struc": { - "$ref": "#/$defs/FloorStrucEnum", - "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed" - }, - "floor_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the floor to provide inertia against temperature fluctuations" - }, - "floor_water_mold": { - "$ref": "#/$defs/FloorWaterMoldEnum", - "description": "Signs of the presence of mold or mildew in a room" - }, - "fluor": { - "$ref": "#/$defs/QuantityValue", - "description": "Raw or converted fluorescence of water" - }, - "freq_clean": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually." - }, - "freq_cook": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of times a meal is cooked per week" - }, - "fungicide_regm": { - "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "furniture": { - "$ref": "#/$defs/FurnitureEnum", - "description": "The types of furniture present in the sampled room" - }, - "gaseous_environment": { - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "gaseous_substances": { - "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "gender_restroom": { - "$ref": "#/$defs/GenderRestroomEnum", - "description": "The gender type of the restroom" - }, - "genetic_mod": { - "$ref": "#/$defs/TextValue", - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection" - }, - "geo_loc_name": { - "$ref": "#/$defs/TextValue", - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" - }, - "glucosidase_act": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of glucosidase activity" - }, - "gold_biosample_identifiers": { - "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", - "items": { - "pattern": "^gold:Gb[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "gravidity": { - "$ref": "#/$defs/TextValue", - "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used" - }, - "gravity": { - "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "growth_facil": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research" - }, - "growth_habit": { - "$ref": "#/$defs/GrowthHabitEnum", - "description": "Characteristic shape, appearance or growth form of a plant species" - }, - "growth_hormone_regm": { - "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "habitat": { - "type": "string" - }, - "hall_count": { - "$ref": "#/$defs/TextValue", - "description": "The total count of hallways and cooridors in the built structure" - }, - "handidness": { - "$ref": "#/$defs/HandidnessEnum", - "description": "The handidness of the individual sampled" - }, - "hc_produced": { - "$ref": "#/$defs/HcProducedEnum", - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr": { - "$ref": "#/$defs/HcrEnum", - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr_fw_salinity": { - "$ref": "#/$defs/QuantityValue", - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS" - }, - "hcr_geol_age": { - "$ref": "#/$defs/HcrGeolAgeEnum", - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr_pressure": { - "$ref": "#/$defs/TextValue", - "description": "Original pressure of the hydrocarbon resource" - }, - "hcr_temp": { - "$ref": "#/$defs/TextValue", - "description": "Original temperature of the hydrocarbon resource" - }, - "heat_cool_type": { - "description": "Methods of conditioning or heating a room or building", - "items": { - "$ref": "#/$defs/HeatCoolTypeEnum" - }, - "type": "array" - }, - "heat_deliv_loc": { - "$ref": "#/$defs/HeatDelivLocEnum", - "description": "The location of heat delivery within the room" - }, - "heat_sys_deliv_meth": { - "description": "The method by which the heat is delivered through the system", - "type": "string" - }, - "heat_system_id": { - "$ref": "#/$defs/TextValue", - "description": "The heating system identifier" - }, - "heavy_metals": { - "description": "Heavy metals present in the sample and their concentrations.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "heavy_metals_meth": { - "description": "Reference or method used in determining heavy metals", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "height_carper_fiber": { - "$ref": "#/$defs/QuantityValue", - "description": "The average carpet fiber height in the indoor environment" - }, - "herbicide_regm": { - "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "horizon_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining the horizon" - }, - "host_age": { - "$ref": "#/$defs/QuantityValue", - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees" - }, - "host_body_habitat": { - "$ref": "#/$defs/TextValue", - "description": "Original body habitat where the sample was obtained from" - }, - "host_body_product": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon" - }, - "host_body_site": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON" - }, - "host_body_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Core body temperature of the host when sample was collected" - }, - "host_color": { - "$ref": "#/$defs/TextValue", - "description": "The color of host" - }, - "host_common_name": { - "$ref": "#/$defs/TextValue", - "description": "Common name of the host." - }, - "host_diet": { - "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "host_disease_stat": { - "$ref": "#/$defs/TextValue", - "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text" - }, - "host_dry_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of dry mass" - }, - "host_family_relation": { - "description": "Familial relationships to other hosts in the same study; can include multiple relationships", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_genotype": { - "$ref": "#/$defs/TextValue", - "description": "Observed genotype" - }, - "host_growth_cond": { - "$ref": "#/$defs/TextValue", - "description": "Literature reference giving growth conditions of the host" - }, - "host_height": { - "$ref": "#/$defs/QuantityValue", - "description": "The height of subject" - }, - "host_last_meal": { - "description": "Content of last meal and time since feeding; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "host_length": { - "$ref": "#/$defs/QuantityValue", - "description": "The length of subject" - }, - "host_life_stage": { - "$ref": "#/$defs/TextValue", - "description": "Description of life stage of host" - }, - "host_name": { - "type": "string" - }, - "host_phenotype": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP" - }, - "host_sex": { - "$ref": "#/$defs/HostSexEnum", - "description": "Gender or physical sex of the host." - }, - "host_shape": { - "$ref": "#/$defs/TextValue", - "description": "Morphological shape of host" - }, - "host_subject_id": { - "$ref": "#/$defs/TextValue", - "description": "A unique identifier by which each subject can be referred to, de-identified." - }, - "host_subspecf_genlin": { - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_substrate": { - "$ref": "#/$defs/TextValue", - "description": "The growth substrate of the host." - }, - "host_symbiont": { - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_taxid": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "NCBI taxon id of the host, e.g. 9606" - }, - "host_tot_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Total mass of the host at collection, the unit depends on host" - }, - "host_wet_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of wet mass" - }, - "humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Amount of water vapour in the air, at the time of sampling" - }, - "humidity_regm": { - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "id": { - "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "igsn_biosample_identifiers": { - "description": "A list of identifiers for the biosample from the IGSN database.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "img_identifiers": { - "description": "A list of identifiers that relate the biosample to records in the IMG database.", - "items": { - "pattern": "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$", - "type": "string" - }, - "type": "array" - }, - "indoor_space": { - "$ref": "#/$defs/IndoorSpaceEnum", - "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" - }, - "indoor_surf": { - "$ref": "#/$defs/IndoorSurfEnum", - "description": "Type of indoor surface" - }, - "indust_eff_percent": { - "$ref": "#/$defs/QuantityValue", - "description": "Percentage of industrial effluents received by wastewater treatment plant" - }, - "infiltrations": { - "description": "The amount of time it takes to complete each infiltration activity", - "items": { - "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", - "type": "string" - }, - "type": "array" - }, - "inorg_particles": { - "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "insdc_biosample_identifiers": { - "description": "identifiers for corresponding sample in INSDC", - "items": { - "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "inside_lux": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded value at sampling time (power density)" - }, - "int_wall_cond": { - "$ref": "#/$defs/IntWallCondEnum", - "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "investigation_field": { - "description": "field describing aspect of the investigation/study to which the sample belongs", - "type": "string" - }, - "isotope_exposure": { - "description": "List isotope exposure or addition applied to your sample.", - "type": "string" - }, - "iw_bt_date_well": { - "$ref": "#/$defs/TimestampValue", - "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery" - }, - "iwf": { - "$ref": "#/$defs/QuantityValue", - "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)" - }, - "last_clean": { - "$ref": "#/$defs/TimestampValue", - "description": "The last time the floor was cleaned (swept, mopped, vacuumed)" - }, - "lat_lon": { - "$ref": "#/$defs/GeolocationValue", - "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" - }, - "lbc_thirty": { - "$ref": "#/$defs/QuantityValue", - "description": "lime buffer capacity, determined after 30 minute incubation" - }, - "lbceq": { - "$ref": "#/$defs/QuantityValue", - "description": "lime buffer capacity, determined at equilibrium after 5 day incubation" - }, - "light_intensity": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of light intensity" - }, - "light_regm": { - "$ref": "#/$defs/TextValue", - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality." - }, - "light_type": { - "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", - "items": { - "$ref": "#/$defs/LightTypeEnum" - }, - "type": "array" - }, - "link_addit_analys": { - "$ref": "#/$defs/TextValue", - "description": "Link to additional analysis results performed on the sample" - }, - "link_class_info": { - "$ref": "#/$defs/TextValue", - "description": "Link to digitized soil maps or other soil classification information" - }, - "link_climate_info": { - "$ref": "#/$defs/TextValue", - "description": "Link to climate resource" - }, - "lithology": { - "$ref": "#/$defs/LithologyEnum", - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "local_class": { - "$ref": "#/$defs/TextValue", - "description": "Soil classification based on local soil classification system" - }, - "local_class_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining the local soil classification" - }, - "location": { - "type": "string" - }, - "magnesium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of magnesium in the sample" - }, - "manganese": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of manganese in the sample" - }, - "max_occup": { - "$ref": "#/$defs/QuantityValue", - "description": "The maximum amount of people allowed in the indoor environment" - }, - "mean_frict_vel": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of mean friction velocity" - }, - "mean_peak_frict_vel": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of mean peak friction velocity" - }, - "mech_struc": { - "$ref": "#/$defs/MechStrucEnum", - "description": "mechanical structure: a moving structure" - }, - "mechanical_damage": { - "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "methane": { - "$ref": "#/$defs/QuantityValue", - "description": "Methane (gas) amount or concentration at the time of sampling" - }, - "micro_biomass_c_meth": { - "description": "Reference or method used in determining microbial biomass carbon", - "type": "string" - }, - "micro_biomass_meth": { - "description": "Reference or method used in determining microbial biomass", - "type": "string" - }, - "micro_biomass_n_meth": { - "description": "Reference or method used in determining microbial biomass nitrogen", - "type": "string" - }, - "microbial_biomass": { - "$ref": "#/$defs/QuantityValue", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units" - }, - "microbial_biomass_c": { - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "type": "string" - }, - "microbial_biomass_n": { - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "type": "string" - }, - "mineral_nutr_regm": { - "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "misc_param": { - "description": "Any other measurement performed or parameter collected, that is not listed here", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "mod_date": { - "description": "The last date on which the database information was modified.", - "type": "string" - }, - "n_alkanes": { - "description": "Concentration of n-alkanes; can include multiple n-alkanes", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ncbi_taxonomy_name": { - "type": "string" - }, - "neon_biosample_identifiers": { - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "nitrate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrate in the sample" - }, - "nitrate_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrate nitrogen in the sample" - }, - "nitrite": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrite in the sample" - }, - "nitrite_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrite nitrogen in the sample" - }, - "nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrogen (total)" - }, - "non_microb_biomass": { - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "type": "string" - }, - "non_microb_biomass_method": { - "description": "Reference or method used in determining biomass", - "type": "string" - }, - "non_min_nutr_regm": { - "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", - "items": { - "type": "string" - }, - "type": "array" - }, - "nucl_acid_amp": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" - }, - "nucl_acid_ext": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" - }, - "nucleic_acid_sequence_source_field": { - "type": "string" - }, - "number_pets": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of pets residing in the sampled space" - }, - "number_plants": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of plant(s) in the sampling space" - }, - "number_resident": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of individuals currently occupying in the sampling location" - }, - "occup_density_samp": { - "$ref": "#/$defs/QuantityValue", - "description": "Average number of occupants at time of sampling per square footage" - }, - "occup_document": { - "$ref": "#/$defs/OccupDocumentEnum", - "description": "The type of documentation of occupancy" - }, - "occup_samp": { - "$ref": "#/$defs/QuantityValue", - "description": "Number of occupants present at time of sample within the given space" - }, - "org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic carbon" - }, - "org_count_qpcr_info": { - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "type": "string" - }, - "org_matter": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic matter" - }, - "org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic nitrogen" - }, - "org_nitro_method": { - "description": "Method used for obtaining organic nitrogen", - "type": "string" - }, - "org_particles": { - "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "organism_count": { - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "items": { - "$ref": "#/$defs/QuantityValue" - }, - "type": "array" - }, - "other_treatment": { - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "type": "string" - }, - "owc_tvdss": { - "$ref": "#/$defs/QuantityValue", - "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)" - }, - "oxy_stat_samp": { - "$ref": "#/$defs/OxyStatSampEnum", - "description": "Oxygenation status of sample" - }, - "oxygen": { - "$ref": "#/$defs/QuantityValue", - "description": "Oxygen (gas) amount or concentration at the time of sampling" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "part_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of particulate organic carbon" - }, - "part_org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of particulate organic nitrogen" - }, - "particle_class": { - "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pcr_cond": { - "$ref": "#/$defs/TextValue", - "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" - }, - "pcr_primers": { - "$ref": "#/$defs/TextValue", - "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" - }, - "permeability": { - "$ref": "#/$defs/TextValue", - "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))" - }, - "perturbation": { - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pesticide_regm": { - "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "petroleum_hydrocarb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of petroleum hydrocarbon" - }, - "ph": { - "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "type": "number" - }, - "ph_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining ph" - }, - "ph_regm": { - "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "phaeopigments": { - "description": "Concentration of phaeopigments; can include multiple phaeopigments", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "phosphate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of phosphate" - }, - "phosplipid_fatt_acid": { - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "photon_flux": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of photon flux" - }, - "plant_growth_med": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary" - }, - "plant_product": { - "$ref": "#/$defs/TextValue", - "description": "Substance produced by the plant, where the sample was obtained from" - }, - "plant_sex": { - "$ref": "#/$defs/PlantSexEnum", - "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite." - }, - "plant_struc": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here." - }, - "pollutants": { - "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pool_dna_extracts": { - "$ref": "#/$defs/TextValue", - "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" - }, - "porosity": { - "$ref": "#/$defs/TextValue", - "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample" - }, - "potassium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of potassium in the sample" - }, - "pour_point": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" - }, - "pre_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater" - }, - "pres_animal_insect": { - "description": "The type and number of animals or insects present in the sampling space.", - "pattern": "^(cat|dog|rodent|snake|other);\\d+$", - "type": "string" - }, - "pressure": { - "$ref": "#/$defs/QuantityValue", - "description": "Pressure to which the sample is subject to, in atmospheres" - }, - "prev_land_use_meth": { - "description": "Reference or method used in determining previous land use and dates", - "type": "string" - }, - "previous_land_use": { - "$ref": "#/$defs/TextValue", - "description": "Previous land use and dates" - }, - "primary_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of primary production, generally measured as isotope uptake" - }, - "primary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed" - }, - "prod_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)" - }, - "prod_start_date": { - "$ref": "#/$defs/TimestampValue", - "description": "Date of field's first production" - }, - "profile_position": { - "$ref": "#/$defs/ProfilePositionEnum", - "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" - }, - "project_id": { - "description": "Proposal IDs or names associated with dataset", - "type": "string" - }, - "proport_woa_temperature": { - "type": "string" - }, - "proposal_dna": { - "type": "string" - }, - "proposal_rna": { - "type": "string" - }, - "quad_pos": { - "$ref": "#/$defs/QuadPosEnum", - "description": "The quadrant position of the sampling room within the building" - }, - "radiation_regm": { - "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "rainfall_regm": { - "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "reactor_type": { - "$ref": "#/$defs/TextValue", - "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage" - }, - "redox_potential": { - "$ref": "#/$defs/QuantityValue", - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" - }, - "rel_air_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air" - }, - "rel_humidity_out": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded outside relative humidity value at the time of sampling" - }, - "rel_samp_loc": { - "$ref": "#/$defs/RelSampLocEnum", - "description": "The sampling location within the train car" - }, - "replicate_number": { - "description": "If sending biological replicates, indicate the rep number here.", - "type": "string" - }, - "reservoir": { - "$ref": "#/$defs/TextValue", - "description": "Name of the reservoir (e.g. Carapebus)" - }, - "resins_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "rna_absorb1": { - "description": "260/280 measurement of RNA sample purity", - "type": "number" - }, - "rna_absorb2": { - "description": "260/230 measurement of RNA sample purity", - "type": "number" - }, - "rna_collect_site": { - "description": "Provide information on the site your RNA sample was collected from", - "type": "string" - }, - "rna_concentration": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "rna_cont_type": { - "$ref": "#/$defs/JgiContTypeEnum", - "description": "Tube or plate (96-well)" - }, - "rna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", - "type": "string" - }, - "rna_container_id": { - "type": "string" - }, - "rna_isolate_meth": { - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "type": "string" - }, - "rna_organisms": { - "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", - "type": "string" - }, - "rna_project_contact": { - "type": "string" - }, - "rna_samp_id": { - "type": "string" - }, - "rna_sample_format": { - "$ref": "#/$defs/RNASampleFormatEnum", - "description": "Solution in which the RNA sample has been suspended" - }, - "rna_sample_name": { - "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "maximum": 2000, - "minimum": 0, - "type": "string" - }, - "rna_seq_project": { - "type": "string" - }, - "rna_seq_project_name": { - "type": "string" - }, - "rna_seq_project_pi": { - "type": "string" - }, - "rna_volume": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "room_air_exch_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "The rate at which outside air replaces indoor air in a given space" - }, - "room_architec_elem": { - "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", - "type": "string" - }, - "room_condt": { - "$ref": "#/$defs/RoomCondtEnum", - "description": "The condition of the room at the time of sampling" - }, - "room_connected": { - "$ref": "#/$defs/RoomConnectedEnum", - "description": "List of rooms connected to the sampling room by a doorway" - }, - "room_count": { - "$ref": "#/$defs/TextValue", - "description": "The total count of rooms in the built structure including all room types" - }, - "room_dim": { - "$ref": "#/$defs/TextValue", - "description": "The length, width and height of sampling room" - }, - "room_door_dist": { - "$ref": "#/$defs/TextValue", - "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms" - }, - "room_door_share": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) sharing a door with the sampling room" - }, - "room_hallway": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) located in the same hallway as sampling room" - }, - "room_loc": { - "$ref": "#/$defs/RoomLocEnum", - "description": "The position of the room within the building" - }, - "room_moist_dam_hist": { - "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", - "type": "integer" - }, - "room_net_area": { - "$ref": "#/$defs/TextValue", - "description": "The net floor area of sampling room. Net area excludes wall thicknesses" - }, - "room_occup": { - "$ref": "#/$defs/QuantityValue", - "description": "Count of room occupancy at time of sampling" - }, - "room_samp_pos": { - "$ref": "#/$defs/RoomSampPosEnum", - "description": "The horizontal sampling position in the room relative to architectural elements" - }, - "room_type": { - "$ref": "#/$defs/RoomTypeEnum", - "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure" - }, - "room_vol": { - "$ref": "#/$defs/TextValue", - "description": "Volume of sampling room" - }, - "room_wall_share": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) sharing a wall with the sampling room" - }, - "room_window_count": { - "description": "Number of windows in the room", - "type": "integer" - }, - "root_cond": { - "$ref": "#/$defs/TextValue", - "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container." - }, - "root_med_carbon": { - "$ref": "#/$defs/TextValue", - "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose." - }, - "root_med_macronutr": { - "$ref": "#/$defs/TextValue", - "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L)." - }, - "root_med_micronutr": { - "$ref": "#/$defs/TextValue", - "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L)." - }, - "root_med_ph": { - "$ref": "#/$defs/QuantityValue", - "description": "pH measurement of the culture rooting medium; e.g. 5.5." - }, - "root_med_regl": { - "$ref": "#/$defs/TextValue", - "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA." - }, - "root_med_solid": { - "$ref": "#/$defs/TextValue", - "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar." - }, - "root_med_suppl": { - "$ref": "#/$defs/TextValue", - "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L)." - }, - "salinity": { - "$ref": "#/$defs/QuantityValue", - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." - }, - "salinity_category": { - "description": "Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", - "type": "string" - }, - "salinity_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining salinity" - }, - "salt_regm": { - "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "samp_capt_status": { - "$ref": "#/$defs/SampCaptStatusEnum", - "description": "Reason for the sample" - }, - "samp_collec_device": { - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "type": "string" - }, - "samp_collec_method": { - "description": "The method employed for collecting the sample.", - "type": "string" - }, - "samp_collect_point": { - "$ref": "#/$defs/SampCollectPointEnum", - "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_dis_stage": { - "$ref": "#/$defs/SampDisStageEnum", - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." - }, - "samp_floor": { - "$ref": "#/$defs/SampFloorEnum", - "description": "The floor of the building, where the sampling room is located" - }, - "samp_loc_corr_rate": { - "$ref": "#/$defs/TextValue", - "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays" - }, - "samp_mat_process": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." - }, - "samp_md": { - "$ref": "#/$defs/QuantityValue", - "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_name": { - "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", - "type": "string" - }, - "samp_preserv": { - "$ref": "#/$defs/TextValue", - "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)" - }, - "samp_room_id": { - "$ref": "#/$defs/TextValue", - "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans" - }, - "samp_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." - }, - "samp_sort_meth": { - "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "samp_store_dur": { - "$ref": "#/$defs/TextValue", - "description": "Duration for which the sample was stored" - }, - "samp_store_loc": { - "$ref": "#/$defs/TextValue", - "description": "Location at which sample was stored, usually name of a specific freezer/room" - }, - "samp_store_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature at which sample was stored, e.g. -80 degree Celsius" - }, - "samp_subtype": { - "$ref": "#/$defs/SampSubtypeEnum", - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_taxon_id": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls." - }, - "samp_time_out": { - "$ref": "#/$defs/TextValue", - "description": "The recent and long term history of outside sampling" - }, - "samp_transport_cond": { - "$ref": "#/$defs/TextValue", - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)" - }, - "samp_tvdss": { - "$ref": "#/$defs/TextValue", - "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m" - }, - "samp_type": { - "$ref": "#/$defs/TextValue", - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)." - }, - "samp_vol_we_dna_ext": { - "$ref": "#/$defs/QuantityValue", - "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." - }, - "samp_weather": { - "$ref": "#/$defs/SampWeatherEnum", - "description": "The weather on the sampling day" - }, - "samp_well_name": { - "$ref": "#/$defs/TextValue", - "description": "Name of the well (e.g. BXA1123) where sample was taken" - }, - "sample_collection_site": { - "type": "string" - }, - "sample_link": { - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_shipped": { - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", - "type": "string" - }, - "sample_type": { - "$ref": "#/$defs/SampleTypeEnum", - "description": "Type of sample being submitted" - }, - "saturates_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "season": { - "$ref": "#/$defs/TextValue", - "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)." - }, - "season_environment": { - "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "season_precpt": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." - }, - "season_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Mean seasonal temperature" - }, - "season_use": { - "$ref": "#/$defs/SeasonUseEnum", - "description": "The seasons the space is occupied" - }, - "secondary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process for substantially degrading the biological content of the sewage" - }, - "sediment_type": { - "$ref": "#/$defs/SedimentTypeEnum", - "description": "Information about the sediment type based on major constituents" - }, - "seq_meth": { - "$ref": "#/$defs/TextValue", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." - }, - "seq_quality_check": { - "$ref": "#/$defs/TextValue", - "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" - }, - "sequencing_field": { - "type": "string" - }, - "sewage_type": { - "$ref": "#/$defs/TextValue", - "description": "Type of wastewater treatment plant as municipial or industrial" - }, - "shad_dev_water_mold": { - "description": "Signs of the presence of mold or mildew on the shading device", - "type": "string" - }, - "shading_device_cond": { - "$ref": "#/$defs/ShadingDeviceCondEnum", - "description": "The physical condition of the shading device at the time of sampling" - }, - "shading_device_loc": { - "$ref": "#/$defs/TextValue", - "description": "The location of the shading device in relation to the built structure" - }, - "shading_device_mat": { - "$ref": "#/$defs/TextValue", - "description": "The material the shading device is composed of" - }, - "shading_device_type": { - "$ref": "#/$defs/ShadingDeviceTypeEnum", - "description": "The type of shading device" - }, - "sieving": { - "$ref": "#/$defs/TextValue", - "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved" - }, - "silicate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of silicate" - }, - "size_frac": { - "$ref": "#/$defs/TextValue", - "description": "Filtering pore size used in sample preparation" - }, - "size_frac_low": { - "$ref": "#/$defs/QuantityValue", - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" - }, - "size_frac_up": { - "$ref": "#/$defs/QuantityValue", - "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" - }, - "slope_aspect": { - "$ref": "#/$defs/QuantityValue", - "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration." - }, - "slope_gradient": { - "$ref": "#/$defs/QuantityValue", - "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer" - }, - "sludge_retent_time": { - "$ref": "#/$defs/QuantityValue", - "description": "The time activated sludge remains in reactor" - }, - "sodium": { - "$ref": "#/$defs/QuantityValue", - "description": "Sodium concentration in the sample" - }, - "soil_horizon": { - "$ref": "#/$defs/SoilHorizonEnum", - "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath" - }, - "soil_text_measure": { - "$ref": "#/$defs/QuantityValue", - "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional." - }, - "soil_texture_meth": { - "description": "Reference or method used in determining soil texture", - "type": "string" - }, - "soil_type": { - "$ref": "#/$defs/TextValue", - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." - }, - "soil_type_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining soil series name or other lower-level classification" - }, - "solar_irradiance": { - "$ref": "#/$defs/QuantityValue", - "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval" - }, - "soluble_inorg_mat": { - "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "soluble_iron_micromol": { - "type": "string" - }, - "soluble_org_mat": { - "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "soluble_react_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of soluble reactive phosphorus" - }, - "source_mat_id": { - "$ref": "#/$defs/TextValue", - "description": "A globally unique identifier assigned to the biological sample." - }, - "space_typ_state": { - "$ref": "#/$defs/TextValue", - "description": "Customary or normal state of the space" - }, - "specific": { - "$ref": "#/$defs/SpecificEnum", - "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents" - }, - "specific_ecosystem": { - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "type": "string" - }, - "specific_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound." - }, - "sr_dep_env": { - "$ref": "#/$defs/SrDepEnvEnum", - "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_geol_age": { - "$ref": "#/$defs/SrGeolAgeEnum", - "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_kerog_type": { - "$ref": "#/$defs/SrKerogTypeEnum", - "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_lithology": { - "$ref": "#/$defs/SrLithologyEnum", - "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "standing_water_regm": { - "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "start_date_inc": { - "description": "Date the incubation was started. Only relevant for incubation samples.", - "type": "string" - }, - "start_time_inc": { - "description": "Time the incubation was started. Only relevant for incubation samples.", - "type": "string" - }, - "store_cond": { - "$ref": "#/$defs/TextValue", - "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." - }, - "substructure_type": { - "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", - "items": { - "$ref": "#/$defs/SubstructureTypeEnum" - }, - "type": "array" - }, - "subsurface_depth": { - "$ref": "#/$defs/QuantityValue" - }, - "sulfate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of sulfate in the sample" - }, - "sulfate_fw": { - "$ref": "#/$defs/QuantityValue", - "description": "Original sulfate concentration in the hydrocarbon resource" - }, - "sulfide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of sulfide in the sample" - }, - "surf_air_cont": { - "description": "Contaminant identified on surface", - "items": { - "$ref": "#/$defs/SurfAirContEnum" - }, - "type": "array" - }, - "surf_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Surfaces: water activity as a function of air and material moisture" - }, - "surf_material": { - "$ref": "#/$defs/SurfMaterialEnum", - "description": "Surface materials at the point of sampling" - }, - "surf_moisture": { - "$ref": "#/$defs/QuantityValue", - "description": "Water held on a surface" - }, - "surf_moisture_ph": { - "description": "ph measurement of surface", - "type": "number" - }, - "surf_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the surface at the time of sampling" - }, - "suspend_part_matter": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of suspended particulate matter" - }, - "suspend_solids": { - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "tan": { - "$ref": "#/$defs/QuantityValue", - "description": "Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" - }, - "target_gene": { - "$ref": "#/$defs/TextValue", - "description": "Targeted gene or locus name for marker gene studies" - }, - "target_subfragment": { - "$ref": "#/$defs/TextValue", - "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" - }, - "technical_reps": { - "description": "If sending technical replicates of the same sample, indicate the replicate count.", - "type": "string" - }, - "temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the sample at the time of sampling." - }, - "temp_out": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded temperature value at sampling time outside" - }, - "tertiary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment" - }, - "tidal_stage": { - "$ref": "#/$defs/TidalStageEnum", - "description": "Stage of tide" - }, - "tillage": { - "description": "Note method(s) used for tilling", - "items": { - "$ref": "#/$defs/TillageEnum" - }, - "type": "array" - }, - "tiss_cult_growth_med": { - "$ref": "#/$defs/TextValue", - "description": "Description of plant tissue culture growth media used" - }, - "toluene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of toluene in the sample" - }, - "tot_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Total carbon content" - }, - "tot_depth_water_col": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of total depth of water column" - }, - "tot_diss_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" - }, - "tot_inorg_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total inorganic nitrogen content" - }, - "tot_iron": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of total iron in the sample" - }, - "tot_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen" - }, - "tot_nitro_cont_meth": { - "description": "Reference or method used in determining the total nitrogen", - "type": "string" - }, - "tot_nitro_content": { - "$ref": "#/$defs/QuantityValue", - "description": "Total nitrogen content of the sample" - }, - "tot_org_c_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining total organic carbon" - }, - "tot_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" - }, - "tot_part_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Total particulate carbon content" - }, - "tot_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" - }, - "tot_phosphate": { - "$ref": "#/$defs/QuantityValue", - "description": "Total amount or concentration of phosphate" - }, - "tot_sulfur": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of total sulfur in the sample" - }, - "train_line": { - "$ref": "#/$defs/TrainLineEnum", - "description": "The subway line name" - }, - "train_stat_loc": { - "$ref": "#/$defs/TrainStatLocEnum", - "description": "The train station collection location" - }, - "train_stop_loc": { - "$ref": "#/$defs/TrainStopLocEnum", - "description": "The train stop collection location" - }, - "turbidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles" - }, - "tvdss_of_hcr_press": { - "$ref": "#/$defs/QuantityValue", - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m)." - }, - "tvdss_of_hcr_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m)." - }, - "typ_occup_density": { - "description": "Customary or normal density of occupants", - "type": "number" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "ventilation_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Ventilation rate of the system in the sampled premises" - }, - "ventilation_type": { - "$ref": "#/$defs/TextValue", - "description": "Ventilation system used in the sampled premises" - }, - "vfa": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of Volatile Fatty Acids in the sample" - }, - "vfa_fw": { - "$ref": "#/$defs/QuantityValue", - "description": "Original volatile fatty acid concentration in the hydrocarbon resource" - }, - "vis_media": { - "$ref": "#/$defs/VisMediaEnum", - "description": "The building visual media" - }, - "viscosity": { - "$ref": "#/$defs/TextValue", - "description": "A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)" - }, - "volatile_org_comp": { - "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "wall_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The total area of the sampled room's walls" - }, - "wall_const_type": { - "$ref": "#/$defs/WallConstTypeEnum", - "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating." - }, - "wall_finish_mat": { - "$ref": "#/$defs/WallFinishMatEnum", - "description": "The material utilized to finish the outer most layer of the wall" - }, - "wall_height": { - "$ref": "#/$defs/QuantityValue", - "description": "The average height of the walls in the sampled room" - }, - "wall_loc": { - "$ref": "#/$defs/WallLocEnum", - "description": "The relative location of the wall within the room" - }, - "wall_surf_treatment": { - "$ref": "#/$defs/WallSurfTreatmentEnum", - "description": "The surface treatment of interior wall" - }, - "wall_texture": { - "$ref": "#/$defs/WallTextureEnum", - "description": "The feel, appearance, or consistency of a wall surface" - }, - "wall_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint" - }, - "wall_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on a wall" - }, - "wastewater_type": { - "$ref": "#/$defs/TextValue", - "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc." - }, - "water_cont_soil_meth": { - "description": "Reference or method used in determining the water content of soil", - "type": "string" - }, - "water_content": { - "description": "Water content measurement", - "items": { - "type": "string" - }, - "type": "array" - }, - "water_current": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of magnitude and direction of flow within a fluid" - }, - "water_cut": { - "$ref": "#/$defs/QuantityValue", - "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams" - }, - "water_feat_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The size of the water feature" - }, - "water_feat_type": { - "$ref": "#/$defs/WaterFeatTypeEnum", - "description": "The type of water feature present within the building being sampled" - }, - "water_prod_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Water production rates per well (e.g. 987 m3 / day)" - }, - "water_temp_regm": { - "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "watering_regm": { - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "weekday": { - "$ref": "#/$defs/WeekdayEnum", - "description": "The day of the week when sampling occurred" - }, - "win": { - "$ref": "#/$defs/TextValue", - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)" - }, - "wind_direction": { - "$ref": "#/$defs/TextValue", - "description": "Wind direction is the direction from which a wind originates" - }, - "wind_speed": { - "$ref": "#/$defs/QuantityValue", - "description": "Speed of wind measured at the time of sampling" - }, - "window_cond": { - "$ref": "#/$defs/WindowCondEnum", - "description": "The physical condition of the window at the time of sampling" - }, - "window_cover": { - "$ref": "#/$defs/WindowCoverEnum", - "description": "The type of window covering" - }, - "window_horiz_pos": { - "$ref": "#/$defs/WindowHorizPosEnum", - "description": "The horizontal position of the window on the wall" - }, - "window_loc": { - "$ref": "#/$defs/WindowLocEnum", - "description": "The relative location of the window within the room" - }, - "window_mat": { - "$ref": "#/$defs/WindowMatEnum", - "description": "The type of material used to finish a window" - }, - "window_open_freq": { - "$ref": "#/$defs/TextValue", - "description": "The number of times windows are opened per week" - }, - "window_size": { - "$ref": "#/$defs/TextValue", - "description": "The window's length and width" - }, - "window_status": { - "$ref": "#/$defs/TextValue", - "description": "Defines whether the windows were open or closed during environmental testing" - }, - "window_type": { - "$ref": "#/$defs/WindowTypeEnum", - "description": "The type of windows" - }, - "window_vert_pos": { - "$ref": "#/$defs/WindowVertPosEnum", - "description": "The vertical position of the window on the wall" - }, - "window_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on the window." - }, - "xylene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of xylene in the sample" - }, - "zinc": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of zinc in the sample" - } - }, - "required": [ - "part_of", - "id", - "env_broad_scale", - "env_local_scale", - "env_medium" - ], - "title": "Biosample", - "type": "object" - }, - "BiosampleCategoryEnum": { - "description": "Funding-based, sample location-based, or experimental method-based defined categories", - "enum": [ - "LTER", - "SIP", - "SFA", - "FICUS", - "NEON" - ], - "title": "BiosampleCategoryEnum", - "type": "string" - }, - "BiosampleProcessing": { - "additionalProperties": false, - "description": "A process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:BiosampleProcessing" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "BiosampleProcessing", - "type": "object" - }, - "BioticRelationshipEnum": { - "description": "", - "enum": [ - "free living", - "parasite", - "commensal", - "symbiont" - ], - "title": "BioticRelationshipEnum", - "type": "string" - }, - "BooleanValue": { - "additionalProperties": false, - "description": "A value that is a boolean", - "properties": { - "has_boolean_value": { - "description": "Links a quantity value to a boolean", - "type": "boolean" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "BooleanValue", - "type": "object" - }, - "BuildDocsEnum": { - "description": "", - "enum": [ - "building information model", - "commissioning report", - "complaint logs", - "contract administration", - "cost estimate", - "janitorial schedules or logs", - "maintenance plans", - "schedule", - "sections", - "shop drawings", - "submittals", - "ventilation system", - "windows" - ], - "title": "BuildDocsEnum", - "type": "string" - }, - "BuildOccupTypeEnum": { - "description": "", - "enum": [ - "office", - "market", - "restaurant", - "residence", - "school", - "residential", - "commercial", - "low rise", - "high rise", - "wood framed", - "health care", - "airport", - "sports complex" - ], - "title": "BuildOccupTypeEnum", - "type": "string" - }, - "BuildingSettingEnum": { - "description": "", - "enum": [ - "urban", - "suburban", - "exurban", - "rural" - ], - "title": "BuildingSettingEnum", - "type": "string" - }, - "CeilCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "CeilCondEnum", - "type": "string" - }, - "CeilFinishMatEnum": { - "description": "", - "enum": [ - "drywall", - "mineral fibre", - "tiles", - "PVC", - "plasterboard", - "metal", - "fiberglass", - "stucco", - "mineral wool/calcium silicate", - "wood" - ], - "title": "CeilFinishMatEnum", - "type": "string" - }, - "CeilTextureEnum": { - "description": "", - "enum": [ - "crows feet", - "crows-foot stomp", - "double skip", - "hawk and trowel", - "knockdown", - "popcorn", - "orange peel", - "rosebud stomp", - "Santa-Fe texture", - "skip trowel", - "smooth", - "stomp knockdown", - "swirl" - ], - "title": "CeilTextureEnum", - "type": "string" - }, - "CeilTypeEnum": { - "description": "", - "enum": [ - "cathedral", - "dropped", - "concave", - "barrel-shaped", - "coffered", - "cove", - "stretched" - ], - "title": "CeilTypeEnum", - "type": "string" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "chemical_formula": { - "description": "A generic grouping for molecular formulae and empirical formulae", - "type": "string" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "inchi": { - "type": "string" - }, - "inchi_key": { - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "smiles": { - "description": "A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ChromatographicSeparationProcess": { - "additionalProperties": false, - "description": "The process of using a selective partitioning of the analyte or interferent between two immiscible phases.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:ChromatographicSeparationProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ordered_mobile_phases": { - "description": "The solution(s) that moves through a chromatography column.", - "items": { - "$ref": "#/$defs/Solution" - }, - "type": "array" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "stationary_phase": { - "$ref": "#/$defs/StationaryPhaseEnum", - "description": "The material the stationary phase is comprised of used in chromatography." - }, - "temperature": { - "$ref": "#/$defs/QuantityValue", - "description": "The value of a temperature measurement or temperature used in a process." - } - }, - "required": [ - "id" - ], - "title": "ChromatographicSeparationProcess", - "type": "object" - }, - "CollectingBiosamplesFromSite": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:CollectingBiosamplesFromSite" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "CollectingBiosamplesFromSite", - "type": "object" - }, - "CompoundEnum": { - "description": "", - "enum": [ - "ammonium bicarbonate", - "deionized water", - "methanol", - "trypsin", - "chloridic acid", - "water" - ], - "title": "CompoundEnum", - "type": "string" - }, - "ContainerCategoryEnum": { - "description": "The permitted types of containers used in processing metabolomic samples.", - "enum": [ - "V-bottom conical tube", - "falcon tube" - ], - "title": "ContainerCategoryEnum", - "type": "string" - }, - "ControlledIdentifiedTermValue": { - "additionalProperties": false, - "description": "A controlled term or class from an ontology, requiring the presence of term with an id", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "term": { - "anyOf": [ - { - "$ref": "#/$defs/OntologyClass" - }, - { - "$ref": "#/$defs/EnvironmentalMaterialTerm" - }, - { - "$ref": "#/$defs/ChemicalEntity" - }, - { - "$ref": "#/$defs/Pathway" - }, - { - "$ref": "#/$defs/Reaction" - }, - { - "$ref": "#/$defs/OrthologyGroup" - } - ], - "description": "pointer to an ontology class" - } - }, - "required": [ - "term" - ], - "title": "ControlledIdentifiedTermValue", - "type": "object" - }, - "ControlledTermValue": { - "additionalProperties": false, - "description": "A controlled term or class from an ontology", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "term": { - "anyOf": [ - { - "$ref": "#/$defs/OntologyClass" - }, - { - "$ref": "#/$defs/EnvironmentalMaterialTerm" - }, - { - "$ref": "#/$defs/ChemicalEntity" - }, - { - "$ref": "#/$defs/Pathway" - }, - { - "$ref": "#/$defs/Reaction" - }, - { - "$ref": "#/$defs/OrthologyGroup" - } - ], - "description": "pointer to an ontology class" - } - }, - "title": "ControlledTermValue", - "type": "object" - }, - "CreditAssociation": { - "additionalProperties": false, - "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", - "properties": { - "applied_roles": { - "items": { - "$ref": "#/$defs/CreditEnum" - }, - "type": "array" - }, - "applies_to_person": { - "$ref": "#/$defs/PersonValue" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "required": [ - "applies_to_person", - "applied_roles" - ], - "title": "CreditAssociation", - "type": "object" - }, - "CreditEnum": { - "description": "", - "enum": [ - "Conceptualization", - "Data curation", - "Formal Analysis", - "Funding acquisition", - "Investigation", - "Methodology", - "Project administration", - "Resources", - "Software", - "Supervision", - "Validation", - "Visualization", - "Writing original draft", - "Writing review and editing", - "Principal Investigator", - "Submitter" - ], - "title": "CreditEnum", - "type": "string" - }, - "CurLandUseEnum": { - "description": "", - "enum": [ - "badlands", - "cities", - "conifers", - "crop trees", - "farmstead", - "gravel", - "hardwoods", - "hayland", - "horticultural plants", - "industrial areas", - "intermixed hardwood and conifers", - "marshlands", - "meadows", - "mines/quarries", - "mudflats", - "oil waste areas", - "pastureland", - "permanent snow or ice", - "rainforest", - "rangeland", - "roads/railroads", - "rock", - "row crops", - "saline seeps", - "salt flats", - "sand", - "shrub crops", - "shrub land", - "small grains", - "successional shrub land", - "swamp", - "tropical", - "tundra", - "vegetable crops", - "vine crops" - ], - "title": "CurLandUseEnum", - "type": "string" - }, - "DNASampleFormatEnum": { - "description": "", - "enum": [ - "10 mM Tris-HCl", - "DNAStable", - "Ethanol", - "Low EDTA TE", - "MDA reaction buffer", - "PBS", - "Pellet", - "RNAStable", - "TE", - "Water", - "Gentegra-DNA", - "Gentegra-RNA" - ], - "title": "DNASampleFormatEnum", - "type": "string" - }, - "DataObject": { - "additionalProperties": false, - "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "compression_type": { - "description": "If provided, specifies the compression type", - "type": "string" - }, - "data_object_type": { - "$ref": "#/$defs/FileTypeEnum", - "description": "The type of file represented by the data object." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "file_size_bytes": { - "description": "Size of the file in bytes", - "type": "integer" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "md5_checksum": { - "description": "MD5 checksum of file (pre-compressed)", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "url": { - "type": "string" - }, - "was_generated_by": { - "type": "string" - } - }, - "required": [ - "id", - "name", - "description" - ], - "title": "DataObject", - "type": "object" - }, - "Database": { - "additionalProperties": false, - "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", - "properties": { - "biosample_set": { - "description": "This property links a database object to the set of samples within it.", - "items": { - "$ref": "#/$defs/Biosample" - }, - "type": "array" - }, - "collecting_biosamples_from_site_set": { - "items": { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - "type": "array" - }, - "data_object_set": { - "description": "This property links a database object to the set of data objects within it.", - "items": { - "$ref": "#/$defs/DataObject" - }, - "type": "array" - }, - "extraction_set": { - "description": "This property links a database object to the set of extractions within it.", - "items": { - "$ref": "#/$defs/Extraction" - }, - "type": "array" - }, - "field_research_site_set": { - "items": { - "$ref": "#/$defs/FieldResearchSite" - }, - "type": "array" - }, - "functional_annotation_agg": { - "items": { - "$ref": "#/$defs/FunctionalAnnotationAggMember" - }, - "type": "array" - }, - "functional_annotation_set": { - "description": "This property links a database object to the set of all functional annotations", - "items": { - "$ref": "#/$defs/FunctionalAnnotation" - }, - "type": "array" - }, - "genome_feature_set": { - "description": "This property links a database object to the set of all features", - "items": { - "$ref": "#/$defs/GenomeFeature" - }, - "type": "array" - }, - "library_preparation_set": { - "description": "This property links a database object to the set of DNA extractions within it.", - "items": { - "$ref": "#/$defs/LibraryPreparation" - }, - "type": "array" - }, - "mags_activity_set": { - "description": "This property links a database object to the set of MAGs analysis activities.", - "items": { - "$ref": "#/$defs/MagsAnalysisActivity" - }, - "type": "array" - }, - "metabolomics_analysis_activity_set": { - "description": "This property links a database object to the set of metabolomics analysis activities.", - "items": { - "$ref": "#/$defs/MetabolomicsAnalysisActivity" - }, - "type": "array" - }, - "metagenome_annotation_activity_set": { - "description": "This property links a database object to the set of metagenome annotation activities.", - "items": { - "$ref": "#/$defs/MetagenomeAnnotationActivity" - }, - "type": "array" - }, - "metagenome_assembly_set": { - "description": "This property links a database object to the set of metagenome assembly activities.", - "items": { - "$ref": "#/$defs/MetagenomeAssembly" - }, - "type": "array" - }, - "metagenome_sequencing_activity_set": { - "description": "This property links a database object to the set of metagenome sequencing activities.", - "items": { - "$ref": "#/$defs/MetagenomeSequencingActivity" - }, - "type": "array" - }, - "metaproteomics_analysis_activity_set": { - "description": "This property links a database object to the set of metaproteomics analysis activities.", - "items": { - "$ref": "#/$defs/MetaproteomicsAnalysisActivity" - }, - "type": "array" - }, - "metatranscriptome_activity_set": { - "description": "This property links a database object to the set of metatranscriptome analysis activities.", - "items": { - "$ref": "#/$defs/MetatranscriptomeActivity" - }, - "type": "array" - }, - "nom_analysis_activity_set": { - "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", - "items": { - "$ref": "#/$defs/NomAnalysisActivity" - }, - "type": "array" - }, - "omics_processing_set": { - "description": "This property links a database object to the set of omics processings within it.", - "items": { - "$ref": "#/$defs/OmicsProcessing" - }, - "type": "array" - }, - "planned_process_set": { - "description": "This property links a database object to the set of planned processes within it.", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/Extraction" - }, - { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - { - "$ref": "#/$defs/BiosampleProcessing" - }, - { - "$ref": "#/$defs/SubSamplingProcess" - }, - { - "$ref": "#/$defs/MixingProcess" - }, - { - "$ref": "#/$defs/FiltrationProcess" - }, - { - "$ref": "#/$defs/ChromatographicSeparationProcess" - }, - { - "$ref": "#/$defs/OmicsProcessing" - }, - { - "$ref": "#/$defs/Pooling" - }, - { - "$ref": "#/$defs/LibraryPreparation" - } - ] - }, - "type": "array" - }, - "pooling_set": { - "items": { - "$ref": "#/$defs/Pooling" - }, - "type": "array" - }, - "processed_sample_set": { - "description": "This property links a database object to the set of processed samples within it.", - "items": { - "$ref": "#/$defs/ProcessedSample" - }, - "type": "array" - }, - "read_based_taxonomy_analysis_activity_set": { - "description": "This property links a database object to the set of read based analysis activities.", - "items": { - "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" - }, - "type": "array" - }, - "read_qc_analysis_activity_set": { - "description": "This property links a database object to the set of read QC analysis activities.", - "items": { - "$ref": "#/$defs/ReadQcAnalysisActivity" - }, - "type": "array" - }, - "study_set": { - "description": "This property links a database object to the set of studies within it.", - "items": { - "$ref": "#/$defs/Study" - }, - "type": "array" - } - }, - "title": "Database", - "type": "object" - }, - "DeposEnvEnum": { - "description": "", - "enum": [ - "Continental - Alluvial", - "Continental - Aeolian", - "Continental - Fluvial", - "Continental - Lacustrine", - "Transitional - Deltaic", - "Transitional - Tidal", - "Transitional - Lagoonal", - "Transitional - Beach", - "Transitional - Lake", - "Marine - Shallow", - "Marine - Deep", - "Marine - Reef", - "Other - Evaporite", - "Other - Glacial", - "Other - Volcanic", - "other" - ], - "title": "DeposEnvEnum", - "type": "string" - }, - "DeviceEnum": { - "description": "", - "enum": [ - "Orbital Shaker", - "Thermomixer", - "Vortex", - "Agitation plunger", - "Drying oven", - "CEREX System 96 processor" - ], - "title": "DeviceEnum", - "type": "string" - }, - "Doi": { - "additionalProperties": false, - "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.", - "if": { - "properties": { - "doi_category": { - "anyOf": [ - { - "const": "dataset_doi" - }, - { - "const": "award_doi" - } - ] - } - }, - "required": [ - "doi_category" - ] - }, - "properties": { - "doi_category": { - "$ref": "#/$defs/DoiCategoryEnum", - "description": "The resource type the corresponding doi resolves to." - }, - "doi_provider": { - "$ref": "#/$defs/DoiProviderEnum", - "description": "The authority, or organization, the DOI is associated with." - }, - "doi_value": { - "description": "A digital object identifier, which is intended to persistantly identify some resource on the web.", - "pattern": "^doi:10.\\d{2,9}/.*$", - "type": "string" - } - }, - "required": [ - "doi_value", - "doi_category" - ], - "then": { - "properties": { - "doi_provider": {} - }, - "required": [ - "doi_provider" - ] - }, - "title": "Doi", - "type": "object" - }, - "DoiCategoryEnum": { - "description": "", - "enum": [ - "award_doi", - "dataset_doi", - "publication_doi", - "data_management_plan_doi" - ], - "title": "DoiCategoryEnum", - "type": "string" - }, - "DoiProviderEnum": { - "description": "", - "enum": [ - "emsl", - "jgi", - "kbase", - "osti", - "ess_dive", - "massive", - "gsc", - "zenodo", - "edi" - ], - "title": "DoiProviderEnum", - "type": "string" - }, - "DoorCompTypeEnum": { - "description": "", - "enum": [ - "metal covered", - "revolving", - "sliding", - "telescopic" - ], - "title": "DoorCompTypeEnum", - "type": "string" - }, - "DoorCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "DoorCondEnum", - "type": "string" - }, - "DoorDirectEnum": { - "description": "", - "enum": [ - "inward", - "outward", - "sideways" - ], - "title": "DoorDirectEnum", - "type": "string" - }, - "DoorLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "DoorLocEnum", - "type": "string" - }, - "DoorMatEnum": { - "description": "", - "enum": [ - "aluminum", - "cellular PVC", - "engineered plastic", - "fiberboard", - "fiberglass", - "metal", - "thermoplastic alloy", - "vinyl", - "wood", - "wood/plastic composite" - ], - "title": "DoorMatEnum", - "type": "string" - }, - "DoorMoveEnum": { - "description": "", - "enum": [ - "collapsible", - "folding", - "revolving", - "rolling shutter", - "sliding", - "swinging" - ], - "title": "DoorMoveEnum", - "type": "string" - }, - "DoorTypeEnum": { - "description": "", - "enum": [ - "composite", - "metal", - "wooden" - ], - "title": "DoorTypeEnum", - "type": "string" - }, - "DoorTypeMetalEnum": { - "description": "", - "enum": [ - "collapsible", - "corrugated steel", - "hollow", - "rolling shutters", - "steel plate" - ], - "title": "DoorTypeMetalEnum", - "type": "string" - }, - "DoorTypeWoodEnum": { - "description": "", - "enum": [ - "bettened and ledged", - "battened", - "ledged and braced", - "ledged and framed", - "ledged, braced and frame", - "framed and paneled", - "glashed or sash", - "flush", - "louvered", - "wire gauged" - ], - "title": "DoorTypeWoodEnum", - "type": "string" - }, - "DrainageClassEnum": { - "description": "", - "enum": [ - "very poorly", - "poorly", - "somewhat poorly", - "moderately well", - "well", - "excessively drained" - ], - "title": "DrainageClassEnum", - "type": "string" - }, - "DrawingsEnum": { - "description": "", - "enum": [ - "operation", - "as built", - "construction", - "bid", - "design", - "building navigation map", - "diagram", - "sketch" - ], - "title": "DrawingsEnum", - "type": "string" - }, - "EnvironmentalMaterialTerm": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterialTerm", - "type": "object" - }, - "ExtWallOrientEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west", - "northeast", - "southeast", - "southwest", - "northwest" - ], - "title": "ExtWallOrientEnum", - "type": "string" - }, - "ExtWindowOrientEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west", - "northeast", - "southeast", - "southwest", - "northwest" - ], - "title": "ExtWindowOrientEnum", - "type": "string" - }, - "Extraction": { - "additionalProperties": false, - "description": "A material separation in which a desired component of an input material is separated from the remainder.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:Extraction" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "extractant": { - "$ref": "#/$defs/Solution", - "description": "The active component(s) primarily responsible for transfer of a solute from one phase to the other." - }, - "extraction_method": { - "$ref": "#/$defs/ExtractionTargetEnum" - }, - "extraction_target": { - "$ref": "#/$defs/ExtractionTargetEnum" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "input_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Total mass of sample used in activity." - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the solvent/solute being used, not the input." - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "Extraction", - "type": "object" - }, - "ExtractionTargetEnum": { - "description": "", - "enum": [ - "DNA", - "RNA", - "metabolite", - "protein" - ], - "title": "ExtractionTargetEnum", - "type": "string" - }, - "FailureCategorization": { - "additionalProperties": false, - "description": "", - "properties": { - "qc_failure_what": { - "$ref": "#/$defs/FailureWhatEnum", - "description": "Provides a summary about what caused a lab or workflow process to fail" - }, - "qc_failure_where": { - "$ref": "#/$defs/FailureWhereEnum", - "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." - } - }, - "title": "FailureCategorization", - "type": "object" - }, - "FailureWhatEnum": { - "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", - "enum": [ - "low_read_count", - "malformed_data", - "assembly_size_too_small", - "no_valid_data_generated", - "other" - ], - "title": "FailureWhatEnum", - "type": "string" - }, - "FailureWhereEnum": { - "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", - "enum": [ - "OmicsProcessing", - "Pooling", - "Extraction", - "LibraryPreparation", - "MetagenomeAssembly", - "MetatranscriptomeActivity", - "MagsAnalysisActivity", - "ReadQcAnalysisActivity", - "ReadBasedTaxonomyAnalysisActivity", - "MetagenomeAnnotationActivity" - ], - "title": "FailureWhereEnum", - "type": "string" - }, - "FaoClassEnum": { - "description": "", - "enum": [ - "Acrisols", - "Andosols", - "Arenosols", - "Cambisols", - "Chernozems", - "Ferralsols", - "Fluvisols", - "Gleysols", - "Greyzems", - "Gypsisols", - "Histosols", - "Kastanozems", - "Lithosols", - "Luvisols", - "Nitosols", - "Phaeozems", - "Planosols", - "Podzols", - "Podzoluvisols", - "Rankers", - "Regosols", - "Rendzinas", - "Solonchaks", - "Solonetz", - "Vertisols", - "Yermosols" - ], - "title": "FaoClassEnum", - "type": "string" - }, - "FieldResearchSite": { - "additionalProperties": false, - "description": "A site, outside of a laboratory, from which biosamples may be collected.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "cur_vegetation": { - "$ref": "#/$defs/TextValue", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "elev": { - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "type": "number" - }, - "geo_loc_name": { - "$ref": "#/$defs/TextValue", - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" - }, - "habitat": { - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "lat_lon": { - "$ref": "#/$defs/GeolocationValue", - "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" - }, - "local_class": { - "$ref": "#/$defs/TextValue", - "description": "Soil classification based on local soil classification system" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "soil_type": { - "$ref": "#/$defs/TextValue", - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." - } - }, - "required": [ - "id" - ], - "title": "FieldResearchSite", - "type": "object" - }, - "FileTypeEnum": { - "description": "", - "enum": [ - "Metagenome Raw Reads", - "Metagenome Raw Read 1", - "Metagenome Raw Read 2", - "FT ICR-MS Analysis Results", - "GC-MS Metabolomics Results", - "Metaproteomics Workflow Statistics", - "Protein Report", - "Peptide Report", - "Unfiltered Metaproteomics Results", - "Read Count and RPKM", - "QC non-rRNA R2", - "QC non-rRNA R1", - "Metagenome Bins", - "Metagenome HQMQ Bins Compression File", - "Metagenome LQ Bins Compression File", - "Metagenome Bins Info File", - "CheckM Statistics", - "Metagenome Bins Heatmap", - "Metagenome Bins Barplot", - "Metagenome Bins Krona Plot", - "Read Based Analysis Info File", - "GTDBTK Bacterial Summary", - "GTDBTK Archaeal Summary", - "GOTTCHA2 Krona Plot", - "GOTTCHA2 Classification Report", - "GOTTCHA2 Report Full", - "Kraken2 Krona Plot", - "Centrifuge Krona Plot", - "Centrifuge output report file", - "Kraken2 Classification Report", - "Kraken2 Taxonomic Classification", - "Centrifuge Classification Report", - "Centrifuge Taxonomic Classification", - "Structural Annotation GFF", - "Structural Annotation Stats Json", - "Functional Annotation GFF", - "Annotation Info File", - "Annotation Amino Acid FASTA", - "Annotation Enzyme Commission", - "Annotation KEGG Orthology", - "Assembly Info File", - "Assembly Coverage BAM", - "Assembly AGP", - "Assembly Scaffolds", - "Assembly Contigs", - "Assembly Coverage Stats", - "Contig Mapping File", - "Error Corrected Reads", - "Filtered Sequencing Reads", - "Read Filtering Info File", - "QC Statistics Extended", - "QC Statistics", - "TIGRFam Annotation GFF", - "CRT Annotation GFF", - "Genemark Annotation GFF", - "Prodigal Annotation GFF", - "TRNA Annotation GFF", - "Misc Annotation GFF", - "RFAM Annotation GFF", - "TMRNA Annotation GFF", - "Crispr Terms", - "Product Names", - "Gene Phylogeny tsv", - "Scaffold Lineage tsv", - "Clusters of Orthologous Groups (COG) Annotation GFF", - "KO_EC Annotation GFF", - "CATH FunFams (Functional Families) Annotation GFF", - "SUPERFam Annotation GFF", - "SMART Annotation GFF", - "Pfam Annotation GFF", - "Annotation Statistics", - "Direct Infusion FT ICR-MS Raw Data", - "LC-DDA-MS/MS Raw Data" - ], - "title": "FileTypeEnum", - "type": "string" - }, - "FilterTypeEnum": { - "description": "", - "enum": [ - "particulate air filter", - "chemical air filter", - "low-MERV pleated media", - "HEPA", - "electrostatic", - "gas-phase or ultraviolet air treatments" - ], - "title": "FilterTypeEnum", - "type": "string" - }, - "FiltrationProcess": { - "additionalProperties": false, - "description": "The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "conditionings": { - "description": "Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.", - "items": { - "type": "string" - }, - "type": "array" - }, - "container_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the container an analyte is stored in or an activity takes place in" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:FiltrationProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "filter_material": { - "description": "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.", - "type": "string" - }, - "filter_pore_size": { - "$ref": "#/$defs/QuantityValue", - "description": "A quantitative or qualitative measurement of the physical dimensions of the pores in a material." - }, - "filtration_category": { - "description": "The type of conditioning applied to a filter, device, etc.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "is_pressurized": { - "description": "Whether or not pressure was applied to a thing or process.", - "type": "boolean" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "separation_method": { - "$ref": "#/$defs/SeparationMethodEnum", - "description": "The method that was used to separate a substance from a solution or mixture." - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of sample filtered." - } - }, - "required": [ - "id" - ], - "title": "FiltrationProcess", - "type": "object" - }, - "FloorCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "FloorCondEnum", - "type": "string" - }, - "FloorFinishMatEnum": { - "description": "", - "enum": [ - "tile", - "wood strip or parquet", - "carpet", - "rug", - "laminate wood", - "lineoleum", - "vinyl composition tile", - "sheet vinyl", - "stone", - "bamboo", - "cork", - "terrazo", - "concrete", - "none", - "sealed", - "clear finish", - "paint", - "none or unfinished" - ], - "title": "FloorFinishMatEnum", - "type": "string" - }, - "FloorStrucEnum": { - "description": "", - "enum": [ - "balcony", - "floating floor", - "glass floor", - "raised floor", - "sprung floor", - "wood-framed", - "concrete" - ], - "title": "FloorStrucEnum", - "type": "string" - }, - "FloorWaterMoldEnum": { - "description": "", - "enum": [ - "mold odor", - "wet floor", - "water stains", - "wall discoloration", - "floor discoloration", - "ceiling discoloration", - "peeling paint or wallpaper", - "bulging walls", - "condensation" - ], - "title": "FloorWaterMoldEnum", - "type": "string" - }, - "FreqCleanEnum": { - "description": "", - "enum": [ - "Daily", - "Weekly", - "Monthly", - "Quarterly", - "Annually", - "other" - ], - "title": "FreqCleanEnum", - "type": "string" - }, - "FunctionalAnnotation": { - "additionalProperties": false, - "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", - "properties": { - "has_function": { - "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", - "type": "string" - }, - "subject": { - "type": "string" - }, - "was_generated_by": { - "description": "provenance for the annotation.", - "type": "string" - } - }, - "title": "FunctionalAnnotation", - "type": "object" - }, - "FunctionalAnnotationAggMember": { - "additionalProperties": false, - "description": "", - "properties": { - "count": { - "type": "integer" - }, - "gene_function_id": { - "description": "The identifier for the gene function.", - "type": "string" - }, - "metagenome_annotation_id": { - "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", - "type": "string" - } - }, - "required": [ - "metagenome_annotation_id", - "gene_function_id", - "count" - ], - "title": "FunctionalAnnotationAggMember", - "type": "object" - }, - "FurnitureEnum": { - "description": "", - "enum": [ - "cabinet", - "chair", - "desks" - ], - "title": "FurnitureEnum", - "type": "string" - }, - "GenderRestroomEnum": { - "description": "", - "enum": [ - "all gender", - "female", - "gender neurtral", - "male", - "male and female", - "unisex" - ], - "title": "GenderRestroomEnum", - "type": "string" - }, - "GeneProduct": { - "additionalProperties": false, - "description": "A molecule encoded by a gene that has an evolved function", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneProduct", - "type": "object" - }, - "GenomeFeature": { - "additionalProperties": false, - "description": "A feature localized to an interval along a genome", - "properties": { - "encodes": { - "description": "The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA", - "type": "string" - }, - "end": { - "description": "The end of the feature in positive 1-based integer coordinates", - "minimum": 1, - "type": "integer" - }, - "feature_type": { - "description": "TODO: Yuri to write", - "type": "string" - }, - "phase": { - "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.", - "maximum": 2, - "minimum": 0, - "type": "integer" - }, - "seqid": { - "description": "The ID of the landmark used to establish the coordinate system for the current feature.", - "type": "string" - }, - "start": { - "description": "The start of the feature in positive 1-based integer coordinates", - "minimum": 1, - "type": "integer" - }, - "strand": { - "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).", - "type": "string" - } - }, - "required": [ - "end", - "seqid", - "start" - ], - "title": "GenomeFeature", - "type": "object" - }, - "GeolocationValue": { - "additionalProperties": false, - "description": "A normalized value for a location on the earth's surface", - "properties": { - "has_raw_value": { - "description": "The raw value for a geolocation should follow {latitude} {longitude}", - "type": "string" - }, - "latitude": { - "description": "latitude", - "type": "number" - }, - "longitude": { - "description": "longitude", - "type": "number" - } - }, - "required": [ - "latitude", - "longitude" - ], - "title": "GeolocationValue", - "type": "object" - }, - "GrowthHabitEnum": { - "description": "", - "enum": [ - "erect", - "semi-erect", - "spreading", - "prostrate" - ], - "title": "GrowthHabitEnum", - "type": "string" - }, - "HandidnessEnum": { - "description": "", - "enum": [ - "ambidexterity", - "left handedness", - "mixed-handedness", - "right handedness" - ], - "title": "HandidnessEnum", - "type": "string" - }, - "HcProducedEnum": { - "description": "", - "enum": [ - "Oil", - "Gas-Condensate", - "Gas", - "Bitumen", - "Coalbed Methane", - "other" - ], - "title": "HcProducedEnum", - "type": "string" - }, - "HcrEnum": { - "description": "", - "enum": [ - "Oil Reservoir", - "Gas Reservoir", - "Oil Sand", - "Coalbed", - "Shale", - "Tight Oil Reservoir", - "Tight Gas Reservoir", - "other" - ], - "title": "HcrEnum", - "type": "string" - }, - "HcrGeolAgeEnum": { - "description": "", - "enum": [ - "Archean", - "Cambrian", - "Carboniferous", - "Cenozoic", - "Cretaceous", - "Devonian", - "Jurassic", - "Mesozoic", - "Neogene", - "Ordovician", - "Paleogene", - "Paleozoic", - "Permian", - "Precambrian", - "Proterozoic", - "Silurian", - "Triassic", - "other" - ], - "title": "HcrGeolAgeEnum", - "type": "string" - }, - "HeatCoolTypeEnum": { - "description": "", - "enum": [ - "radiant system", - "heat pump", - "forced air system", - "steam forced heat", - "wood stove" - ], - "title": "HeatCoolTypeEnum", - "type": "string" - }, - "HeatDelivLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "HeatDelivLocEnum", - "type": "string" - }, - "HostSexEnum": { - "description": "", - "enum": [ - "female", - "hermaphrodite", - "male", - "neuter" - ], - "title": "HostSexEnum", - "type": "string" - }, - "ImageValue": { - "additionalProperties": false, - "description": "An attribute value representing an image.", - "properties": { - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "display_order": { - "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", - "type": "integer" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "url": { - "type": "string" - } - }, - "title": "ImageValue", - "type": "object" - }, - "IndoorSpaceEnum": { - "description": "", - "enum": [ - "bedroom", - "office", - "bathroom", - "foyer", - "kitchen", - "locker room", - "hallway", - "elevator" - ], - "title": "IndoorSpaceEnum", - "type": "string" - }, - "IndoorSurfEnum": { - "description": "", - "enum": [ - "cabinet", - "ceiling", - "counter top", - "door", - "shelving", - "vent cover", - "window", - "wall" - ], - "title": "IndoorSurfEnum", - "type": "string" - }, - "InstrumentModelEnum": { - "description": "", - "enum": [ - "Orbitrap", - "VortexGenie2", - "PIPETMAN F144059M" - ], - "title": "InstrumentModelEnum", - "type": "string" - }, - "InstrumentVendorEnum": { - "description": "", - "enum": [ - "ThermoFisher", - "VWR", - "PerkinElmer", - "Gilson", - "ScientificIndustries" - ], - "title": "InstrumentVendorEnum", - "type": "string" - }, - "IntWallCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "IntWallCondEnum", - "type": "string" - }, - "IntegerValue": { - "additionalProperties": false, - "description": "A value that is an integer", - "properties": { - "has_numeric_value": { - "description": "Links a quantity value to a number", - "type": "number" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "IntegerValue", - "type": "object" - }, - "JgiContTypeEnum": { - "description": "", - "enum": [ - "plate", - "tube" - ], - "title": "JgiContTypeEnum", - "type": "string" - }, - "LibraryPreparation": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:LibraryPreparation" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "library_preparation_kit": { - "type": "string" - }, - "library_type": { - "$ref": "#/$defs/LibraryTypeEnum" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "pcr_cycles": { - "type": "integer" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "LibraryPreparation", - "type": "object" - }, - "LibraryTypeEnum": { - "description": "", - "enum": [ - "DNA", - "RNA" - ], - "title": "LibraryTypeEnum", - "type": "string" - }, - "LightTypeEnum": { - "description": "", - "enum": [ - "natural light", - "electric light", - "desk lamp", - "flourescent lights", - "none" - ], - "title": "LightTypeEnum", - "type": "string" - }, - "LithologyEnum": { - "description": "", - "enum": [ - "Basement", - "Chalk", - "Chert", - "Coal", - "Conglomerate", - "Diatomite", - "Dolomite", - "Limestone", - "Sandstone", - "Shale", - "Siltstone", - "Volcanic", - "other" - ], - "title": "LithologyEnum", - "type": "string" - }, - "MagBin": { - "additionalProperties": false, - "description": "", - "properties": { - "bin_name": { - "type": "string" - }, - "bin_quality": { - "type": "string" - }, - "completeness": { - "type": "number" - }, - "contamination": { - "type": "number" - }, - "gene_count": { - "type": "integer" - }, - "gtdbtk_class": { - "type": "string" - }, - "gtdbtk_domain": { - "type": "string" - }, - "gtdbtk_family": { - "type": "string" - }, - "gtdbtk_genus": { - "type": "string" - }, - "gtdbtk_order": { - "type": "string" - }, - "gtdbtk_phylum": { - "type": "string" - }, - "gtdbtk_species": { - "type": "string" - }, - "members_id": { - "type": "string" - }, - "num_16s": { - "type": "integer" - }, - "num_23s": { - "type": "integer" - }, - "num_5s": { - "type": "integer" - }, - "num_t_rna": { - "type": "integer" - }, - "number_of_contig": { - "type": "integer" - }, - "total_bases": { - "type": "integer" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "title": "MagBin", - "type": "object" - }, - "MagsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "binned_contig_num": { - "type": "integer" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "input_contig_num": { - "type": "integer" - }, - "low_depth_contig_num": { - "type": "integer" - }, - "mags_list": { - "items": { - "$ref": "#/$defs/MagBin" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "too_short_contig_num": { - "type": "integer" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "unbinned_contig_num": { - "type": "integer" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MagsAnalysisActivity", - "type": "object" - }, - "MechStrucEnum": { - "description": "", - "enum": [ - "subway", - "coach", - "carriage", - "elevator", - "escalator", - "boat", - "train", - "car", - "bus" - ], - "title": "MechStrucEnum", - "type": "string" - }, - "MetaboliteQuantification": { - "additionalProperties": false, - "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "highest_similarity_score": { - "type": "number" - }, - "metabolite_quantified": { - "description": "the specific metabolite identifier", - "type": "string" - } - }, - "title": "MetaboliteQuantification", - "type": "object" - }, - "MetabolomicsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_calibration": { - "description": "A reference to a file that holds calibration information.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_metabolite_quantifications": { - "items": { - "$ref": "#/$defs/MetaboliteQuantification" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetabolomicsAnalysisActivity", - "type": "object" - }, - "MetagenomeAnnotationActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "gold_analysis_project_identifiers": { - "description": "identifiers for corresponding analysis project in GOLD", - "items": { - "pattern": "^gold:Ga[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeAnnotationActivity", - "type": "object" - }, - "MetagenomeAssembly": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "asm_score": { - "description": "A score for comparing metagenomic assembly quality from same sample.", - "type": "number" - }, - "contig_bp": { - "description": "Total size in bp of all contigs.", - "type": "number" - }, - "contigs": { - "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "ctg_l50": { - "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", - "type": "number" - }, - "ctg_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", - "type": "number" - }, - "ctg_logsum": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_max": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_n50": { - "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", - "type": "number" - }, - "ctg_n90": { - "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", - "type": "number" - }, - "ctg_powsum": { - "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "gap_pct": { - "description": "The gap size percentage of all scaffolds.", - "type": "number" - }, - "gc_avg": { - "description": "Average of GC content of all contigs.", - "type": "number" - }, - "gc_std": { - "description": "Standard deviation of GC content of all contigs.", - "type": "number" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "insdc_assembly_identifiers": { - "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "num_aligned_reads": { - "description": "The sequence count number of input reads aligned to assembled contigs.", - "type": "number" - }, - "num_input_reads": { - "description": "The sequence count number of input reads for assembly.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "scaf_bp": { - "description": "Total size in bp of all scaffolds.", - "type": "number" - }, - "scaf_l50": { - "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", - "type": "number" - }, - "scaf_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", - "type": "number" - }, - "scaf_l_gt50k": { - "description": "Total size in bp of all scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_logsum": { - "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "scaf_max": { - "description": "Maximum scaffold length.", - "type": "number" - }, - "scaf_n50": { - "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", - "type": "number" - }, - "scaf_n90": { - "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", - "type": "number" - }, - "scaf_n_gt50k": { - "description": "Total sequence count of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_pct_gt50k": { - "description": "Total sequence size percentage of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_powsum": { - "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "scaffolds": { - "description": "Total sequence count of all scaffolds.", - "type": "number" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeAssembly", - "type": "object" - }, - "MetagenomeSequencingActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeSequencingActivity", - "type": "object" - }, - "MetaproteomicsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_peptide_quantifications": { - "items": { - "$ref": "#/$defs/PeptideQuantification" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "description": "The instrument used to collect the data used in the analysis", - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetaproteomicsAnalysisActivity", - "type": "object" - }, - "MetatranscriptomeActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeActivity", - "type": "object" - }, - "MetatranscriptomeAnnotationActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "gold_analysis_project_identifiers": { - "description": "identifiers for corresponding analysis project in GOLD", - "items": { - "pattern": "^gold:Ga[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeAnnotationActivity", - "type": "object" - }, - "MetatranscriptomeAssembly": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "asm_score": { - "description": "A score for comparing metagenomic assembly quality from same sample.", - "type": "number" - }, - "contig_bp": { - "description": "Total size in bp of all contigs.", - "type": "number" - }, - "contigs": { - "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "ctg_l50": { - "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", - "type": "number" - }, - "ctg_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", - "type": "number" - }, - "ctg_logsum": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_max": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_n50": { - "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", - "type": "number" - }, - "ctg_n90": { - "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", - "type": "number" - }, - "ctg_powsum": { - "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "gap_pct": { - "description": "The gap size percentage of all scaffolds.", - "type": "number" - }, - "gc_avg": { - "description": "Average of GC content of all contigs.", - "type": "number" - }, - "gc_std": { - "description": "Standard deviation of GC content of all contigs.", - "type": "number" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "insdc_assembly_identifiers": { - "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "num_aligned_reads": { - "description": "The sequence count number of input reads aligned to assembled contigs.", - "type": "number" - }, - "num_input_reads": { - "description": "The sequence count number of input reads for assembly.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "scaf_bp": { - "description": "Total size in bp of all scaffolds.", - "type": "number" - }, - "scaf_l50": { - "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", - "type": "number" - }, - "scaf_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", - "type": "number" - }, - "scaf_l_gt50k": { - "description": "Total size in bp of all scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_logsum": { - "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "scaf_max": { - "description": "Maximum scaffold length.", - "type": "number" - }, - "scaf_n50": { - "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", - "type": "number" - }, - "scaf_n90": { - "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", - "type": "number" - }, - "scaf_n_gt50k": { - "description": "Total sequence count of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_pct_gt50k": { - "description": "Total sequence size percentage of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_powsum": { - "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "scaffolds": { - "description": "Total sequence count of all scaffolds.", - "type": "number" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeAssembly", - "type": "object" - }, - "MixingProcess": { - "additionalProperties": false, - "description": "The combining of components, particles or layers into a more homogeneous state.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:MixingProcess" - ], - "type": "string" - }, - "duration": { - "$ref": "#/$defs/QuantityValue", - "description": "The elapsed time of an activity." - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "The mixed sample.", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MixingProcess", - "type": "object" - }, - "NomAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_calibration": { - "description": "A reference to a file that holds calibration information.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "description": "The instrument used to collect the data used in the analysis", - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "NomAnalysisActivity", - "type": "object" - }, - "OccupDocumentEnum": { - "description": "", - "enum": [ - "automated count", - "estimate", - "manual count", - "videos" - ], - "title": "OccupDocumentEnum", - "type": "string" - }, - "OmicsProcessing": { - "additionalProperties": false, - "description": "The methods and processes used to generate omics data from a biosample or organism.", - "properties": { - "add_date": { - "description": "The date on which the information was added to the database.", - "type": "string" - }, - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "chimera_check": { - "$ref": "#/$defs/TextValue", - "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:OmicsProcessing" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "gold_sequencing_project_identifiers": { - "description": "identifiers for corresponding sequencing project in GOLD", - "items": { - "pattern": "^gold:Gp[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "insdc_bioproject_identifiers": { - "description": "identifiers for corresponding project in INSDC Bioproject", - "items": { - "pattern": "^bioproject:PRJ[DEN][A-Z][0-9]+$", - "type": "string" - }, - "type": "array" - }, - "insdc_experiment_identifiers": { - "items": { - "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", - "type": "string" - }, - "type": "array" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "mod_date": { - "description": "The last date on which the database information was modified.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ncbi_project_name": { - "type": "string" - }, - "nucl_acid_amp": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" - }, - "nucl_acid_ext": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" - }, - "omics_type": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "The type of omics data" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "pcr_cond": { - "$ref": "#/$defs/TextValue", - "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" - }, - "pcr_primers": { - "$ref": "#/$defs/TextValue", - "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" - }, - "principal_investigator": { - "$ref": "#/$defs/PersonValue", - "description": "Principal Investigator who led the study and/or generated the dataset." - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "samp_vol_we_dna_ext": { - "$ref": "#/$defs/QuantityValue", - "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." - }, - "seq_meth": { - "$ref": "#/$defs/TextValue", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." - }, - "seq_quality_check": { - "$ref": "#/$defs/TextValue", - "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "target_gene": { - "$ref": "#/$defs/TextValue", - "description": "Targeted gene or locus name for marker gene studies" - }, - "target_subfragment": { - "$ref": "#/$defs/TextValue", - "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "required": [ - "has_input", - "id" - ], - "title": "OmicsProcessing", - "type": "object" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "OrganismCountEnum": { - "description": "", - "enum": [ - "ATP", - "MPN", - "other" - ], - "title": "OrganismCountEnum", - "type": "string" - }, - "OrthologyGroup": { - "additionalProperties": false, - "description": "A set of genes or gene products in which all members are orthologous", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OrthologyGroup", - "type": "object" - }, - "OxyStatSampEnum": { - "description": "", - "enum": [ - "aerobic", - "anaerobic", - "other" - ], - "title": "OxyStatSampEnum", - "type": "string" - }, - "Pathway": { - "additionalProperties": false, - "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "has_part": { - "description": "A pathway can be broken down to a series of reaction step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "has_part", - "id" - ], - "title": "Pathway", - "type": "object" - }, - "PeptideQuantification": { - "additionalProperties": false, - "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", - "properties": { - "all_proteins": { - "description": "the list of protein identifiers that are associated with the peptide sequence", - "items": { - "type": "string" - }, - "type": "array" - }, - "best_protein": { - "description": "the specific protein identifier most correctly associated with the peptide sequence", - "type": "string" - }, - "min_q_value": { - "description": "smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool", - "type": "number" - }, - "peptide_sequence": { - "type": "string" - }, - "peptide_spectral_count": { - "description": "sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file", - "type": "integer" - }, - "peptide_sum_masic_abundance": { - "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool", - "type": "integer" - } - }, - "title": "PeptideQuantification", - "type": "object" - }, - "PersonValue": { - "additionalProperties": false, - "description": "An attribute value representing a person", - "properties": { - "email": { - "description": "An email address for an entity such as a person. This should be the primary email address used.", - "type": "string" - }, - "has_raw_value": { - "description": "The full name of the Investigator in format FIRST LAST.", - "type": "string" - }, - "name": { - "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", - "type": "string" - }, - "orcid": { - "description": "The ORCID of a person.", - "type": "string" - }, - "profile_image_url": { - "description": "A url that points to an image of a person.", - "type": "string" - }, - "websites": { - "description": "A list of websites that are associated with the entity.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "type": "array" - } - }, - "title": "PersonValue", - "type": "object" - }, - "PlantGrowthMedEnum": { - "description": "", - "enum": [ - "other artificial liquid medium", - "other artificial solid medium", - "peat moss", - "perlite", - "pumice", - "sand", - "soil", - "vermiculite", - "water" - ], - "title": "PlantGrowthMedEnum", - "type": "string" - }, - "PlantSexEnum": { - "description": "", - "enum": [ - "Androdioecious", - "Androecious", - "Androgynous", - "Androgynomonoecious", - "Andromonoecious", - "Bisexual", - "Dichogamous", - "Diclinous", - "Dioecious", - "Gynodioecious", - "Gynoecious", - "Gynomonoecious", - "Hermaphroditic", - "Imperfect", - "Monoclinous", - "Monoecious", - "Perfect", - "Polygamodioecious", - "Polygamomonoecious", - "Polygamous", - "Protandrous", - "Protogynous", - "Subandroecious", - "Subdioecious", - "Subgynoecious", - "Synoecious", - "Trimonoecious", - "Trioecious", - "Unisexual" - ], - "title": "PlantSexEnum", - "type": "string" - }, - "Pooling": { - "additionalProperties": false, - "description": "physical combination of several instances of like material.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:Pooling" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "minItems": 2, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "maxItems": 1, - "minItems": 1, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "Pooling", - "type": "object" - }, - "ProcessedSample": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "biomaterial_purity": { - "$ref": "#/$defs/QuantityValue" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "dna_absorb1": { - "description": "260/280 measurement of DNA sample purity", - "type": "number" - }, - "dna_concentration": { - "maximum": 2000, - "minimum": 0, - "type": "number" - }, - "external_database_identifiers": { - "description": "Link to corresponding identifier in external database", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcessedSample", - "type": "object" - }, - "ProcessingInstitutionEnum": { - "description": "", - "enum": [ - "UCSD", - "JGI", - "EMSL", - "Battelle", - "ANL", - "UCD_Genome_Center" - ], - "title": "ProcessingInstitutionEnum", - "type": "string" - }, - "ProfilePositionEnum": { - "description": "", - "enum": [ - "summit", - "shoulder", - "backslope", - "footslope", - "toeslope" - ], - "title": "ProfilePositionEnum", - "type": "string" - }, - "ProteinQuantification": { - "additionalProperties": false, - "description": "This is used to link a metaproteomics analysis workflow to a specific protein", - "properties": { - "all_proteins": { - "description": "the grouped list of protein identifiers associated with the peptide sequences that were grouped to a best protein", - "items": { - "type": "string" - }, - "type": "array" - }, - "best_protein": { - "description": "the specific protein identifier most correctly grouped to its associated peptide sequences", - "type": "string" - }, - "peptide_sequence_count": { - "description": "count of peptide sequences grouped to the best_protein", - "type": "integer" - }, - "protein_spectral_count": { - "description": "sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file", - "type": "integer" - }, - "protein_sum_masic_abundance": { - "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool", - "type": "integer" - } - }, - "title": "ProteinQuantification", - "type": "object" - }, - "Protocol": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "url": { - "type": "string" - } - }, - "title": "Protocol", - "type": "object" - }, - "QuadPosEnum": { - "description": "", - "enum": [ - "North side", - "West side", - "South side", - "East side" - ], - "title": "QuadPosEnum", - "type": "string" - }, - "QuantityValue": { - "additionalProperties": false, - "description": "A simple quantity, e.g. 2cm", - "properties": { - "has_maximum_numeric_value": { - "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", - "type": "number" - }, - "has_minimum_numeric_value": { - "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", - "type": "number" - }, - "has_numeric_value": { - "description": "The number part of the quantity", - "type": "number" - }, - "has_raw_value": { - "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", - "type": "string" - }, - "has_unit": { - "description": "The unit of the quantity", - "type": "string" - } - }, - "title": "QuantityValue", - "type": "object" - }, - "RNASampleFormatEnum": { - "description": "", - "enum": [ - "10 mM Tris-HCl", - "DNAStable", - "Ethanol", - "Low EDTA TE", - "MDA reaction buffer", - "PBS", - "Pellet", - "RNAStable", - "TE", - "Water", - "Gentegra-DNA", - "Gentegra-RNA" - ], - "title": "RNASampleFormatEnum", - "type": "string" - }, - "Reaction": { - "additionalProperties": false, - "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "direction": { - "description": "One of l->r, r->l, bidirectional, neutral", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "is_balanced": { - "type": "boolean" - }, - "is_diastereoselective": { - "type": "boolean" - }, - "is_fully_characterized": { - "description": "False if includes R-groups", - "type": "boolean" - }, - "is_stereo": { - "type": "boolean" - }, - "is_transport": { - "type": "boolean" - }, - "left_participants": { - "items": { - "$ref": "#/$defs/ReactionParticipant" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "right_participants": { - "items": { - "$ref": "#/$defs/ReactionParticipant" - }, - "type": "array" - }, - "smarts_string": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Reaction", - "type": "object" - }, - "ReactionParticipant": { - "additionalProperties": false, - "description": "Instances of this link a reaction to a chemical entity participant", - "properties": { - "chemical": { - "description": "from reaction participant class", - "type": "string" - }, - "stoichiometry": { - "description": "from reaction participant class", - "type": "integer" - } - }, - "title": "ReactionParticipant", - "type": "object" - }, - "ReadBasedTaxonomyAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "ReadBasedTaxonomyAnalysisActivity", - "type": "object" - }, - "ReadQcAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "input_base_count": { - "description": "The nucleotide base count number of input reads for QC analysis.", - "type": "number" - }, - "input_read_bases": { - "description": "TODO ", - "type": "number" - }, - "input_read_count": { - "description": "The sequence count number of input reads for QC analysis.", - "type": "number" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "output_base_count": { - "description": "After QC analysis nucleotide base count number.", - "type": "number" - }, - "output_read_bases": { - "description": "TODO", - "type": "number" - }, - "output_read_count": { - "description": "After QC analysis sequence count number.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "ReadQcAnalysisActivity", - "type": "object" - }, - "RelSampLocEnum": { - "description": "", - "enum": [ - "edge of car", - "center of car", - "under a seat" - ], - "title": "RelSampLocEnum", - "type": "string" - }, - "RoomCondtEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture", - "visible signs of mold/mildew" - ], - "title": "RoomCondtEnum", - "type": "string" - }, - "RoomConnectedEnum": { - "description": "", - "enum": [ - "attic", - "bathroom", - "closet", - "conference room", - "elevator", - "examining room", - "hallway", - "kitchen", - "mail room", - "office", - "stairwell" - ], - "title": "RoomConnectedEnum", - "type": "string" - }, - "RoomLocEnum": { - "description": "", - "enum": [ - "corner room", - "interior room", - "exterior wall" - ], - "title": "RoomLocEnum", - "type": "string" - }, - "RoomSampPosEnum": { - "description": "", - "enum": [ - "north corner", - "south corner", - "west corner", - "east corner", - "northeast corner", - "northwest corner", - "southeast corner", - "southwest corner", - "center" - ], - "title": "RoomSampPosEnum", - "type": "string" - }, - "RoomTypeEnum": { - "description": "", - "enum": [ - "attic", - "bathroom", - "closet", - "conference room", - "elevator", - "examining room", - "hallway", - "kitchen", - "mail room", - "private office", - "open office", - "stairwell", - ",restroom", - "lobby", - "vestibule", - "mechanical or electrical room", - "data center", - "laboratory_wet", - "laboratory_dry", - "gymnasium", - "natatorium", - "auditorium", - "lockers", - "cafe", - "warehouse" - ], - "title": "RoomTypeEnum", - "type": "string" - }, - "SampCaptStatusEnum": { - "description": "", - "enum": [ - "active surveillance in response to an outbreak", - "active surveillance not initiated by an outbreak", - "farm sample", - "market sample", - "other" - ], - "title": "SampCaptStatusEnum", - "type": "string" - }, - "SampCollectPointEnum": { - "description": "", - "enum": [ - "well", - "test well", - "drilling rig", - "wellhead", - "separator", - "storage tank", - "other" - ], - "title": "SampCollectPointEnum", - "type": "string" - }, - "SampDisStageEnum": { - "description": "", - "enum": [ - "dissemination", - "growth and reproduction", - "infection", - "inoculation", - "penetration", - "other" - ], - "title": "SampDisStageEnum", - "type": "string" - }, - "SampFloorEnum": { - "description": "", - "enum": [ - "1st floor", - "2nd floor", - "basement", - "lobby" - ], - "title": "SampFloorEnum", - "type": "string" - }, - "SampMdEnum": { - "description": "", - "enum": [ - "DF", - "RT", - "KB", - "MSL", - "other" - ], - "title": "SampMdEnum", - "type": "string" - }, - "SampSubtypeEnum": { - "description": "", - "enum": [ - "oil phase", - "water phase", - "biofilm", - "not applicable", - "other" - ], - "title": "SampSubtypeEnum", - "type": "string" - }, - "SampWeatherEnum": { - "description": "", - "enum": [ - "clear sky", - "cloudy", - "foggy", - "hail", - "rain", - "snow", - "sleet", - "sunny", - "windy" - ], - "title": "SampWeatherEnum", - "type": "string" - }, - "SampleTypeEnum": { - "description": "", - "enum": [ - "soil", - "soil - water extract", - "plant associated", - "sediment", - "water" - ], - "title": "SampleTypeEnum", - "type": "string" - }, - "SeasonUseEnum": { - "description": "", - "enum": [ - "Spring", - "Summer", - "Fall", - "Winter" - ], - "title": "SeasonUseEnum", - "type": "string" - }, - "SedimentTypeEnum": { - "description": "", - "enum": [ - "biogenous", - "cosmogenous", - "hydrogenous", - "lithogenous" - ], - "title": "SedimentTypeEnum", - "type": "string" - }, - "SeparationMethodEnum": { - "description": "The tool/substance used to separate or filter a solution or mixture.", - "enum": [ - "PTFE 96-well filter plate" - ], - "title": "SeparationMethodEnum", - "type": "string" - }, - "ShadingDeviceCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "ShadingDeviceCondEnum", - "type": "string" - }, - "ShadingDeviceTypeEnum": { - "description": "", - "enum": [ - "bahama shutters", - "exterior roll blind", - "gambrel awning", - "hood awning", - "porchroller awning", - "sarasota shutters", - "slatted aluminum", - "solid aluminum awning", - "sun screen", - "tree", - "trellis", - "venetian awning" - ], - "title": "ShadingDeviceTypeEnum", - "type": "string" - }, - "SoilHorizonEnum": { - "description": "", - "enum": [ - "O horizon", - "A horizon", - "E horizon", - "B horizon", - "C horizon", - "R layer", - "Permafrost", - "M horizon" - ], - "title": "SoilHorizonEnum", - "type": "string" - }, - "Solution": { - "additionalProperties": false, - "description": "A mixture that is homogeneous, made up of two or more scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent.", - "properties": { - "has_solution_components": { - "description": "Relationship from a Solution to one or more constituent solution components", - "items": { - "$ref": "#/$defs/SolutionComponent" - }, - "minItems": 1, - "type": "array" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of a substance." - } - }, - "required": [ - "has_solution_components" - ], - "title": "Solution", - "type": "object" - }, - "SolutionComponent": { - "additionalProperties": false, - "description": "One constituent of a solution", - "properties": { - "compound": { - "$ref": "#/$defs/CompoundEnum", - "description": "A substance that consists of more than one atom or ion. Includes solvents and solutes. Can be combined into solutions." - }, - "concentration": { - "$ref": "#/$defs/QuantityValue", - "description": "The concentration of a substance used in a process" - } - }, - "required": [ - "compound" - ], - "title": "SolutionComponent", - "type": "object" - }, - "SpecificEnum": { - "description": "", - "enum": [ - "operation", - "as built", - "construction", - "bid", - "design", - "photos" - ], - "title": "SpecificEnum", - "type": "string" - }, - "SrDepEnvEnum": { - "description": "", - "enum": [ - "Lacustine", - "Fluvioldeltaic", - "Fluviomarine", - "Marine", - "other" - ], - "title": "SrDepEnvEnum", - "type": "string" - }, - "SrGeolAgeEnum": { - "description": "", - "enum": [ - "Archean", - "Cambrian", - "Carboniferous", - "Cenozoic", - "Cretaceous", - "Devonian", - "Jurassic", - "Mesozoic", - "Neogene", - "Ordovician", - "Paleogene", - "Paleozoic", - "Permian", - "Precambrian", - "Proterozoic", - "Silurian", - "Triassic", - "other" - ], - "title": "SrGeolAgeEnum", - "type": "string" - }, - "SrKerogTypeEnum": { - "description": "", - "enum": [ - "Type I", - "Type II", - "Type III", - "Type IV", - "other" - ], - "title": "SrKerogTypeEnum", - "type": "string" - }, - "SrLithologyEnum": { - "description": "", - "enum": [ - "Clastic", - "Carbonate", - "Coal", - "Biosilicieous", - "other" - ], - "title": "SrLithologyEnum", - "type": "string" - }, - "StationaryPhaseEnum": { - "description": "The type of stationary phase used in a solid phase extraction process.", - "enum": [ - "C18", - "C8", - "C4", - "C2", - "C1", - "C30", - "C60", - "CNT", - "CN", - "Diol", - "HILIC", - "NH2", - "Phenyl", - "PS-DVB", - "SAX", - "SCX", - "Silica", - "WCX", - "WAX", - "ZIC-HILIC", - "ZIC-pHILIC", - "ZIC-cHILIC" - ], - "title": "StationaryPhaseEnum", - "type": "string" - }, - "StatusEnum": { - "description": "", - "enum": [ - "pass", - "fail" - ], - "title": "StatusEnum", - "type": "string" - }, - "Study": { - "additionalProperties": false, - "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", - "properties": { - "alternative_descriptions": { - "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "alternative_identifiers": { - "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "alternative_names": { - "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "alternative_titles": { - "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "associated_dois": { - "description": "A list of DOIs associated with a resource, such as a list of DOIS associated with a Study.", - "items": { - "$ref": "#/$defs/Doi" - }, - "type": "array" - }, - "description": { - "description": "A brief, link-free summary of a Study", - "type": "string" - }, - "ecosystem": { - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_category": { - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_subtype": { - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_type": { - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "type": "string" - }, - "emsl_project_identifiers": { - "description": "Identifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project", - "items": { - "pattern": "^emsl\\.project:[0-9]{5}$", - "type": "string" - }, - "type": "array" - }, - "funding_sources": { - "description": "A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.", - "items": { - "type": "string" - }, - "type": "array" - }, - "gnps_task_identifiers": { - "description": "identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results", - "items": { - "pattern": "^gnps\\.task:[a-f0-9]+$", - "type": "string" - }, - "type": "array" - }, - "gold_study_identifiers": { - "description": "identifiers for corresponding project(s) in GOLD", - "items": { - "pattern": "^gold:Gs[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_credit_associations": { - "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", - "items": { - "$ref": "#/$defs/CreditAssociation" - }, - "type": "array" - }, - "homepage_website": { - "description": "The website address (URL) of an entity's homepage.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "maxItems": 1, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "insdc_bioproject_identifiers": { - "description": "Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study.", - "items": { - "pattern": "^bioproject:PRJ[DEN][A-Z][0-9]+$", - "type": "string" - }, - "type": "array" - }, - "jgi_portal_study_identifiers": { - "description": "Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.", - "items": { - "pattern": "^jgi.proposal:\\d+$", - "type": "string" - }, - "type": "array" - }, - "mgnify_project_identifiers": { - "description": "identifiers for corresponding project in MGnify", - "items": { - "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "neon_study_identifiers": { - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "notes": { - "description": "from study class", - "type": "string" - }, - "objective": { - "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", - "type": "string" - }, - "part_of": { - "description": "Links a study or consortium to a parent (or umbrella) study or consortium.", - "items": { - "type": "string" - }, - "type": "array" - }, - "principal_investigator": { - "$ref": "#/$defs/PersonValue", - "description": "Principal Investigator who led the study and/or generated the dataset." - }, - "related_identifiers": { - "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", - "type": "string" - }, - "relevant_protocols": { - "items": { - "type": "string" - }, - "type": "array" - }, - "specific_ecosystem": { - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "type": "string" - }, - "study_category": { - "$ref": "#/$defs/StudyCategoryEnum", - "description": "The type of research initiative" - }, - "study_image": { - "description": "Links a study to one or more images.", - "items": { - "$ref": "#/$defs/ImageValue" - }, - "type": "array" - }, - "title": { - "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "websites": { - "description": "A list of websites that are associated with the entity.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id", - "study_category" - ], - "title": "Study", - "type": "object" - }, - "StudyCategoryEnum": { - "description": "", - "enum": [ - "research_study", - "consortium" - ], - "title": "StudyCategoryEnum", - "type": "string" - }, - "SubSamplingProcess": { - "additionalProperties": false, - "description": "Separating a sample aliquot from the starting material for downstream activity.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "contained_in": { - "$ref": "#/$defs/ContainerCategoryEnum", - "description": "A type of container. i.e. test tube, falcon tube, etc." - }, - "container_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the container an analyte is stored in or an activity takes place in" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:SubSamplingProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "The subsample.", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The output mass of the SubSampling Process." - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "temperature": { - "$ref": "#/$defs/QuantityValue", - "description": "The value of a temperature measurement or temperature used in a process." - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The output volume of the SubSampling Process." - } - }, - "required": [ - "id" - ], - "title": "SubSamplingProcess", - "type": "object" - }, - "SubstructureTypeEnum": { - "description": "", - "enum": [ - "crawlspace", - "slab on grade", - "basement" - ], - "title": "SubstructureTypeEnum", - "type": "string" - }, - "SurfAirContEnum": { - "description": "", - "enum": [ - "dust", - "organic matter", - "particulate matter", - "volatile organic compounds", - "biological contaminants", - "radon", - "nutrients", - "biocides" - ], - "title": "SurfAirContEnum", - "type": "string" - }, - "SurfMaterialEnum": { - "description": "", - "enum": [ - "adobe", - "carpet", - "cinder blocks", - "concrete", - "hay bales", - "glass", - "metal", - "paint", - "plastic", - "stainless steel", - "stone", - "stucco", - "tile", - "vinyl", - "wood" - ], - "title": "SurfMaterialEnum", - "type": "string" - }, - "TextValue": { - "additionalProperties": false, - "description": "A basic string value", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "language": { - "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", - "type": "string" - } - }, - "title": "TextValue", - "type": "object" - }, - "TidalStageEnum": { - "description": "", - "enum": [ - "low tide", - "ebb tide", - "flood tide", - "high tide" - ], - "title": "TidalStageEnum", - "type": "string" - }, - "TillageEnum": { - "description": "", - "enum": [ - "drill", - "cutting disc", - "ridge till", - "strip tillage", - "zonal tillage", - "chisel", - "tined", - "mouldboard", - "disc plough" - ], - "title": "TillageEnum", - "type": "string" - }, - "TimestampValue": { - "additionalProperties": false, - "description": "A value that is a timestamp. The range should be ISO-8601", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "TimestampValue", - "type": "object" - }, - "TrainLineEnum": { - "description": "", - "enum": [ - "red", - "green", - "orange" - ], - "title": "TrainLineEnum", - "type": "string" - }, - "TrainStatLocEnum": { - "description": "", - "enum": [ - "south station above ground", - "south station underground", - "south station amtrak", - "forest hills", - "riverside" - ], - "title": "TrainStatLocEnum", - "type": "string" - }, - "TrainStopLocEnum": { - "description": "", - "enum": [ - "end", - "mid", - "downtown" - ], - "title": "TrainStopLocEnum", - "type": "string" - }, - "UrlValue": { - "additionalProperties": false, - "description": "A value that is a string that conforms to URL syntax", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "UrlValue", - "type": "object" - }, - "VisMediaEnum": { - "description": "", - "enum": [ - "photos", - "videos", - "commonly of the building", - "site context (adjacent buildings, vegetation, terrain, streets)", - "interiors", - "equipment", - "3D scans" - ], - "title": "VisMediaEnum", - "type": "string" - }, - "WallConstTypeEnum": { - "description": "", - "enum": [ - "frame construction", - "joisted masonry", - "light noncombustible", - "masonry noncombustible", - "modified fire resistive", - "fire resistive" - ], - "title": "WallConstTypeEnum", - "type": "string" - }, - "WallFinishMatEnum": { - "description": "", - "enum": [ - "plaster", - "gypsum plaster", - "veneer plaster", - "gypsum board", - "tile", - "terrazzo", - "stone facing", - "acoustical treatment", - "wood", - "metal", - "masonry" - ], - "title": "WallFinishMatEnum", - "type": "string" - }, - "WallLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "WallLocEnum", - "type": "string" - }, - "WallSurfTreatmentEnum": { - "description": "", - "enum": [ - "painted", - "wall paper", - "no treatment", - "paneling", - "stucco", - "fabric" - ], - "title": "WallSurfTreatmentEnum", - "type": "string" - }, - "WallTextureEnum": { - "description": "", - "enum": [ - "crows feet", - "crows-foot stomp", - "", - "double skip", - "hawk and trowel", - "knockdown", - "popcorn", - "orange peel", - "rosebud stomp", - "Santa-Fe texture", - "skip trowel", - "smooth", - "stomp knockdown", - "swirl" - ], - "title": "WallTextureEnum", - "type": "string" - }, - "WaterFeatTypeEnum": { - "description": "", - "enum": [ - "fountain", - "pool", - "standing feature", - "stream", - "waterfall" - ], - "title": "WaterFeatTypeEnum", - "type": "string" - }, - "WeekdayEnum": { - "description": "", - "enum": [ - "Monday", - "Tuesday", - "Wednesday", - "Thursday", - "Friday", - "Saturday", - "Sunday" - ], - "title": "WeekdayEnum", - "type": "string" - }, - "WindowCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "WindowCondEnum", - "type": "string" - }, - "WindowCoverEnum": { - "description": "", - "enum": [ - "blinds", - "curtains", - "none" - ], - "title": "WindowCoverEnum", - "type": "string" - }, - "WindowHorizPosEnum": { - "description": "", - "enum": [ - "left", - "middle", - "right" - ], - "title": "WindowHorizPosEnum", - "type": "string" - }, - "WindowLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "WindowLocEnum", - "type": "string" - }, - "WindowMatEnum": { - "description": "", - "enum": [ - "clad", - "fiberglass", - "metal", - "vinyl", - "wood" - ], - "title": "WindowMatEnum", - "type": "string" - }, - "WindowTypeEnum": { - "description": "", - "enum": [ - "single-hung sash window", - "horizontal sash window", - "fixed window" - ], - "title": "WindowTypeEnum", - "type": "string" - }, - "WindowVertPosEnum": { - "description": "", - "enum": [ - "bottom", - "middle", - "top", - "low", - "high" - ], - "title": "WindowVertPosEnum", - "type": "string" - }, - "YesNoEnum": { - "description": "replaces DnaDnaseEnum and DnaseRnaEnum", - "enum": [ - "no", - "yes" - ], - "title": "YesNoEnum", - "type": "string" - } - }, - "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": true, - "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", - "metamodel_version": "1.7.0", - "properties": { - "biosample_set": { - "description": "This property links a database object to the set of samples within it.", - "items": { - "$ref": "#/$defs/Biosample" - }, - "type": "array" - }, - "collecting_biosamples_from_site_set": { - "items": { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - "type": "array" - }, - "data_object_set": { - "description": "This property links a database object to the set of data objects within it.", - "items": { - "$ref": "#/$defs/DataObject" - }, - "type": "array" - }, - "extraction_set": { - "description": "This property links a database object to the set of extractions within it.", - "items": { - "$ref": "#/$defs/Extraction" - }, - "type": "array" - }, - "field_research_site_set": { - "items": { - "$ref": "#/$defs/FieldResearchSite" - }, - "type": "array" - }, - "functional_annotation_agg": { - "items": { - "$ref": "#/$defs/FunctionalAnnotationAggMember" - }, - "type": "array" - }, - "functional_annotation_set": { - "description": "This property links a database object to the set of all functional annotations", - "items": { - "$ref": "#/$defs/FunctionalAnnotation" - }, - "type": "array" - }, - "genome_feature_set": { - "description": "This property links a database object to the set of all features", - "items": { - "$ref": "#/$defs/GenomeFeature" - }, - "type": "array" - }, - "library_preparation_set": { - "description": "This property links a database object to the set of DNA extractions within it.", - "items": { - "$ref": "#/$defs/LibraryPreparation" - }, - "type": "array" - }, - "mags_activity_set": { - "description": "This property links a database object to the set of MAGs analysis activities.", - "items": { - "$ref": "#/$defs/MagsAnalysisActivity" - }, - "type": "array" - }, - "metabolomics_analysis_activity_set": { - "description": "This property links a database object to the set of metabolomics analysis activities.", - "items": { - "$ref": "#/$defs/MetabolomicsAnalysisActivity" - }, - "type": "array" - }, - "metagenome_annotation_activity_set": { - "description": "This property links a database object to the set of metagenome annotation activities.", - "items": { - "$ref": "#/$defs/MetagenomeAnnotationActivity" - }, - "type": "array" - }, - "metagenome_assembly_set": { - "description": "This property links a database object to the set of metagenome assembly activities.", - "items": { - "$ref": "#/$defs/MetagenomeAssembly" - }, - "type": "array" - }, - "metagenome_sequencing_activity_set": { - "description": "This property links a database object to the set of metagenome sequencing activities.", - "items": { - "$ref": "#/$defs/MetagenomeSequencingActivity" - }, - "type": "array" - }, - "metaproteomics_analysis_activity_set": { - "description": "This property links a database object to the set of metaproteomics analysis activities.", - "items": { - "$ref": "#/$defs/MetaproteomicsAnalysisActivity" - }, - "type": "array" - }, - "metatranscriptome_activity_set": { - "description": "This property links a database object to the set of metatranscriptome analysis activities.", - "items": { - "$ref": "#/$defs/MetatranscriptomeActivity" - }, - "type": "array" - }, - "nom_analysis_activity_set": { - "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", - "items": { - "$ref": "#/$defs/NomAnalysisActivity" - }, - "type": "array" - }, - "omics_processing_set": { - "description": "This property links a database object to the set of omics processings within it.", - "items": { - "$ref": "#/$defs/OmicsProcessing" - }, - "type": "array" - }, - "planned_process_set": { - "description": "This property links a database object to the set of planned processes within it.", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/Extraction" - }, - { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - { - "$ref": "#/$defs/BiosampleProcessing" - }, - { - "$ref": "#/$defs/SubSamplingProcess" - }, - { - "$ref": "#/$defs/MixingProcess" - }, - { - "$ref": "#/$defs/FiltrationProcess" - }, - { - "$ref": "#/$defs/ChromatographicSeparationProcess" - }, - { - "$ref": "#/$defs/OmicsProcessing" - }, - { - "$ref": "#/$defs/Pooling" - }, - { - "$ref": "#/$defs/LibraryPreparation" - } - ] - }, - "type": "array" - }, - "pooling_set": { - "items": { - "$ref": "#/$defs/Pooling" - }, - "type": "array" - }, - "processed_sample_set": { - "description": "This property links a database object to the set of processed samples within it.", - "items": { - "$ref": "#/$defs/ProcessedSample" - }, - "type": "array" - }, - "read_based_taxonomy_analysis_activity_set": { - "description": "This property links a database object to the set of read based analysis activities.", - "items": { - "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" - }, - "type": "array" - }, - "read_qc_analysis_activity_set": { - "description": "This property links a database object to the set of read QC analysis activities.", - "items": { - "$ref": "#/$defs/ReadQcAnalysisActivity" - }, - "type": "array" - }, - "study_set": { - "description": "This property links a database object to the set of studies within it.", - "items": { - "$ref": "#/$defs/Study" - }, - "type": "array" - } - }, - "title": "NMDC", - "type": "object", - "version": "0.0.0" -} \ No newline at end of file diff --git a/nmdc_schema/nmdc_data.py b/nmdc_schema/nmdc_data.py index cbc8454285..afc825a37a 100755 --- a/nmdc_schema/nmdc_data.py +++ b/nmdc_schema/nmdc_data.py @@ -116,9 +116,8 @@ def get_nmdc_jsonschema_bytes(variant: Optional[SchemaVariantIdentifier] = None) >>> bytes_b = get_nmdc_jsonschema_bytes(variant=SchemaVariantIdentifier.nmdc_materialized_patterns) >>> type(bytes_b) is bytes and b"version" in bytes_b True - >>> len(bytes_b) > len(bytes_a) # assumes that including structured patterns makes the file larger - True """ + nmdc_json = get_nmdc_jsonschema_bytesIO(variant=variant) return nmdc_json.getvalue() @@ -137,9 +136,9 @@ def get_nmdc_jsonschema_string(variant: Optional[SchemaVariantIdentifier] = None >>> str_b = get_nmdc_jsonschema_string(variant=SchemaVariantIdentifier.nmdc_materialized_patterns) >>> type(str_b) is str and "version" in str_b True - >>> len(str_b) > len(str_a) # assumes that including structured patterns makes the file larger - True + """ + nmdc_json = get_nmdc_jsonschema_bytes(variant=variant) return nmdc_json.decode("utf-8") diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json deleted file mode 100644 index 97983ed69e..0000000000 --- a/nmdc_schema/nmdc_materialized_patterns.schema.json +++ /dev/null @@ -1,9575 +0,0 @@ -{ - "$defs": { - "AnalysisTypeEnum": { - "description": "", - "enum": [ - "metabolomics", - "metagenomics", - "metagenomics_long_read", - "metaproteomics", - "metatranscriptomics", - "natural organic matter", - "bulk chemistry" - ], - "title": "AnalysisTypeEnum", - "type": "string" - }, - "AnalyticalSample": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):ansm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AnalyticalSample", - "type": "object" - }, - "ArchStrucEnum": { - "description": "", - "enum": [ - "building", - "shed", - "home" - ], - "title": "ArchStrucEnum", - "type": "string" - }, - "AttributeValue": { - "additionalProperties": false, - "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "AttributeValue", - "type": "object" - }, - "BiolStatEnum": { - "description": "", - "enum": [ - "wild", - "natural", - "semi-natural", - "inbred line", - "breeder's line", - "hybrid", - "clonal selection", - "mutant" - ], - "title": "BiolStatEnum", - "type": "string" - }, - "Biosample": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "dna_cont_well": { - "pattern": ".+" - } - }, - "required": [ - "dna_cont_well" - ] - }, - "then": { - "properties": { - "dna_cont_type": { - "const": "plate" - } - }, - "required": [ - "dna_cont_type" - ] - } - }, - { - "if": { - "properties": { - "dna_cont_type": { - "const": "plate" - } - }, - "required": [ - "dna_cont_type" - ] - }, - "then": { - "properties": { - "dna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" - } - }, - "required": [ - "dna_cont_well" - ] - } - }, - { - "if": { - "properties": { - "rna_cont_well": { - "pattern": ".+" - } - }, - "required": [ - "rna_cont_well" - ] - }, - "then": { - "properties": { - "rna_cont_type": { - "const": "plate" - } - }, - "required": [ - "rna_cont_type" - ] - } - }, - { - "if": { - "properties": { - "rna_cont_type": { - "const": "plate" - } - }, - "required": [ - "rna_cont_type" - ] - }, - "then": { - "properties": { - "rna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" - } - }, - "required": [ - "rna_cont_well" - ] - } - } - ], - "description": "Biological source material which can be characterized by an experiment.", - "properties": { - "abs_air_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture" - }, - "add_date": { - "description": "The date on which the information was added to the database.", - "type": "string" - }, - "add_recov_method": { - "$ref": "#/$defs/TextValue", - "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "additional_info": { - "$ref": "#/$defs/TextValue", - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary" - }, - "address": { - "$ref": "#/$defs/TextValue", - "description": "The street name and building number where the sampling occurred." - }, - "adj_room": { - "$ref": "#/$defs/TextValue", - "description": "List of rooms (room number, room name) immediately adjacent to the sampling room" - }, - "aero_struc": { - "$ref": "#/$defs/TextValue", - "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together" - }, - "agrochem_addition": { - "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "air_PM_concen": { - "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "air_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the air at the time of sampling" - }, - "air_temp_regm": { - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "al_sat": { - "$ref": "#/$defs/QuantityValue", - "description": "The relative abundance of aluminum in the sample" - }, - "al_sat_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining Aluminum saturation" - }, - "alkalinity": { - "$ref": "#/$defs/QuantityValue", - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" - }, - "alkalinity_method": { - "$ref": "#/$defs/TextValue", - "description": "Method used for alkalinity measurement" - }, - "alkyl_diethers": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of alkyl diethers" - }, - "alt": { - "$ref": "#/$defs/QuantityValue", - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" - }, - "alternative_identifiers": { - "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "aminopept_act": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of aminopeptidase activity" - }, - "ammonium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ammonium in the sample" - }, - "ammonium_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ammonium nitrogen in the sample" - }, - "amount_light": { - "$ref": "#/$defs/QuantityValue", - "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area" - }, - "analysis_type": { - "description": "Select all the data types associated or available for this biosample", - "items": { - "$ref": "#/$defs/AnalysisTypeEnum" - }, - "type": "array" - }, - "ances_data": { - "$ref": "#/$defs/TextValue", - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)" - }, - "annual_precpt": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." - }, - "annual_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Mean annual temperature" - }, - "antibiotic_regm": { - "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "api": { - "$ref": "#/$defs/QuantityValue", - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)" - }, - "arch_struc": { - "$ref": "#/$defs/ArchStrucEnum", - "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction" - }, - "aromatics_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "asphaltenes_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "atmospheric_data": { - "description": "Measurement of atmospheric data; can include multiple data", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "avg_dew_point": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day" - }, - "avg_occup": { - "$ref": "#/$defs/TextValue", - "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room." - }, - "avg_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day" - }, - "bac_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Bacterial production in the water column measured by isotope uptake" - }, - "bac_resp": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of bacterial respiration in the water column" - }, - "bacteria_carb_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of bacterial carbon production" - }, - "barometric_press": { - "$ref": "#/$defs/QuantityValue", - "description": "Force per unit area exerted against a surface by the weight of air above that surface" - }, - "basin": { - "$ref": "#/$defs/TextValue", - "description": "Name of the basin (e.g. Campos)" - }, - "bathroom_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of bathrooms in the building" - }, - "bedroom_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of bedrooms in the building" - }, - "benzene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of benzene in the sample" - }, - "biochem_oxygen_dem": { - "$ref": "#/$defs/QuantityValue", - "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period" - }, - "biocide": { - "$ref": "#/$defs/TextValue", - "description": "List of biocides (commercial name of product and supplier) and date of administration" - }, - "biocide_admin_method": { - "$ref": "#/$defs/TextValue", - "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)" - }, - "biol_stat": { - "$ref": "#/$defs/BiolStatEnum", - "description": "The level of genome modification." - }, - "biomass": { - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "biosample_categories": { - "items": { - "$ref": "#/$defs/BiosampleCategoryEnum" - }, - "type": "array" - }, - "biotic_regm": { - "$ref": "#/$defs/TextValue", - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." - }, - "biotic_relationship": { - "$ref": "#/$defs/BioticRelationshipEnum", - "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" - }, - "bishomohopanol": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of bishomohopanol" - }, - "blood_press_diast": { - "$ref": "#/$defs/QuantityValue", - "description": "Resting diastolic blood pressure, measured as mm mercury" - }, - "blood_press_syst": { - "$ref": "#/$defs/QuantityValue", - "description": "Resting systolic blood pressure, measured as mm mercury" - }, - "bromide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of bromide" - }, - "build_docs": { - "$ref": "#/$defs/BuildDocsEnum", - "description": "The building design, construction and operation documents" - }, - "build_occup_type": { - "description": "The primary function for which a building or discrete part of a building is intended to be used", - "items": { - "$ref": "#/$defs/BuildOccupTypeEnum" - }, - "type": "array" - }, - "building_setting": { - "$ref": "#/$defs/BuildingSettingEnum", - "description": "A location (geography) where a building is set" - }, - "built_struc_age": { - "$ref": "#/$defs/QuantityValue", - "description": "The age of the built structure since construction" - }, - "built_struc_set": { - "$ref": "#/$defs/TextValue", - "description": "The characterization of the location of the built structure as high or low human density" - }, - "built_struc_type": { - "$ref": "#/$defs/TextValue", - "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads" - }, - "bulk_elect_conductivity": { - "$ref": "#/$defs/QuantityValue", - "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water." - }, - "calcium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of calcium in the sample" - }, - "carb_dioxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling" - }, - "carb_monoxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Carbon monoxide (gas) amount or concentration at the time of sampling" - }, - "carb_nitro_ratio": { - "$ref": "#/$defs/QuantityValue", - "description": "Ratio of amount or concentrations of carbon to nitrogen" - }, - "ceil_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The area of the ceiling space within the room" - }, - "ceil_cond": { - "$ref": "#/$defs/CeilCondEnum", - "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "ceil_finish_mat": { - "$ref": "#/$defs/CeilFinishMatEnum", - "description": "The type of material used to finish a ceiling" - }, - "ceil_struc": { - "$ref": "#/$defs/TextValue", - "description": "The construction format of the ceiling" - }, - "ceil_texture": { - "$ref": "#/$defs/CeilTextureEnum", - "description": "The feel, appearance, or consistency of a ceiling surface" - }, - "ceil_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow" - }, - "ceil_type": { - "$ref": "#/$defs/CeilTypeEnum", - "description": "The type of ceiling according to the ceiling's appearance or construction" - }, - "ceil_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on the ceiling" - }, - "chem_administration": { - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ] - }, - "type": "array" - }, - "chem_mutagen": { - "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "chem_oxygen_dem": { - "$ref": "#/$defs/QuantityValue", - "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite" - }, - "chem_treat_method": { - "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", - "type": "string" - }, - "chem_treatment": { - "$ref": "#/$defs/TextValue", - "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included" - }, - "chimera_check": { - "$ref": "#/$defs/TextValue", - "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." - }, - "chloride": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of chloride in the sample" - }, - "chlorophyll": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of chlorophyll" - }, - "climate_environment": { - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "collected_from": { - "description": "The Site from which a Biosample was collected", - "pattern": "^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "collection_date": { - "$ref": "#/$defs/TimestampValue", - "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" - }, - "collection_date_inc": { - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "type": "string" - }, - "collection_time": { - "description": "The time of sampling, either as an instance (single point) or interval.", - "type": "string" - }, - "collection_time_inc": { - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "type": "string" - }, - "community": { - "type": "string" - }, - "conduc": { - "$ref": "#/$defs/QuantityValue", - "description": "Electrical conductivity of water" - }, - "cool_syst_id": { - "$ref": "#/$defs/TextValue", - "description": "The cooling system identifier" - }, - "core_field": { - "description": "basic fields", - "type": "string" - }, - "crop_rotation": { - "$ref": "#/$defs/TextValue", - "description": "Whether or not crop is rotated, and if yes, rotation schedule" - }, - "cult_root_med": { - "$ref": "#/$defs/TextValue", - "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors." - }, - "cur_land_use": { - "$ref": "#/$defs/CurLandUseEnum", - "description": "Present state of sample site" - }, - "cur_vegetation": { - "$ref": "#/$defs/TextValue", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" - }, - "cur_vegetation_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in vegetation classification" - }, - "date_last_rain": { - "$ref": "#/$defs/TimestampValue", - "description": "The date of the last time it rained" - }, - "density": { - "$ref": "#/$defs/QuantityValue", - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" - }, - "depos_env": { - "$ref": "#/$defs/DeposEnvEnum", - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "depth": { - "$ref": "#/$defs/QuantityValue", - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "dew_point": { - "$ref": "#/$defs/QuantityValue", - "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water." - }, - "diether_lipids": { - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "diss_carb_dioxide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" - }, - "diss_hydrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved hydrogen" - }, - "diss_inorg_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" - }, - "diss_inorg_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved inorganic nitrogen" - }, - "diss_inorg_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved inorganic phosphorus in the sample" - }, - "diss_iron": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved iron in the sample" - }, - "diss_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" - }, - "diss_org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" - }, - "diss_oxygen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved oxygen" - }, - "diss_oxygen_fluid": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic)." - }, - "dna_absorb1": { - "description": "260/280 measurement of DNA sample purity", - "type": "number" - }, - "dna_absorb2": { - "description": "260/230 measurement of DNA sample purity", - "type": "number" - }, - "dna_collect_site": { - "description": "Provide information on the site your DNA sample was collected from", - "type": "string" - }, - "dna_concentration": { - "maximum": 2000, - "minimum": 0, - "type": "number" - }, - "dna_cont_type": { - "$ref": "#/$defs/JgiContTypeEnum", - "description": "Tube or plate (96-well)" - }, - "dna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", - "type": "string" - }, - "dna_container_id": { - "type": "string" - }, - "dna_dnase": { - "$ref": "#/$defs/YesNoEnum" - }, - "dna_isolate_meth": { - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "type": "string" - }, - "dna_organisms": { - "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", - "type": "string" - }, - "dna_project_contact": { - "type": "string" - }, - "dna_samp_id": { - "type": "string" - }, - "dna_sample_format": { - "$ref": "#/$defs/DNASampleFormatEnum", - "description": "Solution in which the DNA sample has been suspended" - }, - "dna_sample_name": { - "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "type": "string" - }, - "dna_seq_project": { - "type": "string" - }, - "dna_seq_project_name": { - "type": "string" - }, - "dna_seq_project_pi": { - "type": "string" - }, - "dna_volume": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "dnase_rna": { - "$ref": "#/$defs/YesNoEnum" - }, - "door_comp_type": { - "$ref": "#/$defs/DoorCompTypeEnum", - "description": "The composite type of the door" - }, - "door_cond": { - "$ref": "#/$defs/DoorCondEnum", - "description": "The phsical condition of the door" - }, - "door_direct": { - "$ref": "#/$defs/DoorDirectEnum", - "description": "The direction the door opens" - }, - "door_loc": { - "$ref": "#/$defs/DoorLocEnum", - "description": "The relative location of the door in the room" - }, - "door_mat": { - "$ref": "#/$defs/DoorMatEnum", - "description": "The material the door is composed of" - }, - "door_move": { - "$ref": "#/$defs/DoorMoveEnum", - "description": "The type of movement of the door" - }, - "door_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The size of the door" - }, - "door_type": { - "$ref": "#/$defs/DoorTypeEnum", - "description": "The type of door material" - }, - "door_type_metal": { - "$ref": "#/$defs/DoorTypeMetalEnum", - "description": "The type of metal door" - }, - "door_type_wood": { - "$ref": "#/$defs/DoorTypeWoodEnum", - "description": "The type of wood door" - }, - "door_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on a door" - }, - "down_par": { - "$ref": "#/$defs/QuantityValue", - "description": "Visible waveband radiance and irradiance measurements in the water column" - }, - "drainage_class": { - "$ref": "#/$defs/DrainageClassEnum", - "description": "Drainage classification from a standard system such as the USDA system" - }, - "drawings": { - "$ref": "#/$defs/DrawingsEnum", - "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents" - }, - "ecosystem": { - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_category": { - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_subtype": { - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_type": { - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "type": "string" - }, - "efficiency_percent": { - "$ref": "#/$defs/QuantityValue", - "description": "Percentage of volatile solids removed from the anaerobic digestor" - }, - "elev": { - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "type": "number" - }, - "elevator": { - "$ref": "#/$defs/TextValue", - "description": "The number of elevators within the built structure" - }, - "embargoed": { - "description": "If true, the data are embargoed and not available for public access.", - "type": "boolean" - }, - "emsl_biosample_identifiers": { - "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "emulsions": { - "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "env_broad_scale": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS" - }, - "env_local_scale": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS." - }, - "env_medium": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)." - }, - "env_package": { - "$ref": "#/$defs/TextValue", - "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" - }, - "environment_field": { - "description": "field describing environmental aspect of a sample", - "type": "string" - }, - "escalator": { - "$ref": "#/$defs/TextValue", - "description": "The number of escalators within the built structure" - }, - "ethylbenzene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of ethylbenzene in the sample" - }, - "exp_duct": { - "$ref": "#/$defs/QuantityValue", - "description": "The amount of exposed ductwork in the room" - }, - "exp_pipe": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of exposed pipes in the room" - }, - "experimental_factor": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI" - }, - "experimental_factor_other": { - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "type": "string" - }, - "ext_door": { - "$ref": "#/$defs/TextValue", - "description": "The number of exterior doors in the built structure" - }, - "ext_wall_orient": { - "$ref": "#/$defs/ExtWallOrientEnum", - "description": "The orientation of the exterior wall" - }, - "ext_window_orient": { - "$ref": "#/$defs/ExtWindowOrientEnum", - "description": "The compass direction the exterior window of the room is facing" - }, - "extreme_event": { - "description": "Unusual physical events that may have affected microbial populations", - "type": "string" - }, - "fao_class": { - "$ref": "#/$defs/FaoClassEnum", - "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" - }, - "fertilizer_regm": { - "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "field": { - "$ref": "#/$defs/TextValue", - "description": "Name of the hydrocarbon field (e.g. Albacora)" - }, - "filter_method": { - "description": "Type of filter used or how the sample was filtered", - "type": "string" - }, - "filter_type": { - "description": "A device which removes solid particulates or airborne molecular contaminants", - "items": { - "$ref": "#/$defs/FilterTypeEnum" - }, - "type": "array" - }, - "fire": { - "description": "Historical and/or physical evidence of fire", - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$", - "type": "string" - }, - "fireplace_type": { - "$ref": "#/$defs/TextValue", - "description": "A firebox with chimney" - }, - "flooding": { - "description": "Historical and/or physical evidence of flooding", - "type": "string" - }, - "floor_age": { - "$ref": "#/$defs/QuantityValue", - "description": "The time period since installment of the carpet or flooring" - }, - "floor_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The area of the floor space within the room" - }, - "floor_cond": { - "$ref": "#/$defs/FloorCondEnum", - "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "floor_count": { - "$ref": "#/$defs/TextValue", - "description": "The number of floors in the building, including basements and mechanical penthouse" - }, - "floor_finish_mat": { - "$ref": "#/$defs/FloorFinishMatEnum", - "description": "The floor covering type; the finished surface that is walked on" - }, - "floor_struc": { - "$ref": "#/$defs/FloorStrucEnum", - "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed" - }, - "floor_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the floor to provide inertia against temperature fluctuations" - }, - "floor_water_mold": { - "$ref": "#/$defs/FloorWaterMoldEnum", - "description": "Signs of the presence of mold or mildew in a room" - }, - "fluor": { - "$ref": "#/$defs/QuantityValue", - "description": "Raw or converted fluorescence of water" - }, - "freq_clean": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually." - }, - "freq_cook": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of times a meal is cooked per week" - }, - "fungicide_regm": { - "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "furniture": { - "$ref": "#/$defs/FurnitureEnum", - "description": "The types of furniture present in the sampled room" - }, - "gaseous_environment": { - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "gaseous_substances": { - "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "gender_restroom": { - "$ref": "#/$defs/GenderRestroomEnum", - "description": "The gender type of the restroom" - }, - "genetic_mod": { - "$ref": "#/$defs/TextValue", - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection" - }, - "geo_loc_name": { - "$ref": "#/$defs/TextValue", - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" - }, - "glucosidase_act": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of glucosidase activity" - }, - "gold_biosample_identifiers": { - "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", - "items": { - "pattern": "^gold:Gb[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "gravidity": { - "$ref": "#/$defs/TextValue", - "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used" - }, - "gravity": { - "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "growth_facil": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research" - }, - "growth_habit": { - "$ref": "#/$defs/GrowthHabitEnum", - "description": "Characteristic shape, appearance or growth form of a plant species" - }, - "growth_hormone_regm": { - "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "habitat": { - "type": "string" - }, - "hall_count": { - "$ref": "#/$defs/TextValue", - "description": "The total count of hallways and cooridors in the built structure" - }, - "handidness": { - "$ref": "#/$defs/HandidnessEnum", - "description": "The handidness of the individual sampled" - }, - "hc_produced": { - "$ref": "#/$defs/HcProducedEnum", - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr": { - "$ref": "#/$defs/HcrEnum", - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr_fw_salinity": { - "$ref": "#/$defs/QuantityValue", - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS" - }, - "hcr_geol_age": { - "$ref": "#/$defs/HcrGeolAgeEnum", - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "hcr_pressure": { - "$ref": "#/$defs/TextValue", - "description": "Original pressure of the hydrocarbon resource" - }, - "hcr_temp": { - "$ref": "#/$defs/TextValue", - "description": "Original temperature of the hydrocarbon resource" - }, - "heat_cool_type": { - "description": "Methods of conditioning or heating a room or building", - "items": { - "$ref": "#/$defs/HeatCoolTypeEnum" - }, - "type": "array" - }, - "heat_deliv_loc": { - "$ref": "#/$defs/HeatDelivLocEnum", - "description": "The location of heat delivery within the room" - }, - "heat_sys_deliv_meth": { - "description": "The method by which the heat is delivered through the system", - "type": "string" - }, - "heat_system_id": { - "$ref": "#/$defs/TextValue", - "description": "The heating system identifier" - }, - "heavy_metals": { - "description": "Heavy metals present in the sample and their concentrations.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "heavy_metals_meth": { - "description": "Reference or method used in determining heavy metals", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "height_carper_fiber": { - "$ref": "#/$defs/QuantityValue", - "description": "The average carpet fiber height in the indoor environment" - }, - "herbicide_regm": { - "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "horizon_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining the horizon" - }, - "host_age": { - "$ref": "#/$defs/QuantityValue", - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees" - }, - "host_body_habitat": { - "$ref": "#/$defs/TextValue", - "description": "Original body habitat where the sample was obtained from" - }, - "host_body_product": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon" - }, - "host_body_site": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON" - }, - "host_body_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Core body temperature of the host when sample was collected" - }, - "host_color": { - "$ref": "#/$defs/TextValue", - "description": "The color of host" - }, - "host_common_name": { - "$ref": "#/$defs/TextValue", - "description": "Common name of the host." - }, - "host_diet": { - "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "host_disease_stat": { - "$ref": "#/$defs/TextValue", - "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text" - }, - "host_dry_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of dry mass" - }, - "host_family_relation": { - "description": "Familial relationships to other hosts in the same study; can include multiple relationships", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_genotype": { - "$ref": "#/$defs/TextValue", - "description": "Observed genotype" - }, - "host_growth_cond": { - "$ref": "#/$defs/TextValue", - "description": "Literature reference giving growth conditions of the host" - }, - "host_height": { - "$ref": "#/$defs/QuantityValue", - "description": "The height of subject" - }, - "host_last_meal": { - "description": "Content of last meal and time since feeding; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "host_length": { - "$ref": "#/$defs/QuantityValue", - "description": "The length of subject" - }, - "host_life_stage": { - "$ref": "#/$defs/TextValue", - "description": "Description of life stage of host" - }, - "host_name": { - "type": "string" - }, - "host_phenotype": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP" - }, - "host_sex": { - "$ref": "#/$defs/HostSexEnum", - "description": "Gender or physical sex of the host." - }, - "host_shape": { - "$ref": "#/$defs/TextValue", - "description": "Morphological shape of host" - }, - "host_subject_id": { - "$ref": "#/$defs/TextValue", - "description": "A unique identifier by which each subject can be referred to, de-identified." - }, - "host_subspecf_genlin": { - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_substrate": { - "$ref": "#/$defs/TextValue", - "description": "The growth substrate of the host." - }, - "host_symbiont": { - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "items": { - "type": "string" - }, - "type": "array" - }, - "host_taxid": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "NCBI taxon id of the host, e.g. 9606" - }, - "host_tot_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Total mass of the host at collection, the unit depends on host" - }, - "host_wet_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of wet mass" - }, - "humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Amount of water vapour in the air, at the time of sampling" - }, - "humidity_regm": { - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "id": { - "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", - "pattern": "^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "igsn_biosample_identifiers": { - "description": "A list of identifiers for the biosample from the IGSN database.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "img_identifiers": { - "description": "A list of identifiers that relate the biosample to records in the IMG database.", - "items": { - "pattern": "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$", - "type": "string" - }, - "type": "array" - }, - "indoor_space": { - "$ref": "#/$defs/IndoorSpaceEnum", - "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" - }, - "indoor_surf": { - "$ref": "#/$defs/IndoorSurfEnum", - "description": "Type of indoor surface" - }, - "indust_eff_percent": { - "$ref": "#/$defs/QuantityValue", - "description": "Percentage of industrial effluents received by wastewater treatment plant" - }, - "infiltrations": { - "description": "The amount of time it takes to complete each infiltration activity", - "items": { - "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", - "type": "string" - }, - "type": "array" - }, - "inorg_particles": { - "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "insdc_biosample_identifiers": { - "description": "identifiers for corresponding sample in INSDC", - "items": { - "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "inside_lux": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded value at sampling time (power density)" - }, - "int_wall_cond": { - "$ref": "#/$defs/IntWallCondEnum", - "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" - }, - "investigation_field": { - "description": "field describing aspect of the investigation/study to which the sample belongs", - "type": "string" - }, - "isotope_exposure": { - "description": "List isotope exposure or addition applied to your sample.", - "type": "string" - }, - "iw_bt_date_well": { - "$ref": "#/$defs/TimestampValue", - "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery" - }, - "iwf": { - "$ref": "#/$defs/QuantityValue", - "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)" - }, - "last_clean": { - "$ref": "#/$defs/TimestampValue", - "description": "The last time the floor was cleaned (swept, mopped, vacuumed)" - }, - "lat_lon": { - "$ref": "#/$defs/GeolocationValue", - "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" - }, - "lbc_thirty": { - "$ref": "#/$defs/QuantityValue", - "description": "lime buffer capacity, determined after 30 minute incubation" - }, - "lbceq": { - "$ref": "#/$defs/QuantityValue", - "description": "lime buffer capacity, determined at equilibrium after 5 day incubation" - }, - "light_intensity": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of light intensity" - }, - "light_regm": { - "$ref": "#/$defs/TextValue", - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality." - }, - "light_type": { - "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", - "items": { - "$ref": "#/$defs/LightTypeEnum" - }, - "type": "array" - }, - "link_addit_analys": { - "$ref": "#/$defs/TextValue", - "description": "Link to additional analysis results performed on the sample" - }, - "link_class_info": { - "$ref": "#/$defs/TextValue", - "description": "Link to digitized soil maps or other soil classification information" - }, - "link_climate_info": { - "$ref": "#/$defs/TextValue", - "description": "Link to climate resource" - }, - "lithology": { - "$ref": "#/$defs/LithologyEnum", - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "local_class": { - "$ref": "#/$defs/TextValue", - "description": "Soil classification based on local soil classification system" - }, - "local_class_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining the local soil classification" - }, - "location": { - "type": "string" - }, - "magnesium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of magnesium in the sample" - }, - "manganese": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of manganese in the sample" - }, - "max_occup": { - "$ref": "#/$defs/QuantityValue", - "description": "The maximum amount of people allowed in the indoor environment" - }, - "mean_frict_vel": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of mean friction velocity" - }, - "mean_peak_frict_vel": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of mean peak friction velocity" - }, - "mech_struc": { - "$ref": "#/$defs/MechStrucEnum", - "description": "mechanical structure: a moving structure" - }, - "mechanical_damage": { - "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "methane": { - "$ref": "#/$defs/QuantityValue", - "description": "Methane (gas) amount or concentration at the time of sampling" - }, - "micro_biomass_c_meth": { - "description": "Reference or method used in determining microbial biomass carbon", - "type": "string" - }, - "micro_biomass_meth": { - "description": "Reference or method used in determining microbial biomass", - "type": "string" - }, - "micro_biomass_n_meth": { - "description": "Reference or method used in determining microbial biomass nitrogen", - "type": "string" - }, - "microbial_biomass": { - "$ref": "#/$defs/QuantityValue", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units" - }, - "microbial_biomass_c": { - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "type": "string" - }, - "microbial_biomass_n": { - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "type": "string" - }, - "mineral_nutr_regm": { - "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "misc_param": { - "description": "Any other measurement performed or parameter collected, that is not listed here", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "mod_date": { - "description": "The last date on which the database information was modified.", - "type": "string" - }, - "n_alkanes": { - "description": "Concentration of n-alkanes; can include multiple n-alkanes", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ncbi_taxonomy_name": { - "type": "string" - }, - "neon_biosample_identifiers": { - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "nitrate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrate in the sample" - }, - "nitrate_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrate nitrogen in the sample" - }, - "nitrite": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrite in the sample" - }, - "nitrite_nitrogen": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrite nitrogen in the sample" - }, - "nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of nitrogen (total)" - }, - "non_microb_biomass": { - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "type": "string" - }, - "non_microb_biomass_method": { - "description": "Reference or method used in determining biomass", - "type": "string" - }, - "non_min_nutr_regm": { - "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", - "items": { - "type": "string" - }, - "type": "array" - }, - "nucl_acid_amp": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" - }, - "nucl_acid_ext": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" - }, - "nucleic_acid_sequence_source_field": { - "type": "string" - }, - "number_pets": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of pets residing in the sampled space" - }, - "number_plants": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of plant(s) in the sampling space" - }, - "number_resident": { - "$ref": "#/$defs/QuantityValue", - "description": "The number of individuals currently occupying in the sampling location" - }, - "occup_density_samp": { - "$ref": "#/$defs/QuantityValue", - "description": "Average number of occupants at time of sampling per square footage" - }, - "occup_document": { - "$ref": "#/$defs/OccupDocumentEnum", - "description": "The type of documentation of occupancy" - }, - "occup_samp": { - "$ref": "#/$defs/QuantityValue", - "description": "Number of occupants present at time of sample within the given space" - }, - "org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic carbon" - }, - "org_count_qpcr_info": { - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "type": "string" - }, - "org_matter": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic matter" - }, - "org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of organic nitrogen" - }, - "org_nitro_method": { - "description": "Method used for obtaining organic nitrogen", - "type": "string" - }, - "org_particles": { - "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "organism_count": { - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "items": { - "$ref": "#/$defs/QuantityValue" - }, - "type": "array" - }, - "other_treatment": { - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "type": "string" - }, - "owc_tvdss": { - "$ref": "#/$defs/QuantityValue", - "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)" - }, - "oxy_stat_samp": { - "$ref": "#/$defs/OxyStatSampEnum", - "description": "Oxygenation status of sample" - }, - "oxygen": { - "$ref": "#/$defs/QuantityValue", - "description": "Oxygen (gas) amount or concentration at the time of sampling" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "pattern": "^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "part_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of particulate organic carbon" - }, - "part_org_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of particulate organic nitrogen" - }, - "particle_class": { - "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pcr_cond": { - "$ref": "#/$defs/TextValue", - "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" - }, - "pcr_primers": { - "$ref": "#/$defs/TextValue", - "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" - }, - "permeability": { - "$ref": "#/$defs/TextValue", - "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))" - }, - "perturbation": { - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pesticide_regm": { - "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "petroleum_hydrocarb": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of petroleum hydrocarbon" - }, - "ph": { - "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "type": "number" - }, - "ph_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining ph" - }, - "ph_regm": { - "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "phaeopigments": { - "description": "Concentration of phaeopigments; can include multiple phaeopigments", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "phosphate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of phosphate" - }, - "phosplipid_fatt_acid": { - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "photon_flux": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of photon flux" - }, - "plant_growth_med": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary" - }, - "plant_product": { - "$ref": "#/$defs/TextValue", - "description": "Substance produced by the plant, where the sample was obtained from" - }, - "plant_sex": { - "$ref": "#/$defs/PlantSexEnum", - "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite." - }, - "plant_struc": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here." - }, - "pollutants": { - "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "pool_dna_extracts": { - "$ref": "#/$defs/TextValue", - "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" - }, - "porosity": { - "$ref": "#/$defs/TextValue", - "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample" - }, - "potassium": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of potassium in the sample" - }, - "pour_point": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" - }, - "pre_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater" - }, - "pres_animal_insect": { - "description": "The type and number of animals or insects present in the sampling space.", - "pattern": "^(cat|dog|rodent|snake|other);\\d+$", - "type": "string" - }, - "pressure": { - "$ref": "#/$defs/QuantityValue", - "description": "Pressure to which the sample is subject to, in atmospheres" - }, - "prev_land_use_meth": { - "description": "Reference or method used in determining previous land use and dates", - "type": "string" - }, - "previous_land_use": { - "$ref": "#/$defs/TextValue", - "description": "Previous land use and dates" - }, - "primary_prod": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of primary production, generally measured as isotope uptake" - }, - "primary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed" - }, - "prod_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)" - }, - "prod_start_date": { - "$ref": "#/$defs/TimestampValue", - "description": "Date of field's first production" - }, - "profile_position": { - "$ref": "#/$defs/ProfilePositionEnum", - "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" - }, - "project_id": { - "description": "Proposal IDs or names associated with dataset", - "type": "string" - }, - "proport_woa_temperature": { - "type": "string" - }, - "proposal_dna": { - "type": "string" - }, - "proposal_rna": { - "type": "string" - }, - "quad_pos": { - "$ref": "#/$defs/QuadPosEnum", - "description": "The quadrant position of the sampling room within the building" - }, - "radiation_regm": { - "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "rainfall_regm": { - "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "reactor_type": { - "$ref": "#/$defs/TextValue", - "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage" - }, - "redox_potential": { - "$ref": "#/$defs/QuantityValue", - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" - }, - "rel_air_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air" - }, - "rel_humidity_out": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded outside relative humidity value at the time of sampling" - }, - "rel_samp_loc": { - "$ref": "#/$defs/RelSampLocEnum", - "description": "The sampling location within the train car" - }, - "replicate_number": { - "description": "If sending biological replicates, indicate the rep number here.", - "type": "string" - }, - "reservoir": { - "$ref": "#/$defs/TextValue", - "description": "Name of the reservoir (e.g. Carapebus)" - }, - "resins_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "rna_absorb1": { - "description": "260/280 measurement of RNA sample purity", - "type": "number" - }, - "rna_absorb2": { - "description": "260/230 measurement of RNA sample purity", - "type": "number" - }, - "rna_collect_site": { - "description": "Provide information on the site your RNA sample was collected from", - "type": "string" - }, - "rna_concentration": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "rna_cont_type": { - "$ref": "#/$defs/JgiContTypeEnum", - "description": "Tube or plate (96-well)" - }, - "rna_cont_well": { - "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", - "type": "string" - }, - "rna_container_id": { - "type": "string" - }, - "rna_isolate_meth": { - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "type": "string" - }, - "rna_organisms": { - "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", - "type": "string" - }, - "rna_project_contact": { - "type": "string" - }, - "rna_samp_id": { - "type": "string" - }, - "rna_sample_format": { - "$ref": "#/$defs/RNASampleFormatEnum", - "description": "Solution in which the RNA sample has been suspended" - }, - "rna_sample_name": { - "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "maximum": 2000, - "minimum": 0, - "type": "string" - }, - "rna_seq_project": { - "type": "string" - }, - "rna_seq_project_name": { - "type": "string" - }, - "rna_seq_project_pi": { - "type": "string" - }, - "rna_volume": { - "maximum": 1000, - "minimum": 0, - "type": "number" - }, - "room_air_exch_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "The rate at which outside air replaces indoor air in a given space" - }, - "room_architec_elem": { - "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", - "type": "string" - }, - "room_condt": { - "$ref": "#/$defs/RoomCondtEnum", - "description": "The condition of the room at the time of sampling" - }, - "room_connected": { - "$ref": "#/$defs/RoomConnectedEnum", - "description": "List of rooms connected to the sampling room by a doorway" - }, - "room_count": { - "$ref": "#/$defs/TextValue", - "description": "The total count of rooms in the built structure including all room types" - }, - "room_dim": { - "$ref": "#/$defs/TextValue", - "description": "The length, width and height of sampling room" - }, - "room_door_dist": { - "$ref": "#/$defs/TextValue", - "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms" - }, - "room_door_share": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) sharing a door with the sampling room" - }, - "room_hallway": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) located in the same hallway as sampling room" - }, - "room_loc": { - "$ref": "#/$defs/RoomLocEnum", - "description": "The position of the room within the building" - }, - "room_moist_dam_hist": { - "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", - "type": "integer" - }, - "room_net_area": { - "$ref": "#/$defs/TextValue", - "description": "The net floor area of sampling room. Net area excludes wall thicknesses" - }, - "room_occup": { - "$ref": "#/$defs/QuantityValue", - "description": "Count of room occupancy at time of sampling" - }, - "room_samp_pos": { - "$ref": "#/$defs/RoomSampPosEnum", - "description": "The horizontal sampling position in the room relative to architectural elements" - }, - "room_type": { - "$ref": "#/$defs/RoomTypeEnum", - "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure" - }, - "room_vol": { - "$ref": "#/$defs/TextValue", - "description": "Volume of sampling room" - }, - "room_wall_share": { - "$ref": "#/$defs/TextValue", - "description": "List of room(s) (room number, room name) sharing a wall with the sampling room" - }, - "room_window_count": { - "description": "Number of windows in the room", - "type": "integer" - }, - "root_cond": { - "$ref": "#/$defs/TextValue", - "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container." - }, - "root_med_carbon": { - "$ref": "#/$defs/TextValue", - "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose." - }, - "root_med_macronutr": { - "$ref": "#/$defs/TextValue", - "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L)." - }, - "root_med_micronutr": { - "$ref": "#/$defs/TextValue", - "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L)." - }, - "root_med_ph": { - "$ref": "#/$defs/QuantityValue", - "description": "pH measurement of the culture rooting medium; e.g. 5.5." - }, - "root_med_regl": { - "$ref": "#/$defs/TextValue", - "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA." - }, - "root_med_solid": { - "$ref": "#/$defs/TextValue", - "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar." - }, - "root_med_suppl": { - "$ref": "#/$defs/TextValue", - "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L)." - }, - "salinity": { - "$ref": "#/$defs/QuantityValue", - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." - }, - "salinity_category": { - "description": "Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", - "type": "string" - }, - "salinity_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining salinity" - }, - "salt_regm": { - "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "samp_capt_status": { - "$ref": "#/$defs/SampCaptStatusEnum", - "description": "Reason for the sample" - }, - "samp_collec_device": { - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "type": "string" - }, - "samp_collec_method": { - "description": "The method employed for collecting the sample.", - "type": "string" - }, - "samp_collect_point": { - "$ref": "#/$defs/SampCollectPointEnum", - "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_dis_stage": { - "$ref": "#/$defs/SampDisStageEnum", - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." - }, - "samp_floor": { - "$ref": "#/$defs/SampFloorEnum", - "description": "The floor of the building, where the sampling room is located" - }, - "samp_loc_corr_rate": { - "$ref": "#/$defs/TextValue", - "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays" - }, - "samp_mat_process": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." - }, - "samp_md": { - "$ref": "#/$defs/QuantityValue", - "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_name": { - "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", - "type": "string" - }, - "samp_preserv": { - "$ref": "#/$defs/TextValue", - "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)" - }, - "samp_room_id": { - "$ref": "#/$defs/TextValue", - "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans" - }, - "samp_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." - }, - "samp_sort_meth": { - "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "samp_store_dur": { - "$ref": "#/$defs/TextValue", - "description": "Duration for which the sample was stored" - }, - "samp_store_loc": { - "$ref": "#/$defs/TextValue", - "description": "Location at which sample was stored, usually name of a specific freezer/room" - }, - "samp_store_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature at which sample was stored, e.g. -80 degree Celsius" - }, - "samp_subtype": { - "$ref": "#/$defs/SampSubtypeEnum", - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "samp_taxon_id": { - "$ref": "#/$defs/ControlledIdentifiedTermValue", - "description": "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls." - }, - "samp_time_out": { - "$ref": "#/$defs/TextValue", - "description": "The recent and long term history of outside sampling" - }, - "samp_transport_cond": { - "$ref": "#/$defs/TextValue", - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)" - }, - "samp_tvdss": { - "$ref": "#/$defs/TextValue", - "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m" - }, - "samp_type": { - "$ref": "#/$defs/TextValue", - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)." - }, - "samp_vol_we_dna_ext": { - "$ref": "#/$defs/QuantityValue", - "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." - }, - "samp_weather": { - "$ref": "#/$defs/SampWeatherEnum", - "description": "The weather on the sampling day" - }, - "samp_well_name": { - "$ref": "#/$defs/TextValue", - "description": "Name of the well (e.g. BXA1123) where sample was taken" - }, - "sample_collection_site": { - "type": "string" - }, - "sample_link": { - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_shipped": { - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", - "type": "string" - }, - "sample_type": { - "$ref": "#/$defs/SampleTypeEnum", - "description": "Type of sample being submitted" - }, - "saturates_pc": { - "$ref": "#/$defs/TextValue", - "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" - }, - "season": { - "$ref": "#/$defs/TextValue", - "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)." - }, - "season_environment": { - "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "season_precpt": { - "$ref": "#/$defs/QuantityValue", - "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." - }, - "season_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Mean seasonal temperature" - }, - "season_use": { - "$ref": "#/$defs/SeasonUseEnum", - "description": "The seasons the space is occupied" - }, - "secondary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process for substantially degrading the biological content of the sewage" - }, - "sediment_type": { - "$ref": "#/$defs/SedimentTypeEnum", - "description": "Information about the sediment type based on major constituents" - }, - "seq_meth": { - "$ref": "#/$defs/TextValue", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." - }, - "seq_quality_check": { - "$ref": "#/$defs/TextValue", - "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" - }, - "sequencing_field": { - "type": "string" - }, - "sewage_type": { - "$ref": "#/$defs/TextValue", - "description": "Type of wastewater treatment plant as municipial or industrial" - }, - "shad_dev_water_mold": { - "description": "Signs of the presence of mold or mildew on the shading device", - "type": "string" - }, - "shading_device_cond": { - "$ref": "#/$defs/ShadingDeviceCondEnum", - "description": "The physical condition of the shading device at the time of sampling" - }, - "shading_device_loc": { - "$ref": "#/$defs/TextValue", - "description": "The location of the shading device in relation to the built structure" - }, - "shading_device_mat": { - "$ref": "#/$defs/TextValue", - "description": "The material the shading device is composed of" - }, - "shading_device_type": { - "$ref": "#/$defs/ShadingDeviceTypeEnum", - "description": "The type of shading device" - }, - "sieving": { - "$ref": "#/$defs/TextValue", - "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved" - }, - "silicate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of silicate" - }, - "size_frac": { - "$ref": "#/$defs/TextValue", - "description": "Filtering pore size used in sample preparation" - }, - "size_frac_low": { - "$ref": "#/$defs/QuantityValue", - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" - }, - "size_frac_up": { - "$ref": "#/$defs/QuantityValue", - "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" - }, - "slope_aspect": { - "$ref": "#/$defs/QuantityValue", - "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration." - }, - "slope_gradient": { - "$ref": "#/$defs/QuantityValue", - "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer" - }, - "sludge_retent_time": { - "$ref": "#/$defs/QuantityValue", - "description": "The time activated sludge remains in reactor" - }, - "sodium": { - "$ref": "#/$defs/QuantityValue", - "description": "Sodium concentration in the sample" - }, - "soil_horizon": { - "$ref": "#/$defs/SoilHorizonEnum", - "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath" - }, - "soil_text_measure": { - "$ref": "#/$defs/QuantityValue", - "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional." - }, - "soil_texture_meth": { - "description": "Reference or method used in determining soil texture", - "type": "string" - }, - "soil_type": { - "$ref": "#/$defs/TextValue", - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." - }, - "soil_type_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining soil series name or other lower-level classification" - }, - "solar_irradiance": { - "$ref": "#/$defs/QuantityValue", - "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval" - }, - "soluble_inorg_mat": { - "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "soluble_iron_micromol": { - "type": "string" - }, - "soluble_org_mat": { - "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "soluble_react_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of soluble reactive phosphorus" - }, - "source_mat_id": { - "$ref": "#/$defs/TextValue", - "description": "A globally unique identifier assigned to the biological sample." - }, - "space_typ_state": { - "$ref": "#/$defs/TextValue", - "description": "Customary or normal state of the space" - }, - "specific": { - "$ref": "#/$defs/SpecificEnum", - "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents" - }, - "specific_ecosystem": { - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "type": "string" - }, - "specific_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound." - }, - "sr_dep_env": { - "$ref": "#/$defs/SrDepEnvEnum", - "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_geol_age": { - "$ref": "#/$defs/SrGeolAgeEnum", - "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_kerog_type": { - "$ref": "#/$defs/SrKerogTypeEnum", - "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "sr_lithology": { - "$ref": "#/$defs/SrLithologyEnum", - "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" - }, - "standing_water_regm": { - "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "start_date_inc": { - "description": "Date the incubation was started. Only relevant for incubation samples.", - "type": "string" - }, - "start_time_inc": { - "description": "Time the incubation was started. Only relevant for incubation samples.", - "type": "string" - }, - "store_cond": { - "$ref": "#/$defs/TextValue", - "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." - }, - "substructure_type": { - "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", - "items": { - "$ref": "#/$defs/SubstructureTypeEnum" - }, - "type": "array" - }, - "subsurface_depth": { - "$ref": "#/$defs/QuantityValue" - }, - "sulfate": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of sulfate in the sample" - }, - "sulfate_fw": { - "$ref": "#/$defs/QuantityValue", - "description": "Original sulfate concentration in the hydrocarbon resource" - }, - "sulfide": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of sulfide in the sample" - }, - "surf_air_cont": { - "description": "Contaminant identified on surface", - "items": { - "$ref": "#/$defs/SurfAirContEnum" - }, - "type": "array" - }, - "surf_humidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Surfaces: water activity as a function of air and material moisture" - }, - "surf_material": { - "$ref": "#/$defs/SurfMaterialEnum", - "description": "Surface materials at the point of sampling" - }, - "surf_moisture": { - "$ref": "#/$defs/QuantityValue", - "description": "Water held on a surface" - }, - "surf_moisture_ph": { - "description": "ph measurement of surface", - "type": "number" - }, - "surf_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the surface at the time of sampling" - }, - "suspend_part_matter": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of suspended particulate matter" - }, - "suspend_solids": { - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "tan": { - "$ref": "#/$defs/QuantityValue", - "description": "Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" - }, - "target_gene": { - "$ref": "#/$defs/TextValue", - "description": "Targeted gene or locus name for marker gene studies" - }, - "target_subfragment": { - "$ref": "#/$defs/TextValue", - "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" - }, - "technical_reps": { - "description": "If sending technical replicates of the same sample, indicate the replicate count.", - "type": "string" - }, - "temp": { - "$ref": "#/$defs/QuantityValue", - "description": "Temperature of the sample at the time of sampling." - }, - "temp_out": { - "$ref": "#/$defs/QuantityValue", - "description": "The recorded temperature value at sampling time outside" - }, - "tertiary_treatment": { - "$ref": "#/$defs/TextValue", - "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment" - }, - "tidal_stage": { - "$ref": "#/$defs/TidalStageEnum", - "description": "Stage of tide" - }, - "tillage": { - "description": "Note method(s) used for tilling", - "items": { - "$ref": "#/$defs/TillageEnum" - }, - "type": "array" - }, - "tiss_cult_growth_med": { - "$ref": "#/$defs/TextValue", - "description": "Description of plant tissue culture growth media used" - }, - "toluene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of toluene in the sample" - }, - "tot_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Total carbon content" - }, - "tot_depth_water_col": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of total depth of water column" - }, - "tot_diss_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" - }, - "tot_inorg_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total inorganic nitrogen content" - }, - "tot_iron": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of total iron in the sample" - }, - "tot_nitro": { - "$ref": "#/$defs/QuantityValue", - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen" - }, - "tot_nitro_cont_meth": { - "description": "Reference or method used in determining the total nitrogen", - "type": "string" - }, - "tot_nitro_content": { - "$ref": "#/$defs/QuantityValue", - "description": "Total nitrogen content of the sample" - }, - "tot_org_c_meth": { - "$ref": "#/$defs/TextValue", - "description": "Reference or method used in determining total organic carbon" - }, - "tot_org_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" - }, - "tot_part_carb": { - "$ref": "#/$defs/QuantityValue", - "description": "Total particulate carbon content" - }, - "tot_phosp": { - "$ref": "#/$defs/QuantityValue", - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" - }, - "tot_phosphate": { - "$ref": "#/$defs/QuantityValue", - "description": "Total amount or concentration of phosphate" - }, - "tot_sulfur": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of total sulfur in the sample" - }, - "train_line": { - "$ref": "#/$defs/TrainLineEnum", - "description": "The subway line name" - }, - "train_stat_loc": { - "$ref": "#/$defs/TrainStatLocEnum", - "description": "The train station collection location" - }, - "train_stop_loc": { - "$ref": "#/$defs/TrainStopLocEnum", - "description": "The train stop collection location" - }, - "turbidity": { - "$ref": "#/$defs/QuantityValue", - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles" - }, - "tvdss_of_hcr_press": { - "$ref": "#/$defs/QuantityValue", - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m)." - }, - "tvdss_of_hcr_temp": { - "$ref": "#/$defs/QuantityValue", - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m)." - }, - "typ_occup_density": { - "description": "Customary or normal density of occupants", - "type": "number" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "ventilation_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Ventilation rate of the system in the sampled premises" - }, - "ventilation_type": { - "$ref": "#/$defs/TextValue", - "description": "Ventilation system used in the sampled premises" - }, - "vfa": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of Volatile Fatty Acids in the sample" - }, - "vfa_fw": { - "$ref": "#/$defs/QuantityValue", - "description": "Original volatile fatty acid concentration in the hydrocarbon resource" - }, - "vis_media": { - "$ref": "#/$defs/VisMediaEnum", - "description": "The building visual media" - }, - "viscosity": { - "$ref": "#/$defs/TextValue", - "description": "A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)" - }, - "volatile_org_comp": { - "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "wall_area": { - "$ref": "#/$defs/QuantityValue", - "description": "The total area of the sampled room's walls" - }, - "wall_const_type": { - "$ref": "#/$defs/WallConstTypeEnum", - "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating." - }, - "wall_finish_mat": { - "$ref": "#/$defs/WallFinishMatEnum", - "description": "The material utilized to finish the outer most layer of the wall" - }, - "wall_height": { - "$ref": "#/$defs/QuantityValue", - "description": "The average height of the walls in the sampled room" - }, - "wall_loc": { - "$ref": "#/$defs/WallLocEnum", - "description": "The relative location of the wall within the room" - }, - "wall_surf_treatment": { - "$ref": "#/$defs/WallSurfTreatmentEnum", - "description": "The surface treatment of interior wall" - }, - "wall_texture": { - "$ref": "#/$defs/WallTextureEnum", - "description": "The feel, appearance, or consistency of a wall surface" - }, - "wall_thermal_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint" - }, - "wall_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on a wall" - }, - "wastewater_type": { - "$ref": "#/$defs/TextValue", - "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc." - }, - "water_cont_soil_meth": { - "description": "Reference or method used in determining the water content of soil", - "type": "string" - }, - "water_content": { - "description": "Water content measurement", - "items": { - "type": "string" - }, - "type": "array" - }, - "water_current": { - "$ref": "#/$defs/QuantityValue", - "description": "Measurement of magnitude and direction of flow within a fluid" - }, - "water_cut": { - "$ref": "#/$defs/QuantityValue", - "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams" - }, - "water_feat_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The size of the water feature" - }, - "water_feat_type": { - "$ref": "#/$defs/WaterFeatTypeEnum", - "description": "The type of water feature present within the building being sampled" - }, - "water_prod_rate": { - "$ref": "#/$defs/QuantityValue", - "description": "Water production rates per well (e.g. 987 m3 / day)" - }, - "water_temp_regm": { - "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "watering_regm": { - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "items": { - "$ref": "#/$defs/TextValue" - }, - "type": "array" - }, - "weekday": { - "$ref": "#/$defs/WeekdayEnum", - "description": "The day of the week when sampling occurred" - }, - "win": { - "$ref": "#/$defs/TextValue", - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)" - }, - "wind_direction": { - "$ref": "#/$defs/TextValue", - "description": "Wind direction is the direction from which a wind originates" - }, - "wind_speed": { - "$ref": "#/$defs/QuantityValue", - "description": "Speed of wind measured at the time of sampling" - }, - "window_cond": { - "$ref": "#/$defs/WindowCondEnum", - "description": "The physical condition of the window at the time of sampling" - }, - "window_cover": { - "$ref": "#/$defs/WindowCoverEnum", - "description": "The type of window covering" - }, - "window_horiz_pos": { - "$ref": "#/$defs/WindowHorizPosEnum", - "description": "The horizontal position of the window on the wall" - }, - "window_loc": { - "$ref": "#/$defs/WindowLocEnum", - "description": "The relative location of the window within the room" - }, - "window_mat": { - "$ref": "#/$defs/WindowMatEnum", - "description": "The type of material used to finish a window" - }, - "window_open_freq": { - "$ref": "#/$defs/TextValue", - "description": "The number of times windows are opened per week" - }, - "window_size": { - "$ref": "#/$defs/TextValue", - "description": "The window's length and width" - }, - "window_status": { - "$ref": "#/$defs/TextValue", - "description": "Defines whether the windows were open or closed during environmental testing" - }, - "window_type": { - "$ref": "#/$defs/WindowTypeEnum", - "description": "The type of windows" - }, - "window_vert_pos": { - "$ref": "#/$defs/WindowVertPosEnum", - "description": "The vertical position of the window on the wall" - }, - "window_water_mold": { - "$ref": "#/$defs/TextValue", - "description": "Signs of the presence of mold or mildew on the window." - }, - "xylene": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of xylene in the sample" - }, - "zinc": { - "$ref": "#/$defs/QuantityValue", - "description": "Concentration of zinc in the sample" - } - }, - "required": [ - "part_of", - "id", - "env_broad_scale", - "env_local_scale", - "env_medium" - ], - "title": "Biosample", - "type": "object" - }, - "BiosampleCategoryEnum": { - "description": "Funding-based, sample location-based, or experimental method-based defined categories", - "enum": [ - "LTER", - "SIP", - "SFA", - "FICUS", - "NEON" - ], - "title": "BiosampleCategoryEnum", - "type": "string" - }, - "BiosampleProcessing": { - "additionalProperties": false, - "description": "A process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:BiosampleProcessing" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):bsmprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "BiosampleProcessing", - "type": "object" - }, - "BioticRelationshipEnum": { - "description": "", - "enum": [ - "free living", - "parasite", - "commensal", - "symbiont" - ], - "title": "BioticRelationshipEnum", - "type": "string" - }, - "BooleanValue": { - "additionalProperties": false, - "description": "A value that is a boolean", - "properties": { - "has_boolean_value": { - "description": "Links a quantity value to a boolean", - "type": "boolean" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "BooleanValue", - "type": "object" - }, - "BuildDocsEnum": { - "description": "", - "enum": [ - "building information model", - "commissioning report", - "complaint logs", - "contract administration", - "cost estimate", - "janitorial schedules or logs", - "maintenance plans", - "schedule", - "sections", - "shop drawings", - "submittals", - "ventilation system", - "windows" - ], - "title": "BuildDocsEnum", - "type": "string" - }, - "BuildOccupTypeEnum": { - "description": "", - "enum": [ - "office", - "market", - "restaurant", - "residence", - "school", - "residential", - "commercial", - "low rise", - "high rise", - "wood framed", - "health care", - "airport", - "sports complex" - ], - "title": "BuildOccupTypeEnum", - "type": "string" - }, - "BuildingSettingEnum": { - "description": "", - "enum": [ - "urban", - "suburban", - "exurban", - "rural" - ], - "title": "BuildingSettingEnum", - "type": "string" - }, - "CeilCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "CeilCondEnum", - "type": "string" - }, - "CeilFinishMatEnum": { - "description": "", - "enum": [ - "drywall", - "mineral fibre", - "tiles", - "PVC", - "plasterboard", - "metal", - "fiberglass", - "stucco", - "mineral wool/calcium silicate", - "wood" - ], - "title": "CeilFinishMatEnum", - "type": "string" - }, - "CeilTextureEnum": { - "description": "", - "enum": [ - "crows feet", - "crows-foot stomp", - "double skip", - "hawk and trowel", - "knockdown", - "popcorn", - "orange peel", - "rosebud stomp", - "Santa-Fe texture", - "skip trowel", - "smooth", - "stomp knockdown", - "swirl" - ], - "title": "CeilTextureEnum", - "type": "string" - }, - "CeilTypeEnum": { - "description": "", - "enum": [ - "cathedral", - "dropped", - "concave", - "barrel-shaped", - "coffered", - "cove", - "stretched" - ], - "title": "CeilTypeEnum", - "type": "string" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "chemical_formula": { - "description": "A generic grouping for molecular formulae and empirical formulae", - "type": "string" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "inchi": { - "type": "string" - }, - "inchi_key": { - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "smiles": { - "description": "A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ChromatographicSeparationProcess": { - "additionalProperties": false, - "description": "The process of using a selective partitioning of the analyte or interferent between two immiscible phases.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:ChromatographicSeparationProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ordered_mobile_phases": { - "description": "The solution(s) that moves through a chromatography column.", - "items": { - "$ref": "#/$defs/Solution" - }, - "type": "array" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "stationary_phase": { - "$ref": "#/$defs/StationaryPhaseEnum", - "description": "The material the stationary phase is comprised of used in chromatography." - }, - "temperature": { - "$ref": "#/$defs/QuantityValue", - "description": "The value of a temperature measurement or temperature used in a process." - } - }, - "required": [ - "id" - ], - "title": "ChromatographicSeparationProcess", - "type": "object" - }, - "CollectingBiosamplesFromSite": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:CollectingBiosamplesFromSite" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):(frsite|site)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):clsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "CollectingBiosamplesFromSite", - "type": "object" - }, - "CompoundEnum": { - "description": "", - "enum": [ - "ammonium bicarbonate", - "deionized water", - "methanol", - "trypsin", - "chloridic acid", - "water" - ], - "title": "CompoundEnum", - "type": "string" - }, - "ContainerCategoryEnum": { - "description": "The permitted types of containers used in processing metabolomic samples.", - "enum": [ - "V-bottom conical tube", - "falcon tube" - ], - "title": "ContainerCategoryEnum", - "type": "string" - }, - "ControlledIdentifiedTermValue": { - "additionalProperties": false, - "description": "A controlled term or class from an ontology, requiring the presence of term with an id", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "term": { - "anyOf": [ - { - "$ref": "#/$defs/OntologyClass" - }, - { - "$ref": "#/$defs/EnvironmentalMaterialTerm" - }, - { - "$ref": "#/$defs/ChemicalEntity" - }, - { - "$ref": "#/$defs/Pathway" - }, - { - "$ref": "#/$defs/Reaction" - }, - { - "$ref": "#/$defs/OrthologyGroup" - } - ], - "description": "pointer to an ontology class" - } - }, - "required": [ - "term" - ], - "title": "ControlledIdentifiedTermValue", - "type": "object" - }, - "ControlledTermValue": { - "additionalProperties": false, - "description": "A controlled term or class from an ontology", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "term": { - "anyOf": [ - { - "$ref": "#/$defs/OntologyClass" - }, - { - "$ref": "#/$defs/EnvironmentalMaterialTerm" - }, - { - "$ref": "#/$defs/ChemicalEntity" - }, - { - "$ref": "#/$defs/Pathway" - }, - { - "$ref": "#/$defs/Reaction" - }, - { - "$ref": "#/$defs/OrthologyGroup" - } - ], - "description": "pointer to an ontology class" - } - }, - "title": "ControlledTermValue", - "type": "object" - }, - "CreditAssociation": { - "additionalProperties": false, - "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", - "properties": { - "applied_roles": { - "items": { - "$ref": "#/$defs/CreditEnum" - }, - "type": "array" - }, - "applies_to_person": { - "$ref": "#/$defs/PersonValue" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "required": [ - "applies_to_person", - "applied_roles" - ], - "title": "CreditAssociation", - "type": "object" - }, - "CreditEnum": { - "description": "", - "enum": [ - "Conceptualization", - "Data curation", - "Formal Analysis", - "Funding acquisition", - "Investigation", - "Methodology", - "Project administration", - "Resources", - "Software", - "Supervision", - "Validation", - "Visualization", - "Writing original draft", - "Writing review and editing", - "Principal Investigator", - "Submitter" - ], - "title": "CreditEnum", - "type": "string" - }, - "CurLandUseEnum": { - "description": "", - "enum": [ - "badlands", - "cities", - "conifers", - "crop trees", - "farmstead", - "gravel", - "hardwoods", - "hayland", - "horticultural plants", - "industrial areas", - "intermixed hardwood and conifers", - "marshlands", - "meadows", - "mines/quarries", - "mudflats", - "oil waste areas", - "pastureland", - "permanent snow or ice", - "rainforest", - "rangeland", - "roads/railroads", - "rock", - "row crops", - "saline seeps", - "salt flats", - "sand", - "shrub crops", - "shrub land", - "small grains", - "successional shrub land", - "swamp", - "tropical", - "tundra", - "vegetable crops", - "vine crops" - ], - "title": "CurLandUseEnum", - "type": "string" - }, - "DNASampleFormatEnum": { - "description": "", - "enum": [ - "10 mM Tris-HCl", - "DNAStable", - "Ethanol", - "Low EDTA TE", - "MDA reaction buffer", - "PBS", - "Pellet", - "RNAStable", - "TE", - "Water", - "Gentegra-DNA", - "Gentegra-RNA" - ], - "title": "DNASampleFormatEnum", - "type": "string" - }, - "DataObject": { - "additionalProperties": false, - "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "compression_type": { - "description": "If provided, specifies the compression type", - "type": "string" - }, - "data_object_type": { - "$ref": "#/$defs/FileTypeEnum", - "description": "The type of file represented by the data object." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "file_size_bytes": { - "description": "Size of the file in bytes", - "type": "integer" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "md5_checksum": { - "description": "MD5 checksum of file (pre-compressed)", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "url": { - "type": "string" - }, - "was_generated_by": { - "pattern": "^^(nmdc):(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$|^^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "id", - "name", - "description" - ], - "title": "DataObject", - "type": "object" - }, - "Database": { - "additionalProperties": false, - "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", - "properties": { - "biosample_set": { - "description": "This property links a database object to the set of samples within it.", - "items": { - "$ref": "#/$defs/Biosample" - }, - "type": "array" - }, - "collecting_biosamples_from_site_set": { - "items": { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - "type": "array" - }, - "data_object_set": { - "description": "This property links a database object to the set of data objects within it.", - "items": { - "$ref": "#/$defs/DataObject" - }, - "type": "array" - }, - "extraction_set": { - "description": "This property links a database object to the set of extractions within it.", - "items": { - "$ref": "#/$defs/Extraction" - }, - "type": "array" - }, - "field_research_site_set": { - "items": { - "$ref": "#/$defs/FieldResearchSite" - }, - "type": "array" - }, - "functional_annotation_agg": { - "items": { - "$ref": "#/$defs/FunctionalAnnotationAggMember" - }, - "type": "array" - }, - "functional_annotation_set": { - "description": "This property links a database object to the set of all functional annotations", - "items": { - "$ref": "#/$defs/FunctionalAnnotation" - }, - "type": "array" - }, - "genome_feature_set": { - "description": "This property links a database object to the set of all features", - "items": { - "$ref": "#/$defs/GenomeFeature" - }, - "type": "array" - }, - "library_preparation_set": { - "description": "This property links a database object to the set of DNA extractions within it.", - "items": { - "$ref": "#/$defs/LibraryPreparation" - }, - "type": "array" - }, - "mags_activity_set": { - "description": "This property links a database object to the set of MAGs analysis activities.", - "items": { - "$ref": "#/$defs/MagsAnalysisActivity" - }, - "type": "array" - }, - "metabolomics_analysis_activity_set": { - "description": "This property links a database object to the set of metabolomics analysis activities.", - "items": { - "$ref": "#/$defs/MetabolomicsAnalysisActivity" - }, - "type": "array" - }, - "metagenome_annotation_activity_set": { - "description": "This property links a database object to the set of metagenome annotation activities.", - "items": { - "$ref": "#/$defs/MetagenomeAnnotationActivity" - }, - "type": "array" - }, - "metagenome_assembly_set": { - "description": "This property links a database object to the set of metagenome assembly activities.", - "items": { - "$ref": "#/$defs/MetagenomeAssembly" - }, - "type": "array" - }, - "metagenome_sequencing_activity_set": { - "description": "This property links a database object to the set of metagenome sequencing activities.", - "items": { - "$ref": "#/$defs/MetagenomeSequencingActivity" - }, - "type": "array" - }, - "metaproteomics_analysis_activity_set": { - "description": "This property links a database object to the set of metaproteomics analysis activities.", - "items": { - "$ref": "#/$defs/MetaproteomicsAnalysisActivity" - }, - "type": "array" - }, - "metatranscriptome_activity_set": { - "description": "This property links a database object to the set of metatranscriptome analysis activities.", - "items": { - "$ref": "#/$defs/MetatranscriptomeActivity" - }, - "type": "array" - }, - "nom_analysis_activity_set": { - "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", - "items": { - "$ref": "#/$defs/NomAnalysisActivity" - }, - "type": "array" - }, - "omics_processing_set": { - "description": "This property links a database object to the set of omics processings within it.", - "items": { - "$ref": "#/$defs/OmicsProcessing" - }, - "type": "array" - }, - "planned_process_set": { - "description": "This property links a database object to the set of planned processes within it.", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/Extraction" - }, - { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - { - "$ref": "#/$defs/BiosampleProcessing" - }, - { - "$ref": "#/$defs/SubSamplingProcess" - }, - { - "$ref": "#/$defs/MixingProcess" - }, - { - "$ref": "#/$defs/FiltrationProcess" - }, - { - "$ref": "#/$defs/ChromatographicSeparationProcess" - }, - { - "$ref": "#/$defs/OmicsProcessing" - }, - { - "$ref": "#/$defs/Pooling" - }, - { - "$ref": "#/$defs/LibraryPreparation" - } - ] - }, - "type": "array" - }, - "pooling_set": { - "items": { - "$ref": "#/$defs/Pooling" - }, - "type": "array" - }, - "processed_sample_set": { - "description": "This property links a database object to the set of processed samples within it.", - "items": { - "$ref": "#/$defs/ProcessedSample" - }, - "type": "array" - }, - "read_based_taxonomy_analysis_activity_set": { - "description": "This property links a database object to the set of read based analysis activities.", - "items": { - "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" - }, - "type": "array" - }, - "read_qc_analysis_activity_set": { - "description": "This property links a database object to the set of read QC analysis activities.", - "items": { - "$ref": "#/$defs/ReadQcAnalysisActivity" - }, - "type": "array" - }, - "study_set": { - "description": "This property links a database object to the set of studies within it.", - "items": { - "$ref": "#/$defs/Study" - }, - "type": "array" - } - }, - "title": "Database", - "type": "object" - }, - "DeposEnvEnum": { - "description": "", - "enum": [ - "Continental - Alluvial", - "Continental - Aeolian", - "Continental - Fluvial", - "Continental - Lacustrine", - "Transitional - Deltaic", - "Transitional - Tidal", - "Transitional - Lagoonal", - "Transitional - Beach", - "Transitional - Lake", - "Marine - Shallow", - "Marine - Deep", - "Marine - Reef", - "Other - Evaporite", - "Other - Glacial", - "Other - Volcanic", - "other" - ], - "title": "DeposEnvEnum", - "type": "string" - }, - "DeviceEnum": { - "description": "", - "enum": [ - "Orbital Shaker", - "Thermomixer", - "Vortex", - "Agitation plunger", - "Drying oven", - "CEREX System 96 processor" - ], - "title": "DeviceEnum", - "type": "string" - }, - "Doi": { - "additionalProperties": false, - "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.", - "if": { - "properties": { - "doi_category": { - "anyOf": [ - { - "const": "dataset_doi" - }, - { - "const": "award_doi" - } - ] - } - }, - "required": [ - "doi_category" - ] - }, - "properties": { - "doi_category": { - "$ref": "#/$defs/DoiCategoryEnum", - "description": "The resource type the corresponding doi resolves to." - }, - "doi_provider": { - "$ref": "#/$defs/DoiProviderEnum", - "description": "The authority, or organization, the DOI is associated with." - }, - "doi_value": { - "description": "A digital object identifier, which is intended to persistantly identify some resource on the web.", - "pattern": "^doi:10.\\d{2,9}/.*$", - "type": "string" - } - }, - "required": [ - "doi_value", - "doi_category" - ], - "then": { - "properties": { - "doi_provider": {} - }, - "required": [ - "doi_provider" - ] - }, - "title": "Doi", - "type": "object" - }, - "DoiCategoryEnum": { - "description": "", - "enum": [ - "award_doi", - "dataset_doi", - "publication_doi", - "data_management_plan_doi" - ], - "title": "DoiCategoryEnum", - "type": "string" - }, - "DoiProviderEnum": { - "description": "", - "enum": [ - "emsl", - "jgi", - "kbase", - "osti", - "ess_dive", - "massive", - "gsc", - "zenodo", - "edi" - ], - "title": "DoiProviderEnum", - "type": "string" - }, - "DoorCompTypeEnum": { - "description": "", - "enum": [ - "metal covered", - "revolving", - "sliding", - "telescopic" - ], - "title": "DoorCompTypeEnum", - "type": "string" - }, - "DoorCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "DoorCondEnum", - "type": "string" - }, - "DoorDirectEnum": { - "description": "", - "enum": [ - "inward", - "outward", - "sideways" - ], - "title": "DoorDirectEnum", - "type": "string" - }, - "DoorLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "DoorLocEnum", - "type": "string" - }, - "DoorMatEnum": { - "description": "", - "enum": [ - "aluminum", - "cellular PVC", - "engineered plastic", - "fiberboard", - "fiberglass", - "metal", - "thermoplastic alloy", - "vinyl", - "wood", - "wood/plastic composite" - ], - "title": "DoorMatEnum", - "type": "string" - }, - "DoorMoveEnum": { - "description": "", - "enum": [ - "collapsible", - "folding", - "revolving", - "rolling shutter", - "sliding", - "swinging" - ], - "title": "DoorMoveEnum", - "type": "string" - }, - "DoorTypeEnum": { - "description": "", - "enum": [ - "composite", - "metal", - "wooden" - ], - "title": "DoorTypeEnum", - "type": "string" - }, - "DoorTypeMetalEnum": { - "description": "", - "enum": [ - "collapsible", - "corrugated steel", - "hollow", - "rolling shutters", - "steel plate" - ], - "title": "DoorTypeMetalEnum", - "type": "string" - }, - "DoorTypeWoodEnum": { - "description": "", - "enum": [ - "bettened and ledged", - "battened", - "ledged and braced", - "ledged and framed", - "ledged, braced and frame", - "framed and paneled", - "glashed or sash", - "flush", - "louvered", - "wire gauged" - ], - "title": "DoorTypeWoodEnum", - "type": "string" - }, - "DrainageClassEnum": { - "description": "", - "enum": [ - "very poorly", - "poorly", - "somewhat poorly", - "moderately well", - "well", - "excessively drained" - ], - "title": "DrainageClassEnum", - "type": "string" - }, - "DrawingsEnum": { - "description": "", - "enum": [ - "operation", - "as built", - "construction", - "bid", - "design", - "building navigation map", - "diagram", - "sketch" - ], - "title": "DrawingsEnum", - "type": "string" - }, - "EnvironmentalMaterialTerm": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterialTerm", - "type": "object" - }, - "ExtWallOrientEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west", - "northeast", - "southeast", - "southwest", - "northwest" - ], - "title": "ExtWallOrientEnum", - "type": "string" - }, - "ExtWindowOrientEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west", - "northeast", - "southeast", - "southwest", - "northwest" - ], - "title": "ExtWindowOrientEnum", - "type": "string" - }, - "Extraction": { - "additionalProperties": false, - "description": "A material separation in which a desired component of an input material is separated from the remainder.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:Extraction" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "extractant": { - "$ref": "#/$defs/Solution", - "description": "The active component(s) primarily responsible for transfer of a solute from one phase to the other." - }, - "extraction_method": { - "$ref": "#/$defs/ExtractionTargetEnum" - }, - "extraction_target": { - "$ref": "#/$defs/ExtractionTargetEnum" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):extrp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "input_mass": { - "$ref": "#/$defs/QuantityValue", - "description": "Total mass of sample used in activity." - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the solvent/solute being used, not the input." - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "Extraction", - "type": "object" - }, - "ExtractionTargetEnum": { - "description": "", - "enum": [ - "DNA", - "RNA", - "metabolite", - "protein" - ], - "title": "ExtractionTargetEnum", - "type": "string" - }, - "FailureCategorization": { - "additionalProperties": false, - "description": "", - "properties": { - "qc_failure_what": { - "$ref": "#/$defs/FailureWhatEnum", - "description": "Provides a summary about what caused a lab or workflow process to fail" - }, - "qc_failure_where": { - "$ref": "#/$defs/FailureWhereEnum", - "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." - } - }, - "title": "FailureCategorization", - "type": "object" - }, - "FailureWhatEnum": { - "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", - "enum": [ - "low_read_count", - "malformed_data", - "assembly_size_too_small", - "no_valid_data_generated", - "other" - ], - "title": "FailureWhatEnum", - "type": "string" - }, - "FailureWhereEnum": { - "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", - "enum": [ - "OmicsProcessing", - "Pooling", - "Extraction", - "LibraryPreparation", - "MetagenomeAssembly", - "MetatranscriptomeActivity", - "MagsAnalysisActivity", - "ReadQcAnalysisActivity", - "ReadBasedTaxonomyAnalysisActivity", - "MetagenomeAnnotationActivity" - ], - "title": "FailureWhereEnum", - "type": "string" - }, - "FaoClassEnum": { - "description": "", - "enum": [ - "Acrisols", - "Andosols", - "Arenosols", - "Cambisols", - "Chernozems", - "Ferralsols", - "Fluvisols", - "Gleysols", - "Greyzems", - "Gypsisols", - "Histosols", - "Kastanozems", - "Lithosols", - "Luvisols", - "Nitosols", - "Phaeozems", - "Planosols", - "Podzols", - "Podzoluvisols", - "Rankers", - "Regosols", - "Rendzinas", - "Solonchaks", - "Solonetz", - "Vertisols", - "Yermosols" - ], - "title": "FaoClassEnum", - "type": "string" - }, - "FieldResearchSite": { - "additionalProperties": false, - "description": "A site, outside of a laboratory, from which biosamples may be collected.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "cur_vegetation": { - "$ref": "#/$defs/TextValue", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "elev": { - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "type": "number" - }, - "geo_loc_name": { - "$ref": "#/$defs/TextValue", - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" - }, - "habitat": { - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "lat_lon": { - "$ref": "#/$defs/GeolocationValue", - "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" - }, - "local_class": { - "$ref": "#/$defs/TextValue", - "description": "Soil classification based on local soil classification system" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "pattern": "^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "soil_type": { - "$ref": "#/$defs/TextValue", - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." - } - }, - "required": [ - "id" - ], - "title": "FieldResearchSite", - "type": "object" - }, - "FileTypeEnum": { - "description": "", - "enum": [ - "Metagenome Raw Reads", - "Metagenome Raw Read 1", - "Metagenome Raw Read 2", - "FT ICR-MS Analysis Results", - "GC-MS Metabolomics Results", - "Metaproteomics Workflow Statistics", - "Protein Report", - "Peptide Report", - "Unfiltered Metaproteomics Results", - "Read Count and RPKM", - "QC non-rRNA R2", - "QC non-rRNA R1", - "Metagenome Bins", - "Metagenome HQMQ Bins Compression File", - "Metagenome LQ Bins Compression File", - "Metagenome Bins Info File", - "CheckM Statistics", - "Metagenome Bins Heatmap", - "Metagenome Bins Barplot", - "Metagenome Bins Krona Plot", - "Read Based Analysis Info File", - "GTDBTK Bacterial Summary", - "GTDBTK Archaeal Summary", - "GOTTCHA2 Krona Plot", - "GOTTCHA2 Classification Report", - "GOTTCHA2 Report Full", - "Kraken2 Krona Plot", - "Centrifuge Krona Plot", - "Centrifuge output report file", - "Kraken2 Classification Report", - "Kraken2 Taxonomic Classification", - "Centrifuge Classification Report", - "Centrifuge Taxonomic Classification", - "Structural Annotation GFF", - "Structural Annotation Stats Json", - "Functional Annotation GFF", - "Annotation Info File", - "Annotation Amino Acid FASTA", - "Annotation Enzyme Commission", - "Annotation KEGG Orthology", - "Assembly Info File", - "Assembly Coverage BAM", - "Assembly AGP", - "Assembly Scaffolds", - "Assembly Contigs", - "Assembly Coverage Stats", - "Contig Mapping File", - "Error Corrected Reads", - "Filtered Sequencing Reads", - "Read Filtering Info File", - "QC Statistics Extended", - "QC Statistics", - "TIGRFam Annotation GFF", - "CRT Annotation GFF", - "Genemark Annotation GFF", - "Prodigal Annotation GFF", - "TRNA Annotation GFF", - "Misc Annotation GFF", - "RFAM Annotation GFF", - "TMRNA Annotation GFF", - "Crispr Terms", - "Product Names", - "Gene Phylogeny tsv", - "Scaffold Lineage tsv", - "Clusters of Orthologous Groups (COG) Annotation GFF", - "KO_EC Annotation GFF", - "CATH FunFams (Functional Families) Annotation GFF", - "SUPERFam Annotation GFF", - "SMART Annotation GFF", - "Pfam Annotation GFF", - "Annotation Statistics", - "Direct Infusion FT ICR-MS Raw Data", - "LC-DDA-MS/MS Raw Data" - ], - "title": "FileTypeEnum", - "type": "string" - }, - "FilterTypeEnum": { - "description": "", - "enum": [ - "particulate air filter", - "chemical air filter", - "low-MERV pleated media", - "HEPA", - "electrostatic", - "gas-phase or ultraviolet air treatments" - ], - "title": "FilterTypeEnum", - "type": "string" - }, - "FiltrationProcess": { - "additionalProperties": false, - "description": "The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "conditionings": { - "description": "Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.", - "items": { - "type": "string" - }, - "type": "array" - }, - "container_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the container an analyte is stored in or an activity takes place in" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:FiltrationProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "filter_material": { - "description": "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.", - "type": "string" - }, - "filter_pore_size": { - "$ref": "#/$defs/QuantityValue", - "description": "A quantitative or qualitative measurement of the physical dimensions of the pores in a material." - }, - "filtration_category": { - "description": "The type of conditioning applied to a filter, device, etc.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):filtpr-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "is_pressurized": { - "description": "Whether or not pressure was applied to a thing or process.", - "type": "boolean" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "separation_method": { - "$ref": "#/$defs/SeparationMethodEnum", - "description": "The method that was used to separate a substance from a solution or mixture." - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of sample filtered." - } - }, - "required": [ - "id" - ], - "title": "FiltrationProcess", - "type": "object" - }, - "FloorCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "FloorCondEnum", - "type": "string" - }, - "FloorFinishMatEnum": { - "description": "", - "enum": [ - "tile", - "wood strip or parquet", - "carpet", - "rug", - "laminate wood", - "lineoleum", - "vinyl composition tile", - "sheet vinyl", - "stone", - "bamboo", - "cork", - "terrazo", - "concrete", - "none", - "sealed", - "clear finish", - "paint", - "none or unfinished" - ], - "title": "FloorFinishMatEnum", - "type": "string" - }, - "FloorStrucEnum": { - "description": "", - "enum": [ - "balcony", - "floating floor", - "glass floor", - "raised floor", - "sprung floor", - "wood-framed", - "concrete" - ], - "title": "FloorStrucEnum", - "type": "string" - }, - "FloorWaterMoldEnum": { - "description": "", - "enum": [ - "mold odor", - "wet floor", - "water stains", - "wall discoloration", - "floor discoloration", - "ceiling discoloration", - "peeling paint or wallpaper", - "bulging walls", - "condensation" - ], - "title": "FloorWaterMoldEnum", - "type": "string" - }, - "FreqCleanEnum": { - "description": "", - "enum": [ - "Daily", - "Weekly", - "Monthly", - "Quarterly", - "Annually", - "other" - ], - "title": "FreqCleanEnum", - "type": "string" - }, - "FunctionalAnnotation": { - "additionalProperties": false, - "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", - "properties": { - "has_function": { - "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", - "type": "string" - }, - "subject": { - "type": "string" - }, - "was_generated_by": { - "description": "provenance for the annotation.", - "pattern": "^(nmdc):(wfmgan)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - } - }, - "title": "FunctionalAnnotation", - "type": "object" - }, - "FunctionalAnnotationAggMember": { - "additionalProperties": false, - "description": "", - "properties": { - "count": { - "type": "integer" - }, - "gene_function_id": { - "description": "The identifier for the gene function.", - "type": "string" - }, - "metagenome_annotation_id": { - "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", - "pattern": "^(nmdc):(wfmgan)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "metagenome_annotation_id", - "gene_function_id", - "count" - ], - "title": "FunctionalAnnotationAggMember", - "type": "object" - }, - "FurnitureEnum": { - "description": "", - "enum": [ - "cabinet", - "chair", - "desks" - ], - "title": "FurnitureEnum", - "type": "string" - }, - "GenderRestroomEnum": { - "description": "", - "enum": [ - "all gender", - "female", - "gender neurtral", - "male", - "male and female", - "unisex" - ], - "title": "GenderRestroomEnum", - "type": "string" - }, - "GeneProduct": { - "additionalProperties": false, - "description": "A molecule encoded by a gene that has an evolved function", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneProduct", - "type": "object" - }, - "GenomeFeature": { - "additionalProperties": false, - "description": "A feature localized to an interval along a genome", - "properties": { - "encodes": { - "description": "The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA", - "type": "string" - }, - "end": { - "description": "The end of the feature in positive 1-based integer coordinates", - "minimum": 1, - "type": "integer" - }, - "feature_type": { - "description": "TODO: Yuri to write", - "type": "string" - }, - "phase": { - "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.", - "maximum": 2, - "minimum": 0, - "type": "integer" - }, - "seqid": { - "description": "The ID of the landmark used to establish the coordinate system for the current feature.", - "type": "string" - }, - "start": { - "description": "The start of the feature in positive 1-based integer coordinates", - "minimum": 1, - "type": "integer" - }, - "strand": { - "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).", - "type": "string" - } - }, - "required": [ - "end", - "seqid", - "start" - ], - "title": "GenomeFeature", - "type": "object" - }, - "GeolocationValue": { - "additionalProperties": false, - "description": "A normalized value for a location on the earth's surface", - "properties": { - "has_raw_value": { - "description": "The raw value for a geolocation should follow {latitude} {longitude}", - "type": "string" - }, - "latitude": { - "description": "latitude", - "type": "number" - }, - "longitude": { - "description": "longitude", - "type": "number" - } - }, - "required": [ - "latitude", - "longitude" - ], - "title": "GeolocationValue", - "type": "object" - }, - "GrowthHabitEnum": { - "description": "", - "enum": [ - "erect", - "semi-erect", - "spreading", - "prostrate" - ], - "title": "GrowthHabitEnum", - "type": "string" - }, - "HandidnessEnum": { - "description": "", - "enum": [ - "ambidexterity", - "left handedness", - "mixed-handedness", - "right handedness" - ], - "title": "HandidnessEnum", - "type": "string" - }, - "HcProducedEnum": { - "description": "", - "enum": [ - "Oil", - "Gas-Condensate", - "Gas", - "Bitumen", - "Coalbed Methane", - "other" - ], - "title": "HcProducedEnum", - "type": "string" - }, - "HcrEnum": { - "description": "", - "enum": [ - "Oil Reservoir", - "Gas Reservoir", - "Oil Sand", - "Coalbed", - "Shale", - "Tight Oil Reservoir", - "Tight Gas Reservoir", - "other" - ], - "title": "HcrEnum", - "type": "string" - }, - "HcrGeolAgeEnum": { - "description": "", - "enum": [ - "Archean", - "Cambrian", - "Carboniferous", - "Cenozoic", - "Cretaceous", - "Devonian", - "Jurassic", - "Mesozoic", - "Neogene", - "Ordovician", - "Paleogene", - "Paleozoic", - "Permian", - "Precambrian", - "Proterozoic", - "Silurian", - "Triassic", - "other" - ], - "title": "HcrGeolAgeEnum", - "type": "string" - }, - "HeatCoolTypeEnum": { - "description": "", - "enum": [ - "radiant system", - "heat pump", - "forced air system", - "steam forced heat", - "wood stove" - ], - "title": "HeatCoolTypeEnum", - "type": "string" - }, - "HeatDelivLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "HeatDelivLocEnum", - "type": "string" - }, - "HostSexEnum": { - "description": "", - "enum": [ - "female", - "hermaphrodite", - "male", - "neuter" - ], - "title": "HostSexEnum", - "type": "string" - }, - "ImageValue": { - "additionalProperties": false, - "description": "An attribute value representing an image.", - "properties": { - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "display_order": { - "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", - "type": "integer" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "url": { - "type": "string" - } - }, - "title": "ImageValue", - "type": "object" - }, - "IndoorSpaceEnum": { - "description": "", - "enum": [ - "bedroom", - "office", - "bathroom", - "foyer", - "kitchen", - "locker room", - "hallway", - "elevator" - ], - "title": "IndoorSpaceEnum", - "type": "string" - }, - "IndoorSurfEnum": { - "description": "", - "enum": [ - "cabinet", - "ceiling", - "counter top", - "door", - "shelving", - "vent cover", - "window", - "wall" - ], - "title": "IndoorSurfEnum", - "type": "string" - }, - "InstrumentModelEnum": { - "description": "", - "enum": [ - "Orbitrap", - "VortexGenie2", - "PIPETMAN F144059M" - ], - "title": "InstrumentModelEnum", - "type": "string" - }, - "InstrumentVendorEnum": { - "description": "", - "enum": [ - "ThermoFisher", - "VWR", - "PerkinElmer", - "Gilson", - "ScientificIndustries" - ], - "title": "InstrumentVendorEnum", - "type": "string" - }, - "IntWallCondEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture" - ], - "title": "IntWallCondEnum", - "type": "string" - }, - "IntegerValue": { - "additionalProperties": false, - "description": "A value that is an integer", - "properties": { - "has_numeric_value": { - "description": "Links a quantity value to a number", - "type": "number" - }, - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "IntegerValue", - "type": "object" - }, - "JgiContTypeEnum": { - "description": "", - "enum": [ - "plate", - "tube" - ], - "title": "JgiContTypeEnum", - "type": "string" - }, - "LibraryPreparation": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:LibraryPreparation" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):libprp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "library_preparation_kit": { - "type": "string" - }, - "library_type": { - "$ref": "#/$defs/LibraryTypeEnum" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "pcr_cycles": { - "type": "integer" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "LibraryPreparation", - "type": "object" - }, - "LibraryTypeEnum": { - "description": "", - "enum": [ - "DNA", - "RNA" - ], - "title": "LibraryTypeEnum", - "type": "string" - }, - "LightTypeEnum": { - "description": "", - "enum": [ - "natural light", - "electric light", - "desk lamp", - "flourescent lights", - "none" - ], - "title": "LightTypeEnum", - "type": "string" - }, - "LithologyEnum": { - "description": "", - "enum": [ - "Basement", - "Chalk", - "Chert", - "Coal", - "Conglomerate", - "Diatomite", - "Dolomite", - "Limestone", - "Sandstone", - "Shale", - "Siltstone", - "Volcanic", - "other" - ], - "title": "LithologyEnum", - "type": "string" - }, - "MagBin": { - "additionalProperties": false, - "description": "", - "properties": { - "bin_name": { - "type": "string" - }, - "bin_quality": { - "type": "string" - }, - "completeness": { - "type": "number" - }, - "contamination": { - "type": "number" - }, - "gene_count": { - "type": "integer" - }, - "gtdbtk_class": { - "type": "string" - }, - "gtdbtk_domain": { - "type": "string" - }, - "gtdbtk_family": { - "type": "string" - }, - "gtdbtk_genus": { - "type": "string" - }, - "gtdbtk_order": { - "type": "string" - }, - "gtdbtk_phylum": { - "type": "string" - }, - "gtdbtk_species": { - "type": "string" - }, - "members_id": { - "type": "string" - }, - "num_16s": { - "type": "integer" - }, - "num_23s": { - "type": "integer" - }, - "num_5s": { - "type": "integer" - }, - "num_t_rna": { - "type": "integer" - }, - "number_of_contig": { - "type": "integer" - }, - "total_bases": { - "type": "integer" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "title": "MagBin", - "type": "object" - }, - "MagsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "binned_contig_num": { - "type": "integer" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmag-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "input_contig_num": { - "type": "integer" - }, - "low_depth_contig_num": { - "type": "integer" - }, - "mags_list": { - "items": { - "$ref": "#/$defs/MagBin" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "too_short_contig_num": { - "type": "integer" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "unbinned_contig_num": { - "type": "integer" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MagsAnalysisActivity", - "type": "object" - }, - "MechStrucEnum": { - "description": "", - "enum": [ - "subway", - "coach", - "carriage", - "elevator", - "escalator", - "boat", - "train", - "car", - "bus" - ], - "title": "MechStrucEnum", - "type": "string" - }, - "MetaboliteQuantification": { - "additionalProperties": false, - "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "highest_similarity_score": { - "type": "number" - }, - "metabolite_quantified": { - "description": "the specific metabolite identifier", - "type": "string" - } - }, - "title": "MetaboliteQuantification", - "type": "object" - }, - "MetabolomicsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_calibration": { - "description": "A reference to a file that holds calibration information.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_metabolite_quantifications": { - "items": { - "$ref": "#/$defs/MetaboliteQuantification" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmb-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetabolomicsAnalysisActivity", - "type": "object" - }, - "MetagenomeAnnotationActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "gold_analysis_project_identifiers": { - "description": "identifiers for corresponding analysis project in GOLD", - "items": { - "pattern": "^gold:Ga[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmgan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeAnnotationActivity", - "type": "object" - }, - "MetagenomeAssembly": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "asm_score": { - "description": "A score for comparing metagenomic assembly quality from same sample.", - "type": "number" - }, - "contig_bp": { - "description": "Total size in bp of all contigs.", - "type": "number" - }, - "contigs": { - "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "ctg_l50": { - "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", - "type": "number" - }, - "ctg_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", - "type": "number" - }, - "ctg_logsum": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_max": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_n50": { - "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", - "type": "number" - }, - "ctg_n90": { - "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", - "type": "number" - }, - "ctg_powsum": { - "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "gap_pct": { - "description": "The gap size percentage of all scaffolds.", - "type": "number" - }, - "gc_avg": { - "description": "Average of GC content of all contigs.", - "type": "number" - }, - "gc_std": { - "description": "Standard deviation of GC content of all contigs.", - "type": "number" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmgas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "insdc_assembly_identifiers": { - "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "num_aligned_reads": { - "description": "The sequence count number of input reads aligned to assembled contigs.", - "type": "number" - }, - "num_input_reads": { - "description": "The sequence count number of input reads for assembly.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "scaf_bp": { - "description": "Total size in bp of all scaffolds.", - "type": "number" - }, - "scaf_l50": { - "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", - "type": "number" - }, - "scaf_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", - "type": "number" - }, - "scaf_l_gt50k": { - "description": "Total size in bp of all scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_logsum": { - "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "scaf_max": { - "description": "Maximum scaffold length.", - "type": "number" - }, - "scaf_n50": { - "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", - "type": "number" - }, - "scaf_n90": { - "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", - "type": "number" - }, - "scaf_n_gt50k": { - "description": "Total sequence count of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_pct_gt50k": { - "description": "Total sequence size percentage of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_powsum": { - "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "scaffolds": { - "description": "Total sequence count of all scaffolds.", - "type": "number" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeAssembly", - "type": "object" - }, - "MetagenomeSequencingActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmsa-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetagenomeSequencingActivity", - "type": "object" - }, - "MetaproteomicsAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_peptide_quantifications": { - "items": { - "$ref": "#/$defs/PeptideQuantification" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "description": "The instrument used to collect the data used in the analysis", - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetaproteomicsAnalysisActivity", - "type": "object" - }, - "MetatranscriptomeActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeActivity", - "type": "object" - }, - "MetatranscriptomeAnnotationActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "gold_analysis_project_identifiers": { - "description": "identifiers for corresponding analysis project in GOLD", - "items": { - "pattern": "^gold:Ga[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmtan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeAnnotationActivity", - "type": "object" - }, - "MetatranscriptomeAssembly": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "asm_score": { - "description": "A score for comparing metagenomic assembly quality from same sample.", - "type": "number" - }, - "contig_bp": { - "description": "Total size in bp of all contigs.", - "type": "number" - }, - "contigs": { - "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "ctg_l50": { - "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", - "type": "number" - }, - "ctg_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", - "type": "number" - }, - "ctg_logsum": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_max": { - "description": "Maximum contig length.", - "type": "number" - }, - "ctg_n50": { - "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", - "type": "number" - }, - "ctg_n90": { - "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", - "type": "number" - }, - "ctg_powsum": { - "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "gap_pct": { - "description": "The gap size percentage of all scaffolds.", - "type": "number" - }, - "gc_avg": { - "description": "Average of GC content of all contigs.", - "type": "number" - }, - "gc_std": { - "description": "Standard deviation of GC content of all contigs.", - "type": "number" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfmtas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "insdc_assembly_identifiers": { - "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "num_aligned_reads": { - "description": "The sequence count number of input reads aligned to assembled contigs.", - "type": "number" - }, - "num_input_reads": { - "description": "The sequence count number of input reads for assembly.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "scaf_bp": { - "description": "Total size in bp of all scaffolds.", - "type": "number" - }, - "scaf_l50": { - "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", - "type": "number" - }, - "scaf_l90": { - "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", - "type": "number" - }, - "scaf_l_gt50k": { - "description": "Total size in bp of all scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_logsum": { - "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", - "type": "number" - }, - "scaf_max": { - "description": "Maximum scaffold length.", - "type": "number" - }, - "scaf_n50": { - "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", - "type": "number" - }, - "scaf_n90": { - "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", - "type": "number" - }, - "scaf_n_gt50k": { - "description": "Total sequence count of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_pct_gt50k": { - "description": "Total sequence size percentage of scaffolds greater than 50 KB.", - "type": "number" - }, - "scaf_powsum": { - "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", - "type": "number" - }, - "scaffolds": { - "description": "Total sequence count of all scaffolds.", - "type": "number" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "MetatranscriptomeAssembly", - "type": "object" - }, - "MixingProcess": { - "additionalProperties": false, - "description": "The combining of components, particles or layers into a more homogeneous state.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:MixingProcess" - ], - "type": "string" - }, - "duration": { - "$ref": "#/$defs/QuantityValue", - "description": "The elapsed time of an activity." - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "The mixed sample.", - "items": { - "pattern": "^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MixingProcess", - "type": "object" - }, - "NomAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_calibration": { - "description": "A reference to a file that holds calibration information.", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfnom-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "description": "The instrument used to collect the data used in the analysis", - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "execution_resource", - "git_url", - "has_input", - "type", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "NomAnalysisActivity", - "type": "object" - }, - "OccupDocumentEnum": { - "description": "", - "enum": [ - "automated count", - "estimate", - "manual count", - "videos" - ], - "title": "OccupDocumentEnum", - "type": "string" - }, - "OmicsProcessing": { - "additionalProperties": false, - "description": "The methods and processes used to generate omics data from a biosample or organism.", - "properties": { - "add_date": { - "description": "The date on which the information was added to the database.", - "type": "string" - }, - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "chimera_check": { - "$ref": "#/$defs/TextValue", - "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:OmicsProcessing" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "gold_sequencing_project_identifiers": { - "description": "identifiers for corresponding sequencing project in GOLD", - "items": { - "pattern": "^gold:Gp[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):(dobj)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "insdc_bioproject_identifiers": { - "description": "identifiers for corresponding project in INSDC Bioproject", - "items": { - "pattern": "^bioproject:PRJ[DEN][A-Z][0-9]+$", - "type": "string" - }, - "type": "array" - }, - "insdc_experiment_identifiers": { - "items": { - "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", - "type": "string" - }, - "type": "array" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "mod_date": { - "description": "The last date on which the database information was modified.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "ncbi_project_name": { - "type": "string" - }, - "nucl_acid_amp": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" - }, - "nucl_acid_ext": { - "$ref": "#/$defs/TextValue", - "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" - }, - "omics_type": { - "anyOf": [ - { - "$ref": "#/$defs/ControlledTermValue" - }, - { - "$ref": "#/$defs/ControlledIdentifiedTermValue" - } - ], - "description": "The type of omics data" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "pattern": "^(nmdc):(sty)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "pcr_cond": { - "$ref": "#/$defs/TextValue", - "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" - }, - "pcr_primers": { - "$ref": "#/$defs/TextValue", - "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" - }, - "principal_investigator": { - "$ref": "#/$defs/PersonValue", - "description": "Principal Investigator who led the study and/or generated the dataset." - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "samp_vol_we_dna_ext": { - "$ref": "#/$defs/QuantityValue", - "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." - }, - "seq_meth": { - "$ref": "#/$defs/TextValue", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." - }, - "seq_quality_check": { - "$ref": "#/$defs/TextValue", - "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "target_gene": { - "$ref": "#/$defs/TextValue", - "description": "Targeted gene or locus name for marker gene studies" - }, - "target_subfragment": { - "$ref": "#/$defs/TextValue", - "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - } - }, - "required": [ - "has_input", - "id" - ], - "title": "OmicsProcessing", - "type": "object" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "OrganismCountEnum": { - "description": "", - "enum": [ - "ATP", - "MPN", - "other" - ], - "title": "OrganismCountEnum", - "type": "string" - }, - "OrthologyGroup": { - "additionalProperties": false, - "description": "A set of genes or gene products in which all members are orthologous", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OrthologyGroup", - "type": "object" - }, - "OxyStatSampEnum": { - "description": "", - "enum": [ - "aerobic", - "anaerobic", - "other" - ], - "title": "OxyStatSampEnum", - "type": "string" - }, - "Pathway": { - "additionalProperties": false, - "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "has_part": { - "description": "A pathway can be broken down to a series of reaction step", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "has_part", - "id" - ], - "title": "Pathway", - "type": "object" - }, - "PeptideQuantification": { - "additionalProperties": false, - "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", - "properties": { - "all_proteins": { - "description": "the list of protein identifiers that are associated with the peptide sequence", - "items": { - "type": "string" - }, - "type": "array" - }, - "best_protein": { - "description": "the specific protein identifier most correctly associated with the peptide sequence", - "type": "string" - }, - "min_q_value": { - "description": "smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool", - "type": "number" - }, - "peptide_sequence": { - "type": "string" - }, - "peptide_spectral_count": { - "description": "sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file", - "type": "integer" - }, - "peptide_sum_masic_abundance": { - "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool", - "type": "integer" - } - }, - "title": "PeptideQuantification", - "type": "object" - }, - "PersonValue": { - "additionalProperties": false, - "description": "An attribute value representing a person", - "properties": { - "email": { - "description": "An email address for an entity such as a person. This should be the primary email address used.", - "type": "string" - }, - "has_raw_value": { - "description": "The full name of the Investigator in format FIRST LAST.", - "type": "string" - }, - "name": { - "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", - "type": "string" - }, - "orcid": { - "description": "The ORCID of a person.", - "type": "string" - }, - "profile_image_url": { - "description": "A url that points to an image of a person.", - "type": "string" - }, - "websites": { - "description": "A list of websites that are associated with the entity.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "type": "array" - } - }, - "title": "PersonValue", - "type": "object" - }, - "PlantGrowthMedEnum": { - "description": "", - "enum": [ - "other artificial liquid medium", - "other artificial solid medium", - "peat moss", - "perlite", - "pumice", - "sand", - "soil", - "vermiculite", - "water" - ], - "title": "PlantGrowthMedEnum", - "type": "string" - }, - "PlantSexEnum": { - "description": "", - "enum": [ - "Androdioecious", - "Androecious", - "Androgynous", - "Androgynomonoecious", - "Andromonoecious", - "Bisexual", - "Dichogamous", - "Diclinous", - "Dioecious", - "Gynodioecious", - "Gynoecious", - "Gynomonoecious", - "Hermaphroditic", - "Imperfect", - "Monoclinous", - "Monoecious", - "Perfect", - "Polygamodioecious", - "Polygamomonoecious", - "Polygamous", - "Protandrous", - "Protogynous", - "Subandroecious", - "Subdioecious", - "Subgynoecious", - "Synoecious", - "Trimonoecious", - "Trioecious", - "Unisexual" - ], - "title": "PlantSexEnum", - "type": "string" - }, - "Pooling": { - "additionalProperties": false, - "description": "physical combination of several instances of like material.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:Pooling" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "minItems": 2, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "maxItems": 1, - "minItems": 1, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):poolp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - } - }, - "required": [ - "has_input", - "has_output", - "id" - ], - "title": "Pooling", - "type": "object" - }, - "ProcessedSample": { - "additionalProperties": false, - "description": "", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "biomaterial_purity": { - "$ref": "#/$defs/QuantityValue" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "dna_absorb1": { - "description": "260/280 measurement of DNA sample purity", - "type": "number" - }, - "dna_concentration": { - "maximum": 2000, - "minimum": 0, - "type": "number" - }, - "external_database_identifiers": { - "description": "Link to corresponding identifier in external database", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcessedSample", - "type": "object" - }, - "ProcessingInstitutionEnum": { - "description": "", - "enum": [ - "UCSD", - "JGI", - "EMSL", - "Battelle", - "ANL", - "UCD_Genome_Center" - ], - "title": "ProcessingInstitutionEnum", - "type": "string" - }, - "ProfilePositionEnum": { - "description": "", - "enum": [ - "summit", - "shoulder", - "backslope", - "footslope", - "toeslope" - ], - "title": "ProfilePositionEnum", - "type": "string" - }, - "ProteinQuantification": { - "additionalProperties": false, - "description": "This is used to link a metaproteomics analysis workflow to a specific protein", - "properties": { - "all_proteins": { - "description": "the grouped list of protein identifiers associated with the peptide sequences that were grouped to a best protein", - "items": { - "type": "string" - }, - "type": "array" - }, - "best_protein": { - "description": "the specific protein identifier most correctly grouped to its associated peptide sequences", - "type": "string" - }, - "peptide_sequence_count": { - "description": "count of peptide sequences grouped to the best_protein", - "type": "integer" - }, - "protein_spectral_count": { - "description": "sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file", - "type": "integer" - }, - "protein_sum_masic_abundance": { - "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool", - "type": "integer" - } - }, - "title": "ProteinQuantification", - "type": "object" - }, - "Protocol": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "url": { - "type": "string" - } - }, - "title": "Protocol", - "type": "object" - }, - "QuadPosEnum": { - "description": "", - "enum": [ - "North side", - "West side", - "South side", - "East side" - ], - "title": "QuadPosEnum", - "type": "string" - }, - "QuantityValue": { - "additionalProperties": false, - "description": "A simple quantity, e.g. 2cm", - "properties": { - "has_maximum_numeric_value": { - "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", - "type": "number" - }, - "has_minimum_numeric_value": { - "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", - "type": "number" - }, - "has_numeric_value": { - "description": "The number part of the quantity", - "type": "number" - }, - "has_raw_value": { - "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", - "type": "string" - }, - "has_unit": { - "description": "The unit of the quantity", - "type": "string" - } - }, - "title": "QuantityValue", - "type": "object" - }, - "RNASampleFormatEnum": { - "description": "", - "enum": [ - "10 mM Tris-HCl", - "DNAStable", - "Ethanol", - "Low EDTA TE", - "MDA reaction buffer", - "PBS", - "Pellet", - "RNAStable", - "TE", - "Water", - "Gentegra-DNA", - "Gentegra-RNA" - ], - "title": "RNASampleFormatEnum", - "type": "string" - }, - "Reaction": { - "additionalProperties": false, - "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "direction": { - "description": "One of l->r, r->l, bidirectional, neutral", - "type": "string" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "is_balanced": { - "type": "boolean" - }, - "is_diastereoselective": { - "type": "boolean" - }, - "is_fully_characterized": { - "description": "False if includes R-groups", - "type": "boolean" - }, - "is_stereo": { - "type": "boolean" - }, - "is_transport": { - "type": "boolean" - }, - "left_participants": { - "items": { - "$ref": "#/$defs/ReactionParticipant" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "right_participants": { - "items": { - "$ref": "#/$defs/ReactionParticipant" - }, - "type": "array" - }, - "smarts_string": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Reaction", - "type": "object" - }, - "ReactionParticipant": { - "additionalProperties": false, - "description": "Instances of this link a reaction to a chemical entity participant", - "properties": { - "chemical": { - "description": "from reaction participant class", - "type": "string" - }, - "stoichiometry": { - "description": "from reaction participant class", - "type": "integer" - } - }, - "title": "ReactionParticipant", - "type": "object" - }, - "ReadBasedTaxonomyAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfrbt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "ReadBasedTaxonomyAnalysisActivity", - "type": "object" - }, - "ReadQcAnalysisActivity": { - "additionalProperties": false, - "allOf": [ - { - "if": { - "properties": { - "qc_status": { - "const": "pass" - } - }, - "required": [ - "qc_status" - ] - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - }, - { - "if": { - "not": { - "required": [ - "qc_status" - ] - }, - "properties": { - "qc_status": {} - } - }, - "then": { - "properties": { - "has_output": {} - }, - "required": [ - "has_output" - ] - } - } - ], - "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "execution_resource": { - "type": "string" - }, - "git_url": { - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "An output biosample to a processing step", - "items": { - "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):wfrqc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[0-9]{1,})$", - "type": "string" - }, - "input_base_count": { - "description": "The nucleotide base count number of input reads for QC analysis.", - "type": "number" - }, - "input_read_bases": { - "description": "TODO ", - "type": "number" - }, - "input_read_count": { - "description": "The sequence count number of input reads for QC analysis.", - "type": "number" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "output_base_count": { - "description": "After QC analysis nucleotide base count number.", - "type": "number" - }, - "output_read_bases": { - "description": "TODO", - "type": "number" - }, - "output_read_count": { - "description": "After QC analysis sequence count number.", - "type": "number" - }, - "part_of": { - "description": "Links a resource to another resource that either logically or physically includes it.", - "items": { - "type": "string" - }, - "type": "array" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "started_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "used": { - "type": "string" - }, - "version": { - "type": "string" - }, - "was_informed_by": { - "pattern": "^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - } - }, - "required": [ - "type", - "execution_resource", - "git_url", - "has_input", - "id", - "started_at_time", - "ended_at_time" - ], - "title": "ReadQcAnalysisActivity", - "type": "object" - }, - "RelSampLocEnum": { - "description": "", - "enum": [ - "edge of car", - "center of car", - "under a seat" - ], - "title": "RelSampLocEnum", - "type": "string" - }, - "RoomCondtEnum": { - "description": "", - "enum": [ - "new", - "visible wear", - "needs repair", - "damaged", - "rupture", - "visible signs of mold/mildew" - ], - "title": "RoomCondtEnum", - "type": "string" - }, - "RoomConnectedEnum": { - "description": "", - "enum": [ - "attic", - "bathroom", - "closet", - "conference room", - "elevator", - "examining room", - "hallway", - "kitchen", - "mail room", - "office", - "stairwell" - ], - "title": "RoomConnectedEnum", - "type": "string" - }, - "RoomLocEnum": { - "description": "", - "enum": [ - "corner room", - "interior room", - "exterior wall" - ], - "title": "RoomLocEnum", - "type": "string" - }, - "RoomSampPosEnum": { - "description": "", - "enum": [ - "north corner", - "south corner", - "west corner", - "east corner", - "northeast corner", - "northwest corner", - "southeast corner", - "southwest corner", - "center" - ], - "title": "RoomSampPosEnum", - "type": "string" - }, - "RoomTypeEnum": { - "description": "", - "enum": [ - "attic", - "bathroom", - "closet", - "conference room", - "elevator", - "examining room", - "hallway", - "kitchen", - "mail room", - "private office", - "open office", - "stairwell", - ",restroom", - "lobby", - "vestibule", - "mechanical or electrical room", - "data center", - "laboratory_wet", - "laboratory_dry", - "gymnasium", - "natatorium", - "auditorium", - "lockers", - "cafe", - "warehouse" - ], - "title": "RoomTypeEnum", - "type": "string" - }, - "SampCaptStatusEnum": { - "description": "", - "enum": [ - "active surveillance in response to an outbreak", - "active surveillance not initiated by an outbreak", - "farm sample", - "market sample", - "other" - ], - "title": "SampCaptStatusEnum", - "type": "string" - }, - "SampCollectPointEnum": { - "description": "", - "enum": [ - "well", - "test well", - "drilling rig", - "wellhead", - "separator", - "storage tank", - "other" - ], - "title": "SampCollectPointEnum", - "type": "string" - }, - "SampDisStageEnum": { - "description": "", - "enum": [ - "dissemination", - "growth and reproduction", - "infection", - "inoculation", - "penetration", - "other" - ], - "title": "SampDisStageEnum", - "type": "string" - }, - "SampFloorEnum": { - "description": "", - "enum": [ - "1st floor", - "2nd floor", - "basement", - "lobby" - ], - "title": "SampFloorEnum", - "type": "string" - }, - "SampMdEnum": { - "description": "", - "enum": [ - "DF", - "RT", - "KB", - "MSL", - "other" - ], - "title": "SampMdEnum", - "type": "string" - }, - "SampSubtypeEnum": { - "description": "", - "enum": [ - "oil phase", - "water phase", - "biofilm", - "not applicable", - "other" - ], - "title": "SampSubtypeEnum", - "type": "string" - }, - "SampWeatherEnum": { - "description": "", - "enum": [ - "clear sky", - "cloudy", - "foggy", - "hail", - "rain", - "snow", - "sleet", - "sunny", - "windy" - ], - "title": "SampWeatherEnum", - "type": "string" - }, - "SampleTypeEnum": { - "description": "", - "enum": [ - "soil", - "soil - water extract", - "plant associated", - "sediment", - "water" - ], - "title": "SampleTypeEnum", - "type": "string" - }, - "SeasonUseEnum": { - "description": "", - "enum": [ - "Spring", - "Summer", - "Fall", - "Winter" - ], - "title": "SeasonUseEnum", - "type": "string" - }, - "SedimentTypeEnum": { - "description": "", - "enum": [ - "biogenous", - "cosmogenous", - "hydrogenous", - "lithogenous" - ], - "title": "SedimentTypeEnum", - "type": "string" - }, - "SeparationMethodEnum": { - "description": "The tool/substance used to separate or filter a solution or mixture.", - "enum": [ - "PTFE 96-well filter plate" - ], - "title": "SeparationMethodEnum", - "type": "string" - }, - "ShadingDeviceCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "ShadingDeviceCondEnum", - "type": "string" - }, - "ShadingDeviceTypeEnum": { - "description": "", - "enum": [ - "bahama shutters", - "exterior roll blind", - "gambrel awning", - "hood awning", - "porchroller awning", - "sarasota shutters", - "slatted aluminum", - "solid aluminum awning", - "sun screen", - "tree", - "trellis", - "venetian awning" - ], - "title": "ShadingDeviceTypeEnum", - "type": "string" - }, - "SoilHorizonEnum": { - "description": "", - "enum": [ - "O horizon", - "A horizon", - "E horizon", - "B horizon", - "C horizon", - "R layer", - "Permafrost", - "M horizon" - ], - "title": "SoilHorizonEnum", - "type": "string" - }, - "Solution": { - "additionalProperties": false, - "description": "A mixture that is homogeneous, made up of two or more scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent.", - "properties": { - "has_solution_components": { - "description": "Relationship from a Solution to one or more constituent solution components", - "items": { - "$ref": "#/$defs/SolutionComponent" - }, - "minItems": 1, - "type": "array" - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of a substance." - } - }, - "required": [ - "has_solution_components" - ], - "title": "Solution", - "type": "object" - }, - "SolutionComponent": { - "additionalProperties": false, - "description": "One constituent of a solution", - "properties": { - "compound": { - "$ref": "#/$defs/CompoundEnum", - "description": "A substance that consists of more than one atom or ion. Includes solvents and solutes. Can be combined into solutions." - }, - "concentration": { - "$ref": "#/$defs/QuantityValue", - "description": "The concentration of a substance used in a process" - } - }, - "required": [ - "compound" - ], - "title": "SolutionComponent", - "type": "object" - }, - "SpecificEnum": { - "description": "", - "enum": [ - "operation", - "as built", - "construction", - "bid", - "design", - "photos" - ], - "title": "SpecificEnum", - "type": "string" - }, - "SrDepEnvEnum": { - "description": "", - "enum": [ - "Lacustine", - "Fluvioldeltaic", - "Fluviomarine", - "Marine", - "other" - ], - "title": "SrDepEnvEnum", - "type": "string" - }, - "SrGeolAgeEnum": { - "description": "", - "enum": [ - "Archean", - "Cambrian", - "Carboniferous", - "Cenozoic", - "Cretaceous", - "Devonian", - "Jurassic", - "Mesozoic", - "Neogene", - "Ordovician", - "Paleogene", - "Paleozoic", - "Permian", - "Precambrian", - "Proterozoic", - "Silurian", - "Triassic", - "other" - ], - "title": "SrGeolAgeEnum", - "type": "string" - }, - "SrKerogTypeEnum": { - "description": "", - "enum": [ - "Type I", - "Type II", - "Type III", - "Type IV", - "other" - ], - "title": "SrKerogTypeEnum", - "type": "string" - }, - "SrLithologyEnum": { - "description": "", - "enum": [ - "Clastic", - "Carbonate", - "Coal", - "Biosilicieous", - "other" - ], - "title": "SrLithologyEnum", - "type": "string" - }, - "StationaryPhaseEnum": { - "description": "The type of stationary phase used in a solid phase extraction process.", - "enum": [ - "C18", - "C8", - "C4", - "C2", - "C1", - "C30", - "C60", - "CNT", - "CN", - "Diol", - "HILIC", - "NH2", - "Phenyl", - "PS-DVB", - "SAX", - "SCX", - "Silica", - "WCX", - "WAX", - "ZIC-HILIC", - "ZIC-pHILIC", - "ZIC-cHILIC" - ], - "title": "StationaryPhaseEnum", - "type": "string" - }, - "StatusEnum": { - "description": "", - "enum": [ - "pass", - "fail" - ], - "title": "StatusEnum", - "type": "string" - }, - "Study": { - "additionalProperties": false, - "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", - "properties": { - "alternative_descriptions": { - "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "alternative_identifiers": { - "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "alternative_names": { - "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "alternative_titles": { - "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", - "items": { - "type": "string" - }, - "type": "array" - }, - "associated_dois": { - "description": "A list of DOIs associated with a resource, such as a list of DOIS associated with a Study.", - "items": { - "$ref": "#/$defs/Doi" - }, - "type": "array" - }, - "description": { - "description": "A brief, link-free summary of a Study", - "type": "string" - }, - "ecosystem": { - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_category": { - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_subtype": { - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "type": "string" - }, - "ecosystem_type": { - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "type": "string" - }, - "emsl_project_identifiers": { - "description": "Identifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project", - "items": { - "pattern": "^emsl\\.project:[0-9]{5}$", - "type": "string" - }, - "type": "array" - }, - "funding_sources": { - "description": "A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.", - "items": { - "type": "string" - }, - "type": "array" - }, - "gnps_task_identifiers": { - "description": "identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results", - "items": { - "pattern": "^gnps\\.task:[a-f0-9]+$", - "type": "string" - }, - "type": "array" - }, - "gold_study_identifiers": { - "description": "identifiers for corresponding project(s) in GOLD", - "items": { - "pattern": "^gold:Gs[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "has_credit_associations": { - "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", - "items": { - "$ref": "#/$defs/CreditAssociation" - }, - "type": "array" - }, - "homepage_website": { - "description": "The website address (URL) of an entity's homepage.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "maxItems": 1, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "insdc_bioproject_identifiers": { - "description": "Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study.", - "items": { - "pattern": "^bioproject:PRJ[DEN][A-Z][0-9]+$", - "type": "string" - }, - "type": "array" - }, - "jgi_portal_study_identifiers": { - "description": "Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.", - "items": { - "pattern": "^jgi.proposal:\\d+$", - "type": "string" - }, - "type": "array" - }, - "mgnify_project_identifiers": { - "description": "identifiers for corresponding project in MGnify", - "items": { - "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", - "type": "string" - }, - "type": "array" - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "neon_study_identifiers": { - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "notes": { - "description": "from study class", - "type": "string" - }, - "objective": { - "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", - "type": "string" - }, - "part_of": { - "description": "Links a study or consortium to a parent (or umbrella) study or consortium.", - "items": { - "pattern": "^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "principal_investigator": { - "$ref": "#/$defs/PersonValue", - "description": "Principal Investigator who led the study and/or generated the dataset." - }, - "related_identifiers": { - "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", - "type": "string" - }, - "relevant_protocols": { - "items": { - "type": "string" - }, - "type": "array" - }, - "specific_ecosystem": { - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "type": "string" - }, - "study_category": { - "$ref": "#/$defs/StudyCategoryEnum", - "description": "The type of research initiative" - }, - "study_image": { - "description": "Links a study to one or more images.", - "items": { - "$ref": "#/$defs/ImageValue" - }, - "type": "array" - }, - "title": { - "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", - "type": "string" - }, - "type": { - "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", - "type": "string" - }, - "websites": { - "description": "A list of websites that are associated with the entity.", - "items": { - "pattern": "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$", - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id", - "study_category" - ], - "title": "Study", - "type": "object" - }, - "StudyCategoryEnum": { - "description": "", - "enum": [ - "research_study", - "consortium" - ], - "title": "StudyCategoryEnum", - "type": "string" - }, - "SubSamplingProcess": { - "additionalProperties": false, - "description": "Separating a sample aliquot from the starting material for downstream activity.", - "properties": { - "alternative_identifiers": { - "description": "A list of alternative identifiers for the entity.", - "items": { - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "type": "array" - }, - "contained_in": { - "$ref": "#/$defs/ContainerCategoryEnum", - "description": "A type of container. i.e. test tube, falcon tube, etc." - }, - "container_size": { - "$ref": "#/$defs/QuantityValue", - "description": "The volume of the container an analyte is stored in or an activity takes place in" - }, - "description": { - "description": "a human-readable description of a thing", - "type": "string" - }, - "designated_class": { - "enum": [ - "nmdc:SubSamplingProcess" - ], - "type": "string" - }, - "end_date": { - "description": "The date on which any process or activity was ended", - "type": "string" - }, - "has_failure_categorization": { - "items": { - "$ref": "#/$defs/FailureCategorization" - }, - "type": "array" - }, - "has_input": { - "description": "An input to a process.", - "items": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "string" - } - ], - "pattern": "^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "has_output": { - "description": "The subsample.", - "items": { - "pattern": "^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$", - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$", - "type": "string" - }, - "instrument_name": { - "description": "The name of the instrument that was used for processing the sample.", - "type": "string" - }, - "mass": { - "$ref": "#/$defs/QuantityValue", - "description": "The output mass of the SubSampling Process." - }, - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "processing_institution": { - "$ref": "#/$defs/ProcessingInstitutionEnum", - "description": "The organization that processed the sample." - }, - "protocol_link": { - "$ref": "#/$defs/Protocol" - }, - "qc_comment": { - "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", - "type": "string" - }, - "qc_status": { - "$ref": "#/$defs/StatusEnum", - "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" - }, - "start_date": { - "description": "The date on which any process or activity was started", - "type": "string" - }, - "temperature": { - "$ref": "#/$defs/QuantityValue", - "description": "The value of a temperature measurement or temperature used in a process." - }, - "volume": { - "$ref": "#/$defs/QuantityValue", - "description": "The output volume of the SubSampling Process." - } - }, - "required": [ - "id" - ], - "title": "SubSamplingProcess", - "type": "object" - }, - "SubstructureTypeEnum": { - "description": "", - "enum": [ - "crawlspace", - "slab on grade", - "basement" - ], - "title": "SubstructureTypeEnum", - "type": "string" - }, - "SurfAirContEnum": { - "description": "", - "enum": [ - "dust", - "organic matter", - "particulate matter", - "volatile organic compounds", - "biological contaminants", - "radon", - "nutrients", - "biocides" - ], - "title": "SurfAirContEnum", - "type": "string" - }, - "SurfMaterialEnum": { - "description": "", - "enum": [ - "adobe", - "carpet", - "cinder blocks", - "concrete", - "hay bales", - "glass", - "metal", - "paint", - "plastic", - "stainless steel", - "stone", - "stucco", - "tile", - "vinyl", - "wood" - ], - "title": "SurfMaterialEnum", - "type": "string" - }, - "TextValue": { - "additionalProperties": false, - "description": "A basic string value", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - }, - "language": { - "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", - "type": "string" - } - }, - "title": "TextValue", - "type": "object" - }, - "TidalStageEnum": { - "description": "", - "enum": [ - "low tide", - "ebb tide", - "flood tide", - "high tide" - ], - "title": "TidalStageEnum", - "type": "string" - }, - "TillageEnum": { - "description": "", - "enum": [ - "drill", - "cutting disc", - "ridge till", - "strip tillage", - "zonal tillage", - "chisel", - "tined", - "mouldboard", - "disc plough" - ], - "title": "TillageEnum", - "type": "string" - }, - "TimestampValue": { - "additionalProperties": false, - "description": "A value that is a timestamp. The range should be ISO-8601", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "TimestampValue", - "type": "object" - }, - "TrainLineEnum": { - "description": "", - "enum": [ - "red", - "green", - "orange" - ], - "title": "TrainLineEnum", - "type": "string" - }, - "TrainStatLocEnum": { - "description": "", - "enum": [ - "south station above ground", - "south station underground", - "south station amtrak", - "forest hills", - "riverside" - ], - "title": "TrainStatLocEnum", - "type": "string" - }, - "TrainStopLocEnum": { - "description": "", - "enum": [ - "end", - "mid", - "downtown" - ], - "title": "TrainStopLocEnum", - "type": "string" - }, - "UrlValue": { - "additionalProperties": false, - "description": "A value that is a string that conforms to URL syntax", - "properties": { - "has_raw_value": { - "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", - "type": "string" - } - }, - "title": "UrlValue", - "type": "object" - }, - "VisMediaEnum": { - "description": "", - "enum": [ - "photos", - "videos", - "commonly of the building", - "site context (adjacent buildings, vegetation, terrain, streets)", - "interiors", - "equipment", - "3D scans" - ], - "title": "VisMediaEnum", - "type": "string" - }, - "WallConstTypeEnum": { - "description": "", - "enum": [ - "frame construction", - "joisted masonry", - "light noncombustible", - "masonry noncombustible", - "modified fire resistive", - "fire resistive" - ], - "title": "WallConstTypeEnum", - "type": "string" - }, - "WallFinishMatEnum": { - "description": "", - "enum": [ - "plaster", - "gypsum plaster", - "veneer plaster", - "gypsum board", - "tile", - "terrazzo", - "stone facing", - "acoustical treatment", - "wood", - "metal", - "masonry" - ], - "title": "WallFinishMatEnum", - "type": "string" - }, - "WallLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "WallLocEnum", - "type": "string" - }, - "WallSurfTreatmentEnum": { - "description": "", - "enum": [ - "painted", - "wall paper", - "no treatment", - "paneling", - "stucco", - "fabric" - ], - "title": "WallSurfTreatmentEnum", - "type": "string" - }, - "WallTextureEnum": { - "description": "", - "enum": [ - "crows feet", - "crows-foot stomp", - "", - "double skip", - "hawk and trowel", - "knockdown", - "popcorn", - "orange peel", - "rosebud stomp", - "Santa-Fe texture", - "skip trowel", - "smooth", - "stomp knockdown", - "swirl" - ], - "title": "WallTextureEnum", - "type": "string" - }, - "WaterFeatTypeEnum": { - "description": "", - "enum": [ - "fountain", - "pool", - "standing feature", - "stream", - "waterfall" - ], - "title": "WaterFeatTypeEnum", - "type": "string" - }, - "WeekdayEnum": { - "description": "", - "enum": [ - "Monday", - "Tuesday", - "Wednesday", - "Thursday", - "Friday", - "Saturday", - "Sunday" - ], - "title": "WeekdayEnum", - "type": "string" - }, - "WindowCondEnum": { - "description": "", - "enum": [ - "damaged", - "needs repair", - "new", - "rupture", - "visible wear" - ], - "title": "WindowCondEnum", - "type": "string" - }, - "WindowCoverEnum": { - "description": "", - "enum": [ - "blinds", - "curtains", - "none" - ], - "title": "WindowCoverEnum", - "type": "string" - }, - "WindowHorizPosEnum": { - "description": "", - "enum": [ - "left", - "middle", - "right" - ], - "title": "WindowHorizPosEnum", - "type": "string" - }, - "WindowLocEnum": { - "description": "", - "enum": [ - "north", - "south", - "east", - "west" - ], - "title": "WindowLocEnum", - "type": "string" - }, - "WindowMatEnum": { - "description": "", - "enum": [ - "clad", - "fiberglass", - "metal", - "vinyl", - "wood" - ], - "title": "WindowMatEnum", - "type": "string" - }, - "WindowTypeEnum": { - "description": "", - "enum": [ - "single-hung sash window", - "horizontal sash window", - "fixed window" - ], - "title": "WindowTypeEnum", - "type": "string" - }, - "WindowVertPosEnum": { - "description": "", - "enum": [ - "bottom", - "middle", - "top", - "low", - "high" - ], - "title": "WindowVertPosEnum", - "type": "string" - }, - "YesNoEnum": { - "description": "replaces DnaDnaseEnum and DnaseRnaEnum", - "enum": [ - "no", - "yes" - ], - "title": "YesNoEnum", - "type": "string" - } - }, - "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": false, - "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", - "metamodel_version": "1.7.0", - "properties": { - "biosample_set": { - "description": "This property links a database object to the set of samples within it.", - "items": { - "$ref": "#/$defs/Biosample" - }, - "type": "array" - }, - "collecting_biosamples_from_site_set": { - "items": { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - "type": "array" - }, - "data_object_set": { - "description": "This property links a database object to the set of data objects within it.", - "items": { - "$ref": "#/$defs/DataObject" - }, - "type": "array" - }, - "extraction_set": { - "description": "This property links a database object to the set of extractions within it.", - "items": { - "$ref": "#/$defs/Extraction" - }, - "type": "array" - }, - "field_research_site_set": { - "items": { - "$ref": "#/$defs/FieldResearchSite" - }, - "type": "array" - }, - "functional_annotation_agg": { - "items": { - "$ref": "#/$defs/FunctionalAnnotationAggMember" - }, - "type": "array" - }, - "functional_annotation_set": { - "description": "This property links a database object to the set of all functional annotations", - "items": { - "$ref": "#/$defs/FunctionalAnnotation" - }, - "type": "array" - }, - "genome_feature_set": { - "description": "This property links a database object to the set of all features", - "items": { - "$ref": "#/$defs/GenomeFeature" - }, - "type": "array" - }, - "library_preparation_set": { - "description": "This property links a database object to the set of DNA extractions within it.", - "items": { - "$ref": "#/$defs/LibraryPreparation" - }, - "type": "array" - }, - "mags_activity_set": { - "description": "This property links a database object to the set of MAGs analysis activities.", - "items": { - "$ref": "#/$defs/MagsAnalysisActivity" - }, - "type": "array" - }, - "metabolomics_analysis_activity_set": { - "description": "This property links a database object to the set of metabolomics analysis activities.", - "items": { - "$ref": "#/$defs/MetabolomicsAnalysisActivity" - }, - "type": "array" - }, - "metagenome_annotation_activity_set": { - "description": "This property links a database object to the set of metagenome annotation activities.", - "items": { - "$ref": "#/$defs/MetagenomeAnnotationActivity" - }, - "type": "array" - }, - "metagenome_assembly_set": { - "description": "This property links a database object to the set of metagenome assembly activities.", - "items": { - "$ref": "#/$defs/MetagenomeAssembly" - }, - "type": "array" - }, - "metagenome_sequencing_activity_set": { - "description": "This property links a database object to the set of metagenome sequencing activities.", - "items": { - "$ref": "#/$defs/MetagenomeSequencingActivity" - }, - "type": "array" - }, - "metaproteomics_analysis_activity_set": { - "description": "This property links a database object to the set of metaproteomics analysis activities.", - "items": { - "$ref": "#/$defs/MetaproteomicsAnalysisActivity" - }, - "type": "array" - }, - "metatranscriptome_activity_set": { - "description": "This property links a database object to the set of metatranscriptome analysis activities.", - "items": { - "$ref": "#/$defs/MetatranscriptomeActivity" - }, - "type": "array" - }, - "nom_analysis_activity_set": { - "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", - "items": { - "$ref": "#/$defs/NomAnalysisActivity" - }, - "type": "array" - }, - "omics_processing_set": { - "description": "This property links a database object to the set of omics processings within it.", - "items": { - "$ref": "#/$defs/OmicsProcessing" - }, - "type": "array" - }, - "planned_process_set": { - "description": "This property links a database object to the set of planned processes within it.", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/Extraction" - }, - { - "$ref": "#/$defs/CollectingBiosamplesFromSite" - }, - { - "$ref": "#/$defs/BiosampleProcessing" - }, - { - "$ref": "#/$defs/SubSamplingProcess" - }, - { - "$ref": "#/$defs/MixingProcess" - }, - { - "$ref": "#/$defs/FiltrationProcess" - }, - { - "$ref": "#/$defs/ChromatographicSeparationProcess" - }, - { - "$ref": "#/$defs/OmicsProcessing" - }, - { - "$ref": "#/$defs/Pooling" - }, - { - "$ref": "#/$defs/LibraryPreparation" - } - ] - }, - "type": "array" - }, - "pooling_set": { - "items": { - "$ref": "#/$defs/Pooling" - }, - "type": "array" - }, - "processed_sample_set": { - "description": "This property links a database object to the set of processed samples within it.", - "items": { - "$ref": "#/$defs/ProcessedSample" - }, - "type": "array" - }, - "read_based_taxonomy_analysis_activity_set": { - "description": "This property links a database object to the set of read based analysis activities.", - "items": { - "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" - }, - "type": "array" - }, - "read_qc_analysis_activity_set": { - "description": "This property links a database object to the set of read QC analysis activities.", - "items": { - "$ref": "#/$defs/ReadQcAnalysisActivity" - }, - "type": "array" - }, - "study_set": { - "description": "This property links a database object to the set of studies within it.", - "items": { - "$ref": "#/$defs/Study" - }, - "type": "array" - } - }, - "title": "NMDC", - "type": "object", - "version": "0.0.0" -} diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml deleted file mode 100644 index c4e691553c..0000000000 --- a/nmdc_schema/nmdc_materialized_patterns.yaml +++ /dev/null @@ -1,20927 +0,0 @@ -name: NMDC -description: "Schema for National Microbiome Data Collaborative (NMDC).\nThis schema\ - \ is organized into multiple modules, such as:\n\n * a set of core types for representing\ - \ data values\n * a subset of the mixs schema\n * an annotation schema\n * the NMDC\ - \ schema itself, into which the other modules are imported" -title: NMDC Schema -notes: -- not importing any MIxS terms where the relationship between the name (SCN) and the - id isn't 1:1 -id: https://w3id.org/nmdc/nmdc -version: 0.0.0 -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - CATH: - prefix_prefix: CATH - prefix_reference: 'https://bioregistry.io/cath:' - CHEBI: - prefix_prefix: CHEBI - prefix_reference: http://purl.obolibrary.org/obo/CHEBI_ - CHEMBL.COMPOUND: - prefix_prefix: CHEMBL.COMPOUND - prefix_reference: 'https://bioregistry.io/chembl.compound:' - Contaminant: - prefix_prefix: Contaminant - prefix_reference: http://example.org/contaminant/ - DRUGBANK: - prefix_prefix: DRUGBANK - prefix_reference: 'https://bioregistry.io/drugbank:' - EC: - prefix_prefix: EC - prefix_reference: 'https://bioregistry.io/eccode:' - EFO: - prefix_prefix: EFO - prefix_reference: http://www.ebi.ac.uk/efo/ - EGGNOG: - prefix_prefix: EGGNOG - prefix_reference: 'https://bioregistry.io/eggnog:' - ENVO: - prefix_prefix: ENVO - prefix_reference: http://purl.obolibrary.org/obo/ENVO_ - FBcv: - prefix_prefix: FBcv - prefix_reference: http://purl.obolibrary.org/obo/FBcv_ - FMA: - prefix_prefix: FMA - prefix_reference: http://purl.obolibrary.org/obo/FMA_ - GO: - prefix_prefix: GO - prefix_reference: http://purl.obolibrary.org/obo/GO_ - HMDB: - prefix_prefix: HMDB - prefix_reference: 'https://bioregistry.io/hmdb:' - ISA: - prefix_prefix: ISA - prefix_reference: http://example.org/isa/ - KEGG.ORTHOLOGY: - prefix_prefix: KEGG.ORTHOLOGY - prefix_reference: 'https://bioregistry.io/kegg.orthology:' - MASSIVE: - prefix_prefix: MASSIVE - prefix_reference: 'https://bioregistry.io/reference/massive:' - MESH: - prefix_prefix: MESH - prefix_reference: 'https://bioregistry.io/mesh:' - MS: - prefix_prefix: MS - prefix_reference: http://purl.obolibrary.org/obo/MS_ - MetaNetX: - prefix_prefix: MetaNetX - prefix_reference: http://example.org/metanetx/ - NCBITaxon: - prefix_prefix: NCBITaxon - prefix_reference: http://purl.obolibrary.org/obo/NCBITaxon_ - NCIT: - prefix_prefix: NCIT - prefix_reference: http://purl.obolibrary.org/obo/NCIT_ - OBI: - prefix_prefix: OBI - prefix_reference: http://purl.obolibrary.org/obo/OBI_ - ORCID: - prefix_prefix: ORCID - prefix_reference: https://orcid.org/ - PANTHER.FAMILY: - prefix_prefix: PANTHER.FAMILY - prefix_reference: 'https://bioregistry.io/panther.family:' - PATO: - prefix_prefix: PATO - prefix_reference: http://purl.obolibrary.org/obo/PATO_ - PFAM: - prefix_prefix: PFAM - prefix_reference: 'https://bioregistry.io/pfam:' - PO: - prefix_prefix: PO - prefix_reference: http://purl.obolibrary.org/obo/PO_ - PR: - prefix_prefix: PR - prefix_reference: http://purl.obolibrary.org/obo/PR_ - PUBCHEM.COMPOUND: - prefix_prefix: PUBCHEM.COMPOUND - prefix_reference: 'https://bioregistry.io/pubchem.compound:' - RO: - prefix_prefix: RO - prefix_reference: http://purl.obolibrary.org/obo/RO_ - RetroRules: - prefix_prefix: RetroRules - prefix_reference: http://example.org/retrorules/ - SUPFAM: - prefix_prefix: SUPFAM - prefix_reference: 'https://bioregistry.io/supfam:' - TIGRFAM: - prefix_prefix: TIGRFAM - prefix_reference: 'https://bioregistry.io/tigrfam:' - UBERON: - prefix_prefix: UBERON - prefix_reference: http://purl.obolibrary.org/obo/UBERON_ - UO: - prefix_prefix: UO - prefix_reference: http://purl.obolibrary.org/obo/UO_ - bioproject: - prefix_prefix: bioproject - prefix_reference: 'https://identifiers.org/bioproject:' - biosample: - prefix_prefix: biosample - prefix_reference: 'https://bioregistry.io/biosample:' - cas: - prefix_prefix: cas - prefix_reference: 'https://bioregistry.io/cas:' - doi: - prefix_prefix: doi - prefix_reference: 'https://bioregistry.io/doi:' - edam.data: - prefix_prefix: edam.data - prefix_reference: http://edamontology.org/data_ - emsl.project: - prefix_prefix: emsl.project - prefix_reference: 'https://bioregistry.io/emsl.project:' - emsl: - prefix_prefix: emsl - prefix_reference: http://example.org/emsl_in_mongodb/ - emsl_uuid_like: - prefix_prefix: emsl_uuid_like - prefix_reference: http://example.org/emsl_uuid_like/ - generic: - prefix_prefix: generic - prefix_reference: https://example.org/generic/ - gnps.task: - prefix_prefix: gnps.task - prefix_reference: 'https://bioregistry.io/gnps.task:' - gtpo: - prefix_prefix: gtpo - prefix_reference: http://example.org/gtpo/ - igsn: - prefix_prefix: igsn - prefix_reference: https://app.geosamples.org/sample/igsn/ - img.taxon: - prefix_prefix: img.taxon - prefix_reference: 'https://bioregistry.io/img.taxon:' - jgi.proposal: - prefix_prefix: jgi.proposal - prefix_reference: 'https://bioregistry.io/jgi.proposal:' - jgi: - prefix_prefix: jgi - prefix_reference: http://example.org/jgi/ - kegg: - prefix_prefix: kegg - prefix_reference: 'https://bioregistry.io/kegg:' - linkml: - prefix_prefix: linkml - prefix_reference: https://w3id.org/linkml/ - mgnify.proj: - prefix_prefix: mgnify.proj - prefix_reference: 'https://bioregistry.io/mgnify.proj:' - neon.identifier: - prefix_prefix: neon.identifier - prefix_reference: http://example.org/neon/identifier/ - neon.schema: - prefix_prefix: neon.schema - prefix_reference: http://example.org/neon/schema/ - nmdc: - prefix_prefix: nmdc - prefix_reference: https://w3id.org/nmdc/ - prov: - prefix_prefix: prov - prefix_reference: http://www.w3.org/ns/prov# - rdf: - prefix_prefix: rdf - prefix_reference: http://www.w3.org/1999/02/22-rdf-syntax-ns# - rdfs: - prefix_prefix: rdfs - prefix_reference: http://www.w3.org/2000/01/rdf-schema# - skos: - prefix_prefix: skos - prefix_reference: http://www.w3.org/2004/02/skos/core# - xsd: - prefix_prefix: xsd - prefix_reference: http://www.w3.org/2001/XMLSchema# - CHMO: - prefix_prefix: CHMO - prefix_reference: http://purl.obolibrary.org/obo/CHMO_ - wikidata: - prefix_prefix: wikidata - prefix_reference: http://www.wikidata.org/entity/ - my_emsl: - prefix_prefix: my_emsl - prefix_reference: https://release.my.emsl.pnnl.gov/released_data/ - KEGG.COMPOUND: - prefix_prefix: KEGG.COMPOUND - prefix_reference: 'https://bioregistry.io/kegg.compound:' - SIO: - prefix_prefix: SIO - prefix_reference: http://semanticscience.org/resource/SIO_ - UniProtKB: - prefix_prefix: UniProtKB - prefix_reference: 'https://bioregistry.io/uniprot:' - biolink: - prefix_prefix: biolink - prefix_reference: https://w3id.org/biolink/vocab/ - dcterms: - prefix_prefix: dcterms - prefix_reference: http://purl.org/dc/terms/ - qud: - prefix_prefix: qud - prefix_reference: http://qudt.org/1.1/schema/qudt# - schema: - prefix_prefix: schema - prefix_reference: http://schema.org/ - wgs84: - prefix_prefix: wgs84 - prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos# - COG: - prefix_prefix: COG - prefix_reference: 'https://bioregistry.io/cog:' - KEGG.REACTION: - prefix_prefix: KEGG.REACTION - prefix_reference: 'https://bioregistry.io/kegg.reaction:' - KEGG_PATHWAY: - prefix_prefix: KEGG_PATHWAY - prefix_reference: 'https://bioregistry.io/kegg.pathway:' - MetaCyc: - prefix_prefix: MetaCyc - prefix_reference: 'https://bioregistry.io/metacyc.compound:' - RHEA: - prefix_prefix: RHEA - prefix_reference: 'https://bioregistry.io/rhea:' - SEED: - prefix_prefix: SEED - prefix_reference: 'https://bioregistry.io/seed:' - shex: - prefix_prefix: shex - prefix_reference: http://www.w3.org/ns/shex# - MIXS: - prefix_prefix: MIXS - prefix_reference: https://w3id.org/mixs/ - MIXS_yaml: - prefix_prefix: MIXS_yaml - prefix_reference: https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/ - gold: - prefix_prefix: gold - prefix_reference: 'https://bioregistry.io/gold:' -emit_prefixes: -- KEGG.ORTHOLOGY -- MASSIVE -- biosample -- cas -- doi -- gnps.task -- gold -- img.taxon -- jgi.proposal -- kegg -- rdf -- rdfs -- skos -- xsd -default_prefix: nmdc -default_range: string -subsets: - sample subset: - name: sample subset - description: Subset consisting of entities linked to the processing of samples. Currently, - this subset consists of study, omics process, and biosample. - from_schema: https://w3id.org/nmdc/nmdc - data object subset: - name: data object subset - description: Subset consisting of the data objects that either inputs or outputs - of processes or workflows. - from_schema: https://w3id.org/nmdc/nmdc - data_portal_subset: - name: data_portal_subset - description: Subset consisting of entities that Kitware/nmdc-server use to populate - the data portal. - comments: - - Schema authors are responsible for alerting and supporting Kitware and nmdc-server - authors about changes they will have to make if entities labeled with data_portal_subset - are modified. - - Assignment of the data_portal_subset is incomplete in the schema. - from_schema: https://w3id.org/nmdc/nmdc - environment: - name: environment - from_schema: https://w3id.org/nmdc/nmdc - investigation: - name: investigation - from_schema: https://w3id.org/nmdc/nmdc - nucleic acid sequence source: - name: nucleic acid sequence source - from_schema: https://w3id.org/nmdc/nmdc - sequencing: - name: sequencing - from_schema: https://w3id.org/nmdc/nmdc - mixs_environmental_triad: - name: mixs_environmental_triad - title: MIxS Environmental Triad - from_schema: https://w3id.org/nmdc/nmdc - mixs extension: - name: mixs extension - from_schema: https://w3id.org/nmdc/nmdc - checklist: - name: checklist - description: A MIxS checklist. These can be combined with packages - from_schema: https://w3id.org/nmdc/nmdc - package: - name: package - description: A MIxS package. These can be combined with checklists - from_schema: https://w3id.org/nmdc/nmdc - checklist_package_combination: - name: checklist_package_combination - description: A combination of a checklist and a package - from_schema: https://w3id.org/nmdc/nmdc - workflow subset: - name: workflow subset - description: Subset consisting of just the workflow execution activities - from_schema: https://w3id.org/nmdc/nmdc -types: - bytes: - name: bytes - description: An integer value that corresponds to a size in bytes - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - UO:0000233 - base: int - uri: xsd:long - decimal degree: - name: decimal degree - description: A decimal degree expresses latitude or longitude as decimal fractions. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://en.wikipedia.org/wiki/Decimal_degrees - base: float - uri: xsd:decimal - language code: - name: language code - description: A language code conforming to ISO_639-1 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://en.wikipedia.org/wiki/ISO_639-1 - base: str - uri: xsd:language - unit: - name: unit - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - qud:Unit - - UO:0000000 - base: str - uri: xsd:string - string: - name: string - description: A character string - notes: - - In RDF serializations, a slot with range of string is treated as a literal or - type xsd:string. If you are authoring schemas in LinkML YAML, the type is - referenced with the lower case "string". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Text - base: str - uri: xsd:string - integer: - name: integer - description: An integer - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "integer". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Integer - base: int - uri: xsd:integer - boolean: - name: boolean - description: A binary (true or false) value - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "boolean". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Boolean - base: Bool - uri: xsd:boolean - repr: bool - float: - name: float - description: A real number that conforms to the xsd:float specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "float". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Float - base: float - uri: xsd:float - double: - name: double - description: A real number that conforms to the xsd:double specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "double". - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - schema:Float - base: float - uri: xsd:double - decimal: - name: decimal - description: A real number with arbitrary precision that conforms to the xsd:decimal - specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "decimal". - from_schema: https://w3id.org/nmdc/nmdc - broad_mappings: - - schema:Number - base: Decimal - uri: xsd:decimal - time: - name: time - description: A time object represents a (local) time of day, independent of any - particular day - notes: - - URI is dateTime because OWL reasoners do not work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "time". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Time - base: XSDTime - uri: xsd:time - repr: str - date: - name: date - description: a date (year, month and day) in an idealized calendar - notes: - - URI is dateTime because OWL reasoners don't work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:Date - base: XSDDate - uri: xsd:date - repr: str - datetime: - name: datetime - description: The combination of a date and time - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "datetime". - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - schema:DateTime - base: XSDDateTime - uri: xsd:dateTime - repr: str - date_or_datetime: - name: date_or_datetime - description: Either a date or a datetime - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date_or_datetime". - from_schema: https://w3id.org/nmdc/nmdc - base: str - uri: linkml:DateOrDatetime - repr: str - uriorcurie: - name: uriorcurie - description: a URI or a CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uriorcurie". - from_schema: https://w3id.org/nmdc/nmdc - base: URIorCURIE - uri: xsd:anyURI - repr: str - curie: - name: curie - conforms_to: https://www.w3.org/TR/curie/ - description: a compact URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "curie". - comments: - - in RDF serializations this MUST be expanded to a URI - - in non-RDF serializations MAY be serialized as the compact representation - from_schema: https://w3id.org/nmdc/nmdc - base: Curie - uri: xsd:string - repr: str - uri: - name: uri - conforms_to: https://www.ietf.org/rfc/rfc3987.txt - description: a complete URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uri". - comments: - - in RDF serializations a slot with range of uri is treated as a literal or type - xsd:anyURI unless it is an identifier or a reference to an identifier, in which - case it is translated directly to a node - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - schema:URL - base: URI - uri: xsd:anyURI - repr: str - ncname: - name: ncname - description: Prefix part of CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "ncname". - from_schema: https://w3id.org/nmdc/nmdc - base: NCName - uri: xsd:string - repr: str - objectidentifier: - name: objectidentifier - description: A URI or CURIE that represents an object in the model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "objectidentifier". - comments: - - Used for inheritance and type checking - from_schema: https://w3id.org/nmdc/nmdc - base: ElementIdentifier - uri: shex:iri - repr: str - nodeidentifier: - name: nodeidentifier - description: A URI, CURIE or BNODE that represents a node in a model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "nodeidentifier". - from_schema: https://w3id.org/nmdc/nmdc - base: NodeIdentifier - uri: shex:nonLiteral - repr: str - jsonpointer: - name: jsonpointer - conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 - description: A string encoding a JSON Pointer. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to a valid object within the current - instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpointer". - from_schema: https://w3id.org/nmdc/nmdc - base: str - uri: xsd:string - repr: str - jsonpath: - name: jsonpath - conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html - description: A string encoding a JSON Path. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to zero or more valid objects within - the current instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpath". - from_schema: https://w3id.org/nmdc/nmdc - base: str - uri: xsd:string - repr: str - sparqlpath: - name: sparqlpath - conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths - description: A string encoding a SPARQL Property Path. The value of the string - MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects - within the current instance document when encoded as RDF. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "sparqlpath". - from_schema: https://w3id.org/nmdc/nmdc - base: str - uri: xsd:string - repr: str - external_identifier: - name: external_identifier - description: A CURIE representing an external identifier - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://microbiomedata.github.io/nmdc-schema/identifiers/ - typeof: uriorcurie - uri: xsd:anyURI - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ -enums: - InstrumentModelEnum: - name: InstrumentModelEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Orbitrap: - text: Orbitrap - VortexGenie2: - text: VortexGenie2 - PIPETMAN F144059M: - text: PIPETMAN F144059M - InstrumentVendorEnum: - name: InstrumentVendorEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ThermoFisher: - text: ThermoFisher - VWR: - text: VWR - PerkinElmer: - text: PerkinElmer - Gilson: - text: Gilson - ScientificIndustries: - text: ScientificIndustries - StatusEnum: - name: StatusEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - pass: - text: pass - fail: - text: fail - ExtractionTargetEnum: - name: ExtractionTargetEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - DNA: - text: DNA - RNA: - text: RNA - metabolite: - text: metabolite - protein: - text: protein - LibraryTypeEnum: - name: LibraryTypeEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - DNA: - text: DNA - RNA: - text: RNA - JgiContTypeEnum: - name: JgiContTypeEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plate: - text: plate - tube: - text: tube - YesNoEnum: - name: YesNoEnum - description: replaces DnaDnaseEnum and DnaseRnaEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - 'no': - text: 'no' - 'yes': - text: 'yes' - BiosampleCategoryEnum: - name: BiosampleCategoryEnum - description: Funding-based, sample location-based, or experimental method-based - defined categories - notes: - - Currently, these values can associated with biosamples via the biosample_categories - slot - - They might also be applicable to other classes - - They are intended to enable metadata search and or filtering, for example in - the NMDC data portal, https://data.microbiomedata.org/ - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - category tag - permissible_values: - LTER: - text: LTER - meaning: https://lternet.edu/ - title: National Science Foundation's Long Term Ecological Research Network - SIP: - text: SIP - SFA: - text: SFA - description: Science Focus Area projects funded through the Department of - Energy Office of Science Biological and Environmental Research Program - meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance - title: Department of Energy Office of Science Biological and Environmental - Research Program Laboratory Science Focus Areas - FICUS: - text: FICUS - meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview - title: Facilities Integrating Collaborations for User Science - NEON: - text: NEON - meaning: https://www.neonscience.org - title: National Science Foundation's National Ecological Observatory Network - FileTypeEnum: - name: FileTypeEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Metagenome Raw Reads: - text: Metagenome Raw Reads - description: Interleaved paired-end raw sequencing data - annotations: - file_name_pattern: - tag: file_name_pattern - value: ^\.fastq(\.gz)?$ - Metagenome Raw Read 1: - text: Metagenome Raw Read 1 - description: Read 1 raw sequencing data, aka forward reads - annotations: - file_name_pattern: - tag: file_name_pattern - value: ^.+_R1\.fastq(\.gz)?$ - examples: - - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz - Metagenome Raw Read 2: - text: Metagenome Raw Read 2 - description: Read 2 raw sequencing data, aka reverse reads - annotations: - file_name_pattern: - tag: file_name_pattern - value: ^.+_R2\.fastq(\.gz)?$ - examples: - - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz - FT ICR-MS Analysis Results: - text: FT ICR-MS Analysis Results - description: FT ICR-MS-based molecular formula assignment results table - GC-MS Metabolomics Results: - text: GC-MS Metabolomics Results - description: GC-MS-based metabolite assignment results table - Metaproteomics Workflow Statistics: - text: Metaproteomics Workflow Statistics - description: Aggregate workflow statistics file - Protein Report: - text: Protein Report - description: Filtered protein report file - Peptide Report: - text: Peptide Report - description: Filtered peptide report file - Unfiltered Metaproteomics Results: - text: Unfiltered Metaproteomics Results - description: MSGFjobs and MASIC output file - Read Count and RPKM: - text: Read Count and RPKM - description: Annotation read count and RPKM per feature JSON - QC non-rRNA R2: - text: QC non-rRNA R2 - description: QC removed rRNA reads (R2) fastq - QC non-rRNA R1: - text: QC non-rRNA R1 - description: QC removed rRNA reads (R1) fastq - Metagenome Bins: - text: Metagenome Bins - description: Metagenome bin contigs fasta - Metagenome HQMQ Bins Compression File: - text: Metagenome HQMQ Bins Compression File - description: Compressed file containing high qulaity and medium quality metagenome - bins and associated files - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_hqmq_bin.zip' - Metagenome LQ Bins Compression File: - text: Metagenome LQ Bins Compression File - description: Compressed file containing low quality metagenome bins and associated - files - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_lq_bin.zip' - Metagenome Bins Info File: - text: Metagenome Bins Info File - description: File containing version information on the binning workflow - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_bin.info' - CheckM Statistics: - text: CheckM Statistics - description: CheckM statistics report - Metagenome Bins Heatmap: - text: Metagenome Bins Heatmap - description: The Heatmap presents the pdf file containing the KO analysis - results for metagenome bins - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_heatmap.pdf' - Metagenome Bins Barplot: - text: Metagenome Bins Barplot - description: The Bar chart presents the pdf file containing the KO analysis - results for metagenome bins - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_barplot.pdf' - Metagenome Bins Krona Plot: - text: Metagenome Bins Krona Plot - description: The Krona plot presents the HTML file containing the KO analysis - results for metagenome bins - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[mag_wf_activity_id]_kronaplot.html' - Read Based Analysis Info File: - text: Read Based Analysis Info File - description: File containing reads based analysis information - annotations: - file_name_pattern: - tag: file_name_pattern - value: profiler.info - GTDBTK Bacterial Summary: - text: GTDBTK Bacterial Summary - description: GTDBTK bacterial summary - GTDBTK Archaeal Summary: - text: GTDBTK Archaeal Summary - description: GTDBTK archaeal summary - GOTTCHA2 Krona Plot: - text: GOTTCHA2 Krona Plot - description: GOTTCHA2 krona plot HTML file - GOTTCHA2 Classification Report: - text: GOTTCHA2 Classification Report - description: GOTTCHA2 classification report file - GOTTCHA2 Report Full: - text: GOTTCHA2 Report Full - description: GOTTCHA2 report file - Kraken2 Krona Plot: - text: Kraken2 Krona Plot - description: Kraken2 krona plot HTML file - Centrifuge Krona Plot: - text: Centrifuge Krona Plot - description: Centrifuge krona plot HTML file - Centrifuge output report file: - text: Centrifuge output report file - description: Centrifuge output report file - Kraken2 Classification Report: - text: Kraken2 Classification Report - description: Kraken2 output report file - Kraken2 Taxonomic Classification: - text: Kraken2 Taxonomic Classification - description: Kraken2 output read classification file - Centrifuge Classification Report: - text: Centrifuge Classification Report - description: Centrifuge output report file - Centrifuge Taxonomic Classification: - text: Centrifuge Taxonomic Classification - description: Centrifuge output read classification file - Structural Annotation GFF: - text: Structural Annotation GFF - description: GFF3 format file with structural annotations - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_structural_annotation.gff' - Structural Annotation Stats Json: - text: Structural Annotation Stats Json - description: Structural annotations stats json - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_structural_annotation_stats.json' - Functional Annotation GFF: - text: Functional Annotation GFF - description: GFF3 format file with functional annotations - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_functional_annotation.gff' - Annotation Info File: - text: Annotation Info File - description: File containing annotation info - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_imgap.info' - Annotation Amino Acid FASTA: - text: Annotation Amino Acid FASTA - description: FASTA amino acid file for annotated proteins - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_proteins.faa' - Annotation Enzyme Commission: - text: Annotation Enzyme Commission - description: Tab delimited file for EC annotation - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_ec.tsv' - Annotation KEGG Orthology: - text: Annotation KEGG Orthology - description: Tab delimited file for KO annotation - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_ko.tsv' - Assembly Info File: - text: Assembly Info File - description: File containing assembly info - annotations: - file_name_pattern: - tag: file_name_pattern - value: README.txt - Assembly Coverage BAM: - text: Assembly Coverage BAM - description: Sorted bam file of reads mapping back to the final assembly - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_pairedMapped.sam.gz' - Assembly AGP: - text: Assembly AGP - description: An AGP format file that describes the assembly - Assembly Scaffolds: - text: Assembly Scaffolds - description: Final assembly scaffolds fasta - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_assembly.contigs.fasta' - Assembly Contigs: - text: Assembly Contigs - description: Final assembly contigs fasta - annotations: - file_name_pattern: - tag: file_name_pattern - value: assembly.contigs.fasta - Assembly Coverage Stats: - text: Assembly Coverage Stats - description: Assembled contigs coverage information - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_pairedMapped_sorted.bam.cov' - Contig Mapping File: - text: Contig Mapping File - description: Contig mappings between contigs and scaffolds - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_contig_names_mapping.tsv' - Error Corrected Reads: - text: Error Corrected Reads - description: Error corrected reads fastq - annotations: - file_name_pattern: - tag: file_name_pattern - value: input.corr.fastq.gz - Filtered Sequencing Reads: - text: Filtered Sequencing Reads - description: Reads QC result fastq (clean data) - annotations: - file_name_pattern: - tag: file_name_pattern - value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz ' - Read Filtering Info File: - text: Read Filtering Info File - description: File containing read filtering information - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[rqc_wf_activity_id]_readsQC.info' - QC Statistics Extended: - text: QC Statistics Extended - description: Extended report including methods and results for read filtering - annotations: - file_name_pattern: - tag: file_name_pattern - value: /.+?(?=filter)/filtered-report.txt - QC Statistics: - text: QC Statistics - description: Reads QC summary statistics - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[rqc_wf_activity_id]_filterStats2.txt' - TIGRFam Annotation GFF: - text: TIGRFam Annotation GFF - description: GFF3 format file with TIGRfam - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_tigrfam.gff' - CRT Annotation GFF: - text: CRT Annotation GFF - description: GFF3 format file with CRT - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_crt.gff' - Genemark Annotation GFF: - text: Genemark Annotation GFF - description: GFF3 format file with Genemark - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_genemark.gff' - Prodigal Annotation GFF: - text: Prodigal Annotation GFF - description: GFF3 format file with Prodigal - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_prodigal.gff' - TRNA Annotation GFF: - text: TRNA Annotation GFF - description: GFF3 format file with TRNA - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_trna.gff' - Misc Annotation GFF: - text: Misc Annotation GFF - description: GFF3 format file with Misc - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff' - RFAM Annotation GFF: - text: RFAM Annotation GFF - description: GFF3 format file with RFAM - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_rfam.gff' - TMRNA Annotation GFF: - text: TMRNA Annotation GFF - description: GFF3 format file with TMRNA - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_rfam_ncrna_tmrna.gff' - Crispr Terms: - text: Crispr Terms - description: Crispr Terms - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_crt.crisprs' - Product Names: - text: Product Names - description: Product names file - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_product_names.tsv' - Gene Phylogeny tsv: - text: Gene Phylogeny tsv - description: Gene Phylogeny tsv - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_gene_phylogeny.tsv' - Scaffold Lineage tsv: - text: Scaffold Lineage tsv - description: phylogeny at the scaffold level - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_scaffold_lineage.tsv' - Clusters of Orthologous Groups (COG) Annotation GFF: - text: Clusters of Orthologous Groups (COG) Annotation GFF - description: GFF3 format file with COGs - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_cog.gff' - KO_EC Annotation GFF: - text: KO_EC Annotation GFF - description: GFF3 format file with KO_EC - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_ko_ec.gff' - CATH FunFams (Functional Families) Annotation GFF: - text: CATH FunFams (Functional Families) Annotation GFF - description: GFF3 format file with CATH FunFams - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_cath_funfam.gff' - SUPERFam Annotation GFF: - text: SUPERFam Annotation GFF - description: GFF3 format file with SUPERFam - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_supfam.gff' - SMART Annotation GFF: - text: SMART Annotation GFF - description: GFF3 format file with SMART - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_smart.gff' - Pfam Annotation GFF: - text: Pfam Annotation GFF - description: GFF3 format file with Pfam - annotations: - file_name_pattern: - tag: file_name_pattern - value: '[GOLD-AP]_pfam.gff' - Annotation Statistics: - text: Annotation Statistics - description: Annotation statistics report - Direct Infusion FT ICR-MS Raw Data: - text: Direct Infusion FT ICR-MS Raw Data - description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance - mass spectrometry raw data acquired in broadband full scan mode - LC-DDA-MS/MS Raw Data: - text: LC-DDA-MS/MS Raw Data - description: Liquid chromatographically separated MS1 and Data-Dependent MS2 - binary instrument file - CreditEnum: - name: CreditEnum - comments: - - CreditEnums come from https://casrai.org/credit/ - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Conceptualization: - text: Conceptualization - description: Conceptualization - Data curation: - text: Data curation - description: Data curation - Formal Analysis: - text: Formal Analysis - description: Formal Analysis - Funding acquisition: - text: Funding acquisition - description: Funding acquisition - Investigation: - text: Investigation - description: Investigation - Methodology: - text: Methodology - description: Methodology - Project administration: - text: Project administration - description: Project administration - Resources: - text: Resources - description: Resources - Software: - text: Software - description: Software - Supervision: - text: Supervision - description: Supervision - Validation: - text: Validation - description: Validation - Visualization: - text: Visualization - description: Visualization - Writing original draft: - text: Writing original draft - description: Writing – original draft - Writing review and editing: - text: Writing review and editing - description: Writing – review & editing - Principal Investigator: - text: Principal Investigator - description: principal investigator role - meaning: OBI:0000103 - Submitter: - text: Submitter - description: the person(s) who enter study and biosample metadata into the - NMDC submission portal - meaning: EFO:0001741 - StudyCategoryEnum: - name: StudyCategoryEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - research_study: - text: research_study - description: A detailed examination, analysis, or critical inspection of a - hypothesis-driven experiment. - exact_mappings: - - SIO:001066 - - NCIT:C63536 - - ISA:Study - close_mappings: - - OBI:0000355 - consortium: - text: consortium - description: A group formed to undertake a venture that is beyond the capabilities - of the individual members. Each member of the consortium brings a high - level of expertise in a specific area to ensure the successful completion - of the project. - comments: - - A consortium has collections of data, those data do not come from a hypothesis-driven - experiment. - exact_mappings: - - NCIT:C61538 - DoiProviderEnum: - name: DoiProviderEnum - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - nmdc:ProcessingInstitutionEnum - permissible_values: - emsl: - text: emsl - meaning: https://ror.org/04rc0xn13 - title: EMSL - aliases: - - Environmental Molecular Sciences Laboratory - - EMSL - jgi: - text: jgi - meaning: https://ror.org/04xm1d337 - title: JGI - aliases: - - Joint Genome Institute - - JGI - kbase: - text: kbase - meaning: https://ror.org/01znn6x10 - title: KBase - aliases: - - KBase - osti: - text: osti - meaning: https://ror.org/031478740 - title: OSTI - aliases: - - Office of Scientific and Technical Information - - OSTI - ess_dive: - text: ess_dive - meaning: https://ror.org/01t14bp54 - title: ESS-DIVE - aliases: - - ESS-DIVE - - Environmental System Science Data Infrastructure for a Virtual Ecosystem - massive: - text: massive - title: MassIVE - aliases: - - MassIVE - - Mass Spectrometry Virtual Environment - gsc: - text: gsc - title: GSC - aliases: - - GSC - - Genomic Standards Consortium - zenodo: - text: zenodo - title: Zenodo - aliases: - - Zenodo - edi: - text: edi - meaning: https://ror.org/0330j0z60 - title: EDI - aliases: - - EDI - - Environmental Data Initiative - DoiCategoryEnum: - name: DoiCategoryEnum - comments: - - See especially the resourceTypeGeneral section of the DataCite PDF, on pp48-53 - as of 2023-07-19 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf - - https://api.crossref.org/types - permissible_values: - award_doi: - text: award_doi - description: A type of DOI that resolves to a funding authority. - dataset_doi: - text: dataset_doi - description: A type of DOI that resolves to generated data. - publication_doi: - text: publication_doi - description: A type of DOI that resolves to a publication. - data_management_plan_doi: - text: data_management_plan_doi - description: A type of DOI that resolves to a data management plan. - ContainerCategoryEnum: - name: ContainerCategoryEnum - description: The permitted types of containers used in processing metabolomic - samples. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - permissible_values: - V-bottom conical tube: - text: V-bottom conical tube - falcon tube: - text: falcon tube - FailureWhatEnum: - name: FailureWhatEnum - description: The permitted values for describing where a failure occurred during - processing in the lab during analysis workflows. - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low_read_count: - text: low_read_count - description: Number of output reads is not sufficient to continue to the next - analysis step. - malformed_data: - text: malformed_data - description: Workflow failure reading input or writing the output file(s). - assembly_size_too_small: - text: assembly_size_too_small - description: The size of the metagenome or metatranscriptome assembly is too - small to proceed to the next analysis workflow. - no_valid_data_generated: - text: no_valid_data_generated - description: A process ran but did not produce any output. Ie binning ran - but did not produce any medium or high quality bins. - other: - text: other - description: A lab process or analysis workflow has failed in a way that has - not been captured by the available values yet. Please use slot 'qc_comment' - to specify details. - FailureWhereEnum: - name: FailureWhereEnum - description: The permitted values for describing where in the process, either - a lab or analysis workflow step, the failure occurred. - comments: - - At Chris' recommendation permissible values for this enumeration are the same - as Class names. - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - OmicsProcessing: - text: OmicsProcessing - description: A failure has occurred in omics processing, a lab process. - Pooling: - text: Pooling - description: A failure has occurred in pooling, a lab process. - Extraction: - text: Extraction - description: A failure has occurred in extraction, a lab process. - LibraryPreparation: - text: LibraryPreparation - description: A failure has occurred in library preparation, a lab process. - MetagenomeAssembly: - text: MetagenomeAssembly - description: A failure has occurred in metagenome assembly, a workflow process. - MetatranscriptomeActivity: - text: MetatranscriptomeActivity - description: A failure has occurred in metatranscriptome analysis, a workflow - process. - MagsAnalysisActivity: - text: MagsAnalysisActivity - description: A failure has occurred in binning, a workflow process to generate - metagenome-assembled genomes (MAGS). - ReadQcAnalysisActivity: - text: ReadQcAnalysisActivity - description: A failure has occurred in read qc, a workflow process. - ReadBasedTaxonomyAnalysisActivity: - text: ReadBasedTaxonomyAnalysisActivity - description: A failure has occurred in reads based taxonomy, a workflow process. - MetagenomeAnnotationActivity: - text: MetagenomeAnnotationActivity - description: A failure has occurred in annotation, a workflow process. - SeparationMethodEnum: - name: SeparationMethodEnum - description: The tool/substance used to separate or filter a solution or mixture. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - permissible_values: - PTFE 96-well filter plate: - text: PTFE 96-well filter plate - CompoundEnum: - name: CompoundEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ammonium bicarbonate: - text: ammonium bicarbonate - deionized water: - text: deionized water - methanol: - text: methanol - trypsin: - text: trypsin - chloridic acid: - text: chloridic acid - aliases: - - hydrochloric acid - water: - text: water - StationaryPhaseEnum: - name: StationaryPhaseEnum - description: The type of stationary phase used in a solid phase extraction process. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - permissible_values: - C18: - text: C18 - C8: - text: C8 - C4: - text: C4 - C2: - text: C2 - C1: - text: C1 - C30: - text: C30 - C60: - text: C60 - CNT: - text: CNT - CN: - text: CN - Diol: - text: Diol - HILIC: - text: HILIC - NH2: - text: NH2 - Phenyl: - text: Phenyl - PS-DVB: - text: PS-DVB - SAX: - text: SAX - SCX: - text: SCX - Silica: - text: Silica - WCX: - text: WCX - WAX: - text: WAX - ZIC-HILIC: - text: ZIC-HILIC - ZIC-pHILIC: - text: ZIC-pHILIC - ZIC-cHILIC: - text: ZIC-cHILIC - DeviceEnum: - name: DeviceEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Orbital Shaker: - text: Orbital Shaker - Thermomixer: - text: Thermomixer - Vortex: - text: Vortex - Agitation plunger: - text: Agitation plunger - Drying oven: - text: Drying oven - CEREX System 96 processor: - text: CEREX System 96 processor - arch_struc_enum: - name: arch_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - biol_stat_enum: - name: biol_stat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant - biotic_relationship_enum: - name: biotic_relationship_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - build_docs_enum: - name: build_docs_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - building_setting_enum: - name: building_setting_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - ceil_cond_enum: - name: ceil_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - ceil_finish_mat_enum: - name: ceil_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - ceil_texture_enum: - name: ceil_texture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - ceil_type_enum: - name: ceil_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched - cur_land_use_enum: - name: cur_land_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - badlands: - text: badlands - cities: - text: cities - conifers: - text: conifers - annotations: - originally: - tag: originally - value: conifers (e.g. pine,spruce,fir,cypress) - examples: - - value: cypress - - value: fir - - value: pine - - value: spruce - crop trees: - text: crop trees - annotations: - originally: - tag: originally - value: crop trees (nuts,fruit,christmas trees,nursery trees) - examples: - - value: christmas trees - - value: fruit - - value: nursery trees - - value: nuts - farmstead: - text: farmstead - gravel: - text: gravel - hardwoods: - text: hardwoods - annotations: - originally: - tag: originally - value: hardwoods (e.g. oak,hickory,elm,aspen) - examples: - - value: aspen - - value: elm - - value: hickory - - value: oak - hayland: - text: hayland - horticultural plants: - text: horticultural plants - annotations: - originally: - tag: originally - value: horticultural plants (e.g. tulips) - examples: - - value: tulips - industrial areas: - text: industrial areas - intermixed hardwood and conifers: - text: intermixed hardwood and conifers - marshlands: - text: marshlands - annotations: - originally: - tag: originally - value: marshlands (grass,sedges,rushes) - examples: - - value: grass - - value: rushes - - value: sedgees - meadows: - text: meadows - annotations: - originally: - tag: originally - value: meadows (grasses,alfalfa,fescue,bromegrass,timothy) - examples: - - value: alfalfa - - value: bromegrass - - value: fescue - - value: grasses - - value: timothy - mines/quarries: - text: mines/quarries - mudflats: - text: mudflats - oil waste areas: - text: oil waste areas - pastureland: - text: pastureland - annotations: - originally: - tag: originally - value: pastureland (grasslands used for livestock grazing) - comments: - - grasslands used for livestock grazing - permanent snow or ice: - text: permanent snow or ice - rainforest: - text: rainforest - annotations: - originally: - tag: originally - value: rainforest (evergreen forest receiving greater than 406 cm annual - rainfall) - comments: - - evergreen forest receiving greater than 406 cm annual rainfall - rangeland: - text: rangeland - roads/railroads: - text: roads/railroads - rock: - text: rock - row crops: - text: row crops - saline seeps: - text: saline seeps - salt flats: - text: salt flats - sand: - text: sand - shrub crops: - text: shrub crops - annotations: - originally: - tag: originally - value: shrub crops (blueberries,nursery ornamentals,filberts) - examples: - - value: blueberries - - value: filberts - - value: nursery ornamentals - shrub land: - text: shrub land - annotations: - originally: - tag: originally - value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus) - examples: - - value: creosote bush - - value: eucalyptus - - value: mesquite - - value: sage-brush - - value: shrub oak - small grains: - text: small grains - successional shrub land: - text: successional shrub land - annotations: - originally: - tag: originally - value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub - dogwoods,blackberries) - examples: - - value: blackberries - - value: chokecherry - - value: hazels - - value: shrub dogwoods - - value: sumacs - - value: tree saplings - swamp: - text: swamp - annotations: - originally: - tag: originally - value: swamp (permanent or semi-permanent water body dominated by woody - plants) - comments: - - permanent or semi-permanent water body dominated by woody plants - tropical: - text: tropical - annotations: - originally: - tag: originally - value: tropical (e.g. mangrove,palms) - examples: - - value: mangrove - - value: palms - tundra: - text: tundra - annotations: - originally: - tag: originally - value: tundra (mosses,lichens) - examples: - - value: lichens - - value: mosses - vegetable crops: - text: vegetable crops - vine crops: - text: vine crops - annotations: - originally: - tag: originally - value: vine crops (grapes) - examples: - - value: grapes - depos_env_enum: - name: depos_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - door_cond_enum: - name: door_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_direct_enum: - name: door_direct_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - door_loc_enum: - name: door_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - door_mat_enum: - name: door_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass - metal: - text: metal - thermoplastic alloy: - text: thermoplastic alloy - vinyl: - text: vinyl - wood: - text: wood - wood/plastic composite: - text: wood/plastic composite - door_move_enum: - name: door_move_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging - door_type_enum: - name: door_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - door_type_wood_enum: - name: door_type_wood_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bettened and ledged: - text: bettened and ledged - battened: - text: battened - ledged and braced: - text: ledged and braced - ledged and framed: - text: ledged and framed - ledged, braced and frame: - text: ledged, braced and frame - framed and paneled: - text: framed and paneled - glashed or sash: - text: glashed or sash - flush: - text: flush - louvered: - text: louvered - wire gauged: - text: wire gauged - drainage_class_enum: - name: drainage_class_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - drawings_enum: - name: drawings_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - ext_wall_orient_enum: - name: ext_wall_orient_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - ext_window_orient_enum: - name: ext_window_orient_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - fao_class_enum: - name: fao_class_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Acrisols: - text: Acrisols - Andosols: - text: Andosols - Arenosols: - text: Arenosols - Cambisols: - text: Cambisols - Chernozems: - text: Chernozems - Ferralsols: - text: Ferralsols - Fluvisols: - text: Fluvisols - Gleysols: - text: Gleysols - Greyzems: - text: Greyzems - Gypsisols: - text: Gypsisols - Histosols: - text: Histosols - Kastanozems: - text: Kastanozems - Lithosols: - text: Lithosols - Luvisols: - text: Luvisols - Nitosols: - text: Nitosols - Phaeozems: - text: Phaeozems - Planosols: - text: Planosols - Podzols: - text: Podzols - Podzoluvisols: - text: Podzoluvisols - Rankers: - text: Rankers - Regosols: - text: Regosols - Rendzinas: - text: Rendzinas - Solonchaks: - text: Solonchaks - Solonetz: - text: Solonetz - Vertisols: - text: Vertisols - Yermosols: - text: Yermosols - filter_type_enum: - name: filter_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - floor_cond_enum: - name: floor_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_finish_mat_enum: - name: floor_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - tile: - text: tile - wood strip or parquet: - text: wood strip or parquet - carpet: - text: carpet - rug: - text: rug - laminate wood: - text: laminate wood - lineoleum: - text: lineoleum - vinyl composition tile: - text: vinyl composition tile - sheet vinyl: - text: sheet vinyl - stone: - text: stone - bamboo: - text: bamboo - cork: - text: cork - terrazo: - text: terrazo - concrete: - text: concrete - none: - text: none - sealed: - text: sealed - clear finish: - text: clear finish - paint: - text: paint - none or unfinished: - text: none or unfinished - floor_struc_enum: - name: floor_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - floor_water_mold_enum: - name: floor_water_mold_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - freq_clean_enum: - name: freq_clean_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - furniture_enum: - name: furniture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - growth_habit_enum: - name: growth_habit_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - handidness_enum: - name: handidness_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - hc_produced_enum: - name: hc_produced_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - hcr_enum: - name: hcr_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - hcr_geol_age_enum: - name: hcr_geol_age_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic - other: - text: other - heat_cool_type_enum: - name: heat_cool_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - heat_deliv_loc_enum: - name: heat_deliv_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - host_sex_enum: - name: host_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - indoor_space_enum: - name: indoor_space_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - indoor_surf_enum: - name: indoor_surf_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - light_type_enum: - name: light_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - lithology_enum: - name: lithology_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other - mech_struc_enum: - name: mech_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - occup_document_enum: - name: occup_document_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - organism_count_enum: - name: organism_count_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ATP: - text: ATP - MPN: - text: MPN - other: - text: other - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other - plant_growth_med_enum: - name: plant_growth_med_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - plant_sex_enum: - name: plant_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - profile_position_enum: - name: profile_position_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - quad_pos_enum: - name: quad_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - rel_samp_loc_enum: - name: rel_samp_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - room_condt_enum: - name: room_condt_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - visible signs of mold/mildew: - text: visible signs of mold/mildew - room_connected_enum: - name: room_connected_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - room_loc_enum: - name: room_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - room_samp_pos_enum: - name: room_samp_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - room_type_enum: - name: room_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_capt_status_enum: - name: samp_capt_status_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - samp_collect_point_enum: - name: samp_collect_point_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_dis_stage_enum: - name: samp_dis_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - samp_floor_enum: - name: samp_floor_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - samp_md_enum: - name: samp_md_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other - samp_subtype_enum: - name: samp_subtype_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - samp_weather_enum: - name: samp_weather_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - season_use_enum: - name: season_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sediment_type_enum: - name: sediment_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - shading_device_cond_enum: - name: shading_device_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - shading_device_type_enum: - name: shading_device_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bahama shutters: - text: bahama shutters - exterior roll blind: - text: exterior roll blind - gambrel awning: - text: gambrel awning - hood awning: - text: hood awning - porchroller awning: - text: porchroller awning - sarasota shutters: - text: sarasota shutters - slatted aluminum: - text: slatted aluminum - solid aluminum awning: - text: solid aluminum awning - sun screen: - text: sun screen - tree: - text: tree - trellis: - text: trellis - venetian awning: - text: venetian awning - soil_horizon_enum: - name: soil_horizon_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - specific_enum: - name: specific_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - sr_geol_age_enum: - name: sr_geol_age_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic - other: - text: other - sr_kerog_type_enum: - name: sr_kerog_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other - sr_lithology_enum: - name: sr_lithology_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous - other: - text: other - substructure_type_enum: - name: substructure_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - surf_air_cont_enum: - name: surf_air_cont_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - dust: - text: dust - organic matter: - text: organic matter - particulate matter: - text: particulate matter - volatile organic compounds: - text: volatile organic compounds - biological contaminants: - text: biological contaminants - radon: - text: radon - nutrients: - text: nutrients - biocides: - text: biocides - surf_material_enum: - name: surf_material_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - tillage_enum: - name: tillage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - train_line_enum: - name: train_line_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - train_stat_loc_enum: - name: train_stat_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - train_stop_loc_enum: - name: train_stop_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - vis_media_enum: - name: vis_media_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans - wall_const_type_enum: - name: wall_const_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - wall_loc_enum: - name: wall_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - wall_texture_enum: - name: wall_texture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - weekday_enum: - name: weekday_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - window_cond_enum: - name: window_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - window_cover_enum: - name: window_cover_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - window_horiz_pos_enum: - name: window_horiz_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - window_loc_enum: - name: window_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - window_mat_enum: - name: window_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - window_type_enum: - name: window_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - SampleTypeEnum: - name: SampleTypeEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - soil: - text: soil - soil - water extract: - text: soil - water extract - plant associated: - text: plant associated - sediment: - text: sediment - water: - text: water - DNASampleFormatEnum: - name: DNASampleFormatEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - 10 mM Tris-HCl: - text: 10 mM Tris-HCl - DNAStable: - text: DNAStable - Ethanol: - text: Ethanol - Low EDTA TE: - text: Low EDTA TE - MDA reaction buffer: - text: MDA reaction buffer - PBS: - text: PBS - Pellet: - text: Pellet - RNAStable: - text: RNAStable - TE: - text: TE - Water: - text: Water - Gentegra-DNA: - text: Gentegra-DNA - Gentegra-RNA: - text: Gentegra-RNA - RNASampleFormatEnum: - name: RNASampleFormatEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - 10 mM Tris-HCl: - text: 10 mM Tris-HCl - DNAStable: - text: DNAStable - Ethanol: - text: Ethanol - Low EDTA TE: - text: Low EDTA TE - MDA reaction buffer: - text: MDA reaction buffer - PBS: - text: PBS - Pellet: - text: Pellet - RNAStable: - text: RNAStable - TE: - text: TE - Water: - text: Water - Gentegra-DNA: - text: Gentegra-DNA - Gentegra-RNA: - text: Gentegra-RNA - AnalysisTypeEnum: - name: AnalysisTypeEnum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - metabolomics: - text: metabolomics - metagenomics: - text: metagenomics - description: Standard short-read metagenomic sequencing - title: Metagenomics - metagenomics_long_read: - text: metagenomics_long_read - description: Long-read metagenomic sequencing - title: Metagenomics (long read) - metaproteomics: - text: metaproteomics - metatranscriptomics: - text: metatranscriptomics - natural organic matter: - text: natural organic matter - bulk chemistry: - text: bulk chemistry - processing_institution_enum: - name: processing_institution_enum - notes: - - This will become the range of processing_institution.omics processing - - use ROR meanings like https://ror.org/0168r3w48 for UCSD - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - UCSD: - text: UCSD - meaning: https://ror.org/0168r3w48 - title: University of California, San Diego - JGI: - text: JGI - meaning: https://ror.org/04xm1d337 - title: Joint Genome Institute - EMSL: - text: EMSL - meaning: https://ror.org/04rc0xn13 - title: Environmental Molecular Sciences Laboratory - aliases: - - Environmental Molecular Science Laboratory - - Environmental Molecular Sciences Lab - Battelle: - text: Battelle - meaning: https://ror.org/01h5tnr73 - title: Battelle Memorial Institute - ANL: - text: ANL - meaning: https://ror.org/05gvnxz63 - title: Argonne National Laboratory - UCD_Genome_Center: - text: UCD_Genome_Center - meaning: https://genomecenter.ucdavis.edu/ - title: University of California, Davis Genome Center -slots: - has_failure_categorization: - name: has_failure_categorization - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: FailureCategorization - model: - name: model - from_schema: https://w3id.org/nmdc/nmdc - range: InstrumentModelEnum - vendor: - name: vendor - from_schema: https://w3id.org/nmdc/nmdc - range: InstrumentVendorEnum - metagenome_annotation_id: - name: metagenome_annotation_id - description: The identifier for the analysis activity (WorkflowExecutionActivity) - that generated the functional annotation results. - from_schema: https://w3id.org/nmdc/nmdc - domain: FunctionalAnnotationAggMember - range: MetagenomeAnnotationActivity - required: true - gene_function_id: - name: gene_function_id - description: The identifier for the gene function. - examples: - - value: KEGG.ORTHOLOGY:K00627 - from_schema: https://w3id.org/nmdc/nmdc - range: uriorcurie - required: true - count: - name: count - from_schema: https://w3id.org/nmdc/nmdc - range: integer - required: true - functional_annotation_agg: - name: functional_annotation_agg - from_schema: https://w3id.org/nmdc/nmdc - domain: Database - multivalued: true - range: FunctionalAnnotationAggMember - inlined: true - inlined_as_list: true - ecosystem_path_id: - name: ecosystem_path_id - description: A unique id representing the GOLD classifiers associated with a sample. - from_schema: https://w3id.org/nmdc/nmdc - range: string - habitat: - name: habitat - from_schema: https://w3id.org/nmdc/nmdc - range: string - location: - name: location - from_schema: https://w3id.org/nmdc/nmdc - range: string - community: - name: community - from_schema: https://w3id.org/nmdc/nmdc - range: string - ncbi_taxonomy_name: - name: ncbi_taxonomy_name - from_schema: https://w3id.org/nmdc/nmdc - range: string - ncbi_project_name: - name: ncbi_project_name - from_schema: https://w3id.org/nmdc/nmdc - range: string - sample_collection_site: - name: sample_collection_site - from_schema: https://w3id.org/nmdc/nmdc - range: string - sample_collection_year: - name: sample_collection_year - from_schema: https://w3id.org/nmdc/nmdc - range: integer - sample_collection_month: - name: sample_collection_month - from_schema: https://w3id.org/nmdc/nmdc - qc_status: - name: qc_status - description: Stores information about the result of a process (ie the process - of sequencing a library may have for qc_status of 'fail' if not enough data - was generated) - from_schema: https://w3id.org/nmdc/nmdc - range: StatusEnum - library_preparation_kit: - name: library_preparation_kit - from_schema: https://w3id.org/nmdc/nmdc - range: string - extraction_method: - name: extraction_method - from_schema: https://w3id.org/nmdc/nmdc - domain: Extraction - range: ExtractionTargetEnum - pcr_cycles: - name: pcr_cycles - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - OBI:0002475 - range: integer - mass: - name: mass - description: A physical quality that inheres in a bearer by virtue of the proportion - of the bearer's amount of matter. - title: mass - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - PATO:0000125 - range: QuantityValue - input_mass: - name: input_mass - description: Total mass of sample used in activity. - title: sample mass used - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample mass - - sample weight - exact_mappings: - - MS:1000004 - domain: PlannedProcess - range: QuantityValue - library_type: - name: library_type - title: library type - examples: - - value: DNA - from_schema: https://w3id.org/nmdc/nmdc - domain: LibraryPreparation - range: LibraryTypeEnum - zinc: - name: zinc - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mg/kg (ppm) - occurrence: - tag: occurrence - value: '1' - description: Concentration of zinc in the sample - title: zinc - examples: - - value: 2.5 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - zinc - range: QuantityValue - manganese: - name: manganese - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mg/kg (ppm) - occurrence: - tag: occurrence - value: '1' - description: Concentration of manganese in the sample - title: manganese - examples: - - value: 24.7 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - manganese - range: QuantityValue - ammonium_nitrogen: - name: ammonium_nitrogen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mg/kg - occurrence: - tag: occurrence - value: '1' - description: Concentration of ammonium nitrogen in the sample - title: ammonium nitrogen - examples: - - value: 2.3 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - ammonium_nitrogen - - NH4-N - range: QuantityValue - nitrate_nitrogen: - name: nitrate_nitrogen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mg/kg - occurrence: - tag: occurrence - value: '1' - description: Concentration of nitrate nitrogen in the sample - title: nitrate_nitrogen - comments: - - often below some specified limit of detection - examples: - - value: 0.29 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - nitrate_nitrogen - - NO3-N - range: QuantityValue - nitrite_nitrogen: - name: nitrite_nitrogen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mg/kg - occurrence: - tag: occurrence - value: '1' - description: Concentration of nitrite nitrogen in the sample - title: nitrite_nitrogen - examples: - - value: 1.2 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - nitrite_nitrogen - - NO2-N - range: QuantityValue - lbc_thirty: - name: lbc_thirty - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: ppm CaCO3/pH - occurrence: - tag: occurrence - value: '1' - description: lime buffer capacity, determined after 30 minute incubation - title: lime buffer capacity (at 30 minutes) - comments: - - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by - one pH unit - examples: - - value: 543 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF - aliases: - - lbc_thirty - - lbc30 - - lime buffer capacity (at 30 minutes) - range: QuantityValue - lbceq: - name: lbceq - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: ppm CaCO3/pH - occurrence: - tag: occurrence - value: '1' - description: lime buffer capacity, determined at equilibrium after 5 day incubation - title: lime buffer capacity (after 5 day incubation) - comments: - - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by - one pH unit - examples: - - value: 1575 mg/kg - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ornl.gov/content/bio-scales-0 - aliases: - - lbceq - - lime buffer capacity (at 5-day equilibrium) - range: QuantityValue - env_package: - name: env_package - description: MIxS extension for reporting of measurements and observations obtained - from one or more of the environments where the sample was obtained. All environmental - packages listed here are further defined in separate subtables. By giving the - name of the environmental package, a selection of fields can be made from the - subtables and can be reported - notes: - - no longer in MIxS as of 6.0? - in_subset: - - mixs extension - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - environmental package - range: TextValue - embargoed: - name: embargoed - description: If true, the data are embargoed and not available for public access. - todos: - - make this required? - - first apply to Biosample - - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata? - - applying to a Study may not be granular enough - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - recommended: true - collected_from: - name: collected_from - description: The Site from which a Biosample was collected - todos: - - add an OBO slot_uri ? - comments: - - this illustrates implementing a Biosample relation with a (binary) slot - from_schema: https://w3id.org/nmdc/nmdc - domain: Biosample - range: FieldResearchSite - biosample_categories: - name: biosample_categories - title: Categories the biosample belongs to - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: BiosampleCategoryEnum - date_created: - name: date_created - description: from database class - from_schema: https://w3id.org/nmdc/nmdc - etl_software_version: - name: etl_software_version - description: from database class - from_schema: https://w3id.org/nmdc/nmdc - related_identifiers: - name: related_identifiers - description: Identifiers assigned to a thing that is similar to that which is - represented in NMDC. Related identifier are not an identical match and may have - some variation. - title: Related Identifiers - from_schema: https://w3id.org/nmdc/nmdc - domain: Study - notes: - name: notes - description: from study class - from_schema: https://w3id.org/nmdc/nmdc - has_credit_associations: - name: has_credit_associations - annotations: - tooltip: - tag: tooltip - value: Other researchers associated with this study. - description: 'This slot links a study to a credit association. The credit association - will be linked to a person value and to a CRediT Contributor Roles term. Overall - semantics: person should get credit X for their participation in the study' - from_schema: https://w3id.org/nmdc/nmdc - domain: Study - slot_uri: prov:qualifiedAssociation - multivalued: true - range: CreditAssociation - inlined_as_list: true - study_image: - name: study_image - description: Links a study to one or more images. - from_schema: https://w3id.org/nmdc/nmdc - domain: Study - multivalued: true - range: ImageValue - inlined: true - relevant_protocols: - name: relevant_protocols - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: string - funding_sources: - name: funding_sources - description: A list of organizations, along with the award numbers, that underwrite - financial support for projects of a particular type. Typically, they process - applications and award funds to the chosen qualified applicants. - comments: - - Include only the name of the funding organization and the award or contract - number. - examples: - - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701) - - value: U.S. Department of Energy, Office of Science, Office of Biological and - Environmental Research (BER) under contract DE-AC05-00OR2275 - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - NCIT:C39409 - multivalued: true - range: string - applied_roles: - name: applied_roles - annotations: - tooltip: - tag: tooltip - value: 'Identify all CRediT roles associated with this contributor. CRediT - Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: - https://credit.niso.org/' - from_schema: https://w3id.org/nmdc/nmdc - domain: CreditAssociation - multivalued: true - range: CreditEnum - required: true - applies_to_person: - name: applies_to_person - from_schema: https://w3id.org/nmdc/nmdc - domain: CreditAssociation - range: PersonValue - required: true - study_category: - name: study_category - description: The type of research initiative - from_schema: https://w3id.org/nmdc/nmdc - domain: Study - range: StudyCategoryEnum - required: true - object_set: - name: object_set - description: Applies to a property that links a database object to a set of objects. - This is necessary in a json document to provide context for a list, and to allow - for a single json object that combines multiple object types - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - domain: Database - multivalued: true - inlined_as_list: true - planned_process_set: - name: planned_process_set - description: This property links a database object to the set of planned processes - within it. - comments: - - PlannedProcess instances aggregated by this slot will require the designated_class - slot - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: PlannedProcess - biosample_set: - name: biosample_set - description: This property links a database object to the set of samples within - it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: Biosample - study_set: - name: study_set - description: This property links a database object to the set of studies within - it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: Study - field_research_site_set: - name: field_research_site_set - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: FieldResearchSite - collecting_biosamples_from_site_set: - name: collecting_biosamples_from_site_set - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: CollectingBiosamplesFromSite - data_object_set: - name: data_object_set - description: This property links a database object to the set of data objects - within it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: DataObject - genome_feature_set: - name: genome_feature_set - description: This property links a database object to the set of all features - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: GenomeFeature - functional_annotation_set: - name: functional_annotation_set - description: This property links a database object to the set of all functional - annotations - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: FunctionalAnnotation - mags_activity_set: - name: mags_activity_set - description: This property links a database object to the set of MAGs analysis - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MagsAnalysisActivity - metabolomics_analysis_activity_set: - name: metabolomics_analysis_activity_set - description: This property links a database object to the set of metabolomics - analysis activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetabolomicsAnalysisActivity - metaproteomics_analysis_activity_set: - name: metaproteomics_analysis_activity_set - description: This property links a database object to the set of metaproteomics - analysis activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetaproteomicsAnalysisActivity - metagenome_annotation_activity_set: - name: metagenome_annotation_activity_set - description: This property links a database object to the set of metagenome annotation - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetagenomeAnnotationActivity - metagenome_assembly_set: - name: metagenome_assembly_set - description: This property links a database object to the set of metagenome assembly - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetagenomeAssembly - metagenome_sequencing_activity_set: - name: metagenome_sequencing_activity_set - description: This property links a database object to the set of metagenome sequencing - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetagenomeSequencingActivity - metatranscriptome_activity_set: - name: metatranscriptome_activity_set - description: This property links a database object to the set of metatranscriptome - analysis activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: MetatranscriptomeActivity - read_qc_analysis_activity_set: - name: read_qc_analysis_activity_set - description: This property links a database object to the set of read QC analysis - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: ReadQcAnalysisActivity - read_based_taxonomy_analysis_activity_set: - name: read_based_taxonomy_analysis_activity_set - description: This property links a database object to the set of read based analysis - activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: ReadBasedTaxonomyAnalysisActivity - nom_analysis_activity_set: - name: nom_analysis_activity_set - description: This property links a database object to the set of natural organic - matter (NOM) analysis activities. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: NomAnalysisActivity - omics_processing_set: - name: omics_processing_set - description: This property links a database object to the set of omics processings - within it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: OmicsProcessing - pooling_set: - name: pooling_set - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: Pooling - processed_sample_set: - name: processed_sample_set - description: This property links a database object to the set of processed samples - within it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: ProcessedSample - extraction_set: - name: extraction_set - description: This property links a database object to the set of extractions within - it. - from_schema: https://w3id.org/nmdc/nmdc - mixins: - - object_set - domain: Database - range: Extraction - library_preparation_set: - name: library_preparation_set - description: This property links a database object to the set of DNA extractions - within it. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - library_construction_set - mixins: - - object_set - domain: Database - range: LibraryPreparation - omics_type: - name: omics_type - description: The type of omics data - examples: - - value: metatranscriptome - - value: metagenome - from_schema: https://w3id.org/nmdc/nmdc - domain: OmicsProcessing - range: ControlledTermValue - data_object_type: - name: data_object_type - description: The type of file represented by the data object. - examples: - - value: FT ICR-MS Analysis Results - - value: GC-MS Metabolomics Results - from_schema: https://w3id.org/nmdc/nmdc - range: FileTypeEnum - compression_type: - name: compression_type - description: If provided, specifies the compression type - todos: - - consider setting the range to an enum - examples: - - value: gzip - from_schema: https://w3id.org/nmdc/nmdc - range: string - gold_path_field: - name: gold_path_field - description: This is a grouping for any of the gold path fields - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - range: string - ecosystem: - name: ecosystem - description: An ecosystem is a combination of a physical environment (abiotic - factors) and all the organisms (biotic factors) that interact with this environment. - Ecosystem is in position 1/5 in a GOLD path. - comments: - - The abiotic factors play a profound role on the type and composition of organisms - in a given environment. The GOLD Ecosystem at the top of the five-level classification - system is aimed at capturing the broader environment from which an organism - or environmental sample is collected. The three broad groups under Ecosystem - are Environmental, Host-associated, and Engineered. They represent samples collected - from a natural environment or from another organism or from engineered environments - like bioreactors respectively. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/help - is_a: gold_path_field - ecosystem_category: - name: ecosystem_category - description: Ecosystem categories represent divisions within the ecosystem based - on specific characteristics of the environment from where an organism or sample - is isolated. Ecosystem category is in position 2/5 in a GOLD path. - comments: - - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. - Ecosystem categories for Host-associated samples can be individual hosts or - phyla and for engineered samples it may be manipulated environments like bioreactors, - solid waste etc. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/help - is_a: gold_path_field - ecosystem_type: - name: ecosystem_type - description: Ecosystem types represent things having common characteristics within - the Ecosystem Category. These common characteristics based grouping is still - broad but specific to the characteristics of a given environment. Ecosystem - type is in position 3/5 in a GOLD path. - comments: - - The Aquatic ecosystem category (for example) may have ecosystem types like Marine - or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor - air as different Ecosystem Types. In the case of Host-associated samples, ecosystem - type can represent Respiratory system, Digestive system, Roots etc. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/help - is_a: gold_path_field - ecosystem_subtype: - name: ecosystem_subtype - description: Ecosystem subtypes represent further subdivision of Ecosystem types - into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD - path. - comments: - - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided - (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in - the Ecosystem subtype category. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/help - is_a: gold_path_field - specific_ecosystem: - name: specific_ecosystem - description: Specific ecosystems represent specific features of the environment - like aphotic zone in an ocean or gastric mucosa within a host digestive system. - Specific ecosystem is in position 5/5 in a GOLD path. - comments: - - Specific ecosystems help to define samples based on very specific characteristics - of an environment under the five-level classification system. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/help - is_a: gold_path_field - principal_investigator: - name: principal_investigator - description: Principal Investigator who led the study and/or generated the dataset. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - PI - range: PersonValue - associated_dois: - name: associated_dois - description: A list of DOIs associated with a resource, such as a list of DOIS - associated with a Study. - examples: - - value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'': - ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'', - ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'', - ''doi_category'': ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]' - description: Provides a list of two DOIs; specifically, an EMSL award DOI and - a publication DOI. - in_subset: - - data_portal_subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Associated DOIs - - Associated digital object identifiers - domain: Study - multivalued: true - range: Doi - inlined_as_list: true - doi_value: - name: doi_value - description: A digital object identifier, which is intended to persistantly identify - some resource on the web. - examples: - - value: doi:10.46936/10.25585/60000880 - description: The DOI links to an electronic document. - in_subset: - - data_portal_subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - DOI - - digital object identifier - exact_mappings: - - OBI:0002110 - narrow_mappings: - - edam.data:1188 - domain: Doi - range: uriorcurie - required: true - pattern: ^doi:10.\d{2,9}/.*$ - doi_provider: - name: doi_provider - description: The authority, or organization, the DOI is associated with. - examples: - - value: ess_dive - description: The corresponding DOI is associated with ESS-DIVE. - in_subset: - - data_portal_subset - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - NCIT:C74932 - domain: Doi - range: DoiProviderEnum - doi_category: - name: doi_category - description: The resource type the corresponding doi resolves to. - examples: - - value: dataset_doi - description: The corresponding DOI is a dataset resource type. - in_subset: - - data_portal_subset - from_schema: https://w3id.org/nmdc/nmdc - domain: Doi - range: DoiCategoryEnum - required: true - add_date: - name: add_date - description: The date on which the information was added to the database. - from_schema: https://w3id.org/nmdc/nmdc - range: string - mod_date: - name: mod_date - description: The last date on which the database information was modified. - from_schema: https://w3id.org/nmdc/nmdc - range: string - sample_collection_day: - name: sample_collection_day - from_schema: https://w3id.org/nmdc/nmdc - range: integer - sample_collection_hour: - name: sample_collection_hour - from_schema: https://w3id.org/nmdc/nmdc - range: integer - sample_collection_minute: - name: sample_collection_minute - from_schema: https://w3id.org/nmdc/nmdc - range: integer - salinity_category: - name: salinity_category - description: 'Categorical description of the sample''s salinity. Examples: halophile, - halotolerant, hypersaline, huryhaline' - notes: - - maps to gold:salinity - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/microbiomedata/nmdc-metadata/pull/297 - range: string - soluble_iron_micromol: - name: soluble_iron_micromol - from_schema: https://w3id.org/nmdc/nmdc - range: string - host_name: - name: host_name - from_schema: https://w3id.org/nmdc/nmdc - range: string - subsurface_depth: - name: subsurface_depth - from_schema: https://w3id.org/nmdc/nmdc - range: QuantityValue - proport_woa_temperature: - name: proport_woa_temperature - from_schema: https://w3id.org/nmdc/nmdc - range: string - biogas_temperature: - name: biogas_temperature - from_schema: https://w3id.org/nmdc/nmdc - range: string - soil_annual_season_temp: - name: soil_annual_season_temp - from_schema: https://w3id.org/nmdc/nmdc - range: string - biogas_retention_time: - name: biogas_retention_time - from_schema: https://w3id.org/nmdc/nmdc - range: string - completion_date: - name: completion_date - from_schema: https://w3id.org/nmdc/nmdc - range: string - container_size: - name: container_size - description: The volume of the container an analyte is stored in or an activity - takes place in - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - range: QuantityValue - volume: - name: volume - description: The volume of a substance. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - domain: PlannedProcess - range: QuantityValue - temperature: - name: temperature - description: The value of a temperature measurement or temperature used in a process. - notes: - - Not to be confused with the MIXS:0000113 - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - range: QuantityValue - bulk_elect_conductivity: - name: bulk_elect_conductivity - description: Electrical conductivity is a measure of the ability to carry electric - current, which is mostly dictated by the chemistry of and amount of water. - title: bulk electrical conductivity - comments: - - Provide the value output of the field instrument. - examples: - - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm') - description: The conductivity measurement was 0.017 millisiemens per centimeter. - from_schema: https://w3id.org/nmdc/nmdc - range: QuantityValue - infiltrations: - name: infiltrations - description: The amount of time it takes to complete each infiltration activity - examples: - - value: '[''00:01:32'', ''00:00:53'']' - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 - aliases: - - infiltration_1 - - infiltration_2 - multivalued: true - list_elements_ordered: true - range: string - pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ - filter_material: - name: filter_material - description: A porous material on which solid particles present in air or other - fluid which flows through it are largely caught and retained. - comments: - - 'Filters are made with a variety of materials: cellulose and derivatives, glass - fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous - or be made so by mechanical or other means. Membrane/ceramic filters are prepared - with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, - polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. - The pores constitute 80–85% of the filter volume commonly and several pore sizes - are available for air sampling (0.45−0.8 μm are commonly employed).' - from_schema: https://w3id.org/nmdc/nmdc - range: string - filter_pore_size: - name: filter_pore_size - description: A quantitative or qualitative measurement of the physical dimensions - of the pores in a material. - from_schema: https://w3id.org/nmdc/nmdc - domain: FiltrationProcess - range: QuantityValue - conditionings: - name: conditionings - description: Preliminary treatment of either phase with a suitable solution of - the other phase (in the absence of main extractable solute(s)) so that when - the subsequent equilibration is carried out changes in the (volume) phase ratio - or in the concentrations of other components are minimized. - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - list_elements_ordered: true - range: string - separation_method: - name: separation_method - description: The method that was used to separate a substance from a solution - or mixture. - from_schema: https://w3id.org/nmdc/nmdc - domain: FiltrationProcess - range: SeparationMethodEnum - filtration_category: - name: filtration_category - description: The type of conditioning applied to a filter, device, etc. - from_schema: https://w3id.org/nmdc/nmdc - range: string - material_component_separation: - name: material_component_separation - description: A material processing in which components of an input material become - segregated in space - from_schema: https://w3id.org/nmdc/nmdc - range: string - value: - name: value - from_schema: https://w3id.org/nmdc/nmdc - range: QuantityValue - modifier_substance: - name: modifier_substance - description: The type of modification being done - from_schema: https://w3id.org/nmdc/nmdc - range: string - is_pressurized: - name: is_pressurized - description: Whether or not pressure was applied to a thing or process. - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - duration: - name: duration - description: The elapsed time of an activity. - examples: - - value: JsonObj(has_numeric_value=2, has_unit='hours') - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QuantityValue - contained_in: - name: contained_in - description: A type of container. i.e. test tube, falcon tube, etc. - from_schema: https://w3id.org/nmdc/nmdc - range: ContainerCategoryEnum - extractant: - name: extractant - description: The active component(s) primarily responsible for transfer of a solute - from one phase to the other. - from_schema: https://w3id.org/nmdc/nmdc - domain: Extraction - range: Solution - concentration: - name: concentration - description: The concentration of a substance used in a process - from_schema: https://w3id.org/nmdc/nmdc - domain: SolutionComponent - range: QuantityValue - input_volume: - name: input_volume - description: The volume of the input sample. - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QuantityValue - has_solution_components: - name: has_solution_components - description: Relationship from a Solution to one or more constituent solution - components - from_schema: https://w3id.org/nmdc/nmdc - domain: Solution - multivalued: true - range: SolutionComponent - required: true - inlined_as_list: true - minimum_cardinality: 1 - compound: - name: compound - description: A substance that consists of more than one atom or ion. Includes - solvents and solutes. Can be combined into solutions. - from_schema: https://w3id.org/nmdc/nmdc - domain: SolutionComponent - range: CompoundEnum - required: true - ordered_mobile_phases: - name: ordered_mobile_phases - description: The solution(s) that moves through a chromatography column. - from_schema: https://w3id.org/nmdc/nmdc - domain: ChromatographicSeparationProcess - multivalued: true - list_elements_ordered: true - range: Solution - inlined_as_list: true - stationary_phase: - name: stationary_phase - description: The material the stationary phase is comprised of used in chromatography. - from_schema: https://w3id.org/nmdc/nmdc - domain: ChromatographicSeparationProcess - range: StationaryPhaseEnum - total_bases: - name: total_bases - todos: - - this slot needs some basic textual annotations and constraints - from_schema: https://w3id.org/nmdc/nmdc - domain: MagBin - range: integer - members_id: - name: members_id - todos: - - this slot needs some basic textual annotations and constraints - from_schema: https://w3id.org/nmdc/nmdc - domain: MagBin - range: string - bin_name: - name: bin_name - from_schema: https://w3id.org/nmdc/nmdc - range: string - number_of_contig: - name: number_of_contig - from_schema: https://w3id.org/nmdc/nmdc - range: integer - completeness: - name: completeness - from_schema: https://w3id.org/nmdc/nmdc - range: float - contamination: - name: contamination - from_schema: https://w3id.org/nmdc/nmdc - range: float - gene_count: - name: gene_count - from_schema: https://w3id.org/nmdc/nmdc - range: integer - bin_quality: - name: bin_quality - from_schema: https://w3id.org/nmdc/nmdc - range: string - num_16s: - name: num_16s - from_schema: https://w3id.org/nmdc/nmdc - range: integer - num_5s: - name: num_5s - from_schema: https://w3id.org/nmdc/nmdc - range: integer - num_23s: - name: num_23s - from_schema: https://w3id.org/nmdc/nmdc - range: integer - num_t_rna: - name: num_t_rna - from_schema: https://w3id.org/nmdc/nmdc - range: integer - gtdbtk_domain: - name: gtdbtk_domain - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_phylum: - name: gtdbtk_phylum - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_class: - name: gtdbtk_class - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_order: - name: gtdbtk_order - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_family: - name: gtdbtk_family - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_genus: - name: gtdbtk_genus - from_schema: https://w3id.org/nmdc/nmdc - range: string - gtdbtk_species: - name: gtdbtk_species - from_schema: https://w3id.org/nmdc/nmdc - range: string - language: - name: language - description: Should use ISO 639-1 code e.g. "en", "fr" - from_schema: https://w3id.org/nmdc/nmdc - range: language code - has_raw_value: - name: has_raw_value - description: The value that was specified for an annotation in raw form, i.e. - a string. E.g. "2 cm" or "2-4 cm" - from_schema: https://w3id.org/nmdc/nmdc - domain: AttributeValue - range: string - has_unit: - name: has_unit - description: Links a QuantityValue to a unit - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - scale - mappings: - - qud:unit - - schema:unitCode - domain: QuantityValue - range: unit - has_numeric_value: - name: has_numeric_value - description: Links a quantity value to a number - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - qud:quantityValue - - schema:value - domain: QuantityValue - range: float - has_minimum_numeric_value: - name: has_minimum_numeric_value - description: The minimum value part, expressed as number, of the quantity value - when the value covers a range. - from_schema: https://w3id.org/nmdc/nmdc - is_a: has_numeric_value - domain: QuantityValue - has_maximum_numeric_value: - name: has_maximum_numeric_value - description: The maximum value part, expressed as number, of the quantity value - when the value covers a range. - from_schema: https://w3id.org/nmdc/nmdc - is_a: has_numeric_value - domain: QuantityValue - has_boolean_value: - name: has_boolean_value - description: Links a quantity value to a boolean - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - latitude: - name: latitude - description: latitude - examples: - - value: '-33.460524' - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - schema:latitude - domain: GeolocationValue - slot_uri: wgs84:lat - range: decimal degree - longitude: - name: longitude - description: longitude - examples: - - value: '150.168149' - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - schema:longitude - domain: GeolocationValue - slot_uri: wgs84:long - range: decimal degree - term: - name: term - description: pointer to an ontology class - notes: - - 'removed ''slot_uri: rdf:type''' - from_schema: https://w3id.org/nmdc/nmdc - domain: ControlledTermValue - range: OntologyClass - inlined: true - orcid: - name: orcid - description: The ORCID of a person. - from_schema: https://w3id.org/nmdc/nmdc - domain: PersonValue - range: string - email: - name: email - description: An email address for an entity such as a person. This should be the - primary email address used. - from_schema: https://w3id.org/nmdc/nmdc - slot_uri: schema:email - range: string - alternate_emails: - name: alternate_emails - description: One or more other email addresses for an entity. - from_schema: https://w3id.org/nmdc/nmdc - range: string - profile_image_url: - name: profile_image_url - description: A url that points to an image of a person. - from_schema: https://w3id.org/nmdc/nmdc - domain: PersonValue - range: string - has_input: - name: has_input - description: An input to a process. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - input - domain: NamedThing - multivalued: true - range: NamedThing - has_output: - name: has_output - description: An output biosample to a processing step - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - output - domain: NamedThing - multivalued: true - range: NamedThing - part_of: - name: part_of - description: Links a resource to another resource that either logically or physically - includes it. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - is part of - domain: NamedThing - slot_uri: dcterms:isPartOf - multivalued: true - range: NamedThing - execution_resource: - name: execution_resource - examples: - - value: NERSC-Cori - from_schema: https://w3id.org/nmdc/nmdc - domain: Activity - range: string - url: - name: url - notes: - - See issue 207 - this clashes with the mixs field - from_schema: https://w3id.org/nmdc/nmdc - range: string - display_order: - name: display_order - description: When rendering information, this attribute to specify the order in - which the information should be rendered. - from_schema: https://w3id.org/nmdc/nmdc - domain: ImageValue - range: integer - git_url: - name: git_url - examples: - - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1 - from_schema: https://w3id.org/nmdc/nmdc - range: string - file_size_bytes: - name: file_size_bytes - description: Size of the file in bytes - from_schema: https://w3id.org/nmdc/nmdc - domain: DataObject - range: bytes - md5_checksum: - name: md5_checksum - description: MD5 checksum of file (pre-compressed) - from_schema: https://w3id.org/nmdc/nmdc - range: string - keywords: - name: keywords - description: A list of keywords that used to associate the entity. Keywords SHOULD - come from controlled vocabularies, including MESH, ENVO. - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - dcterms:subject - multivalued: true - range: string - objective: - name: objective - description: The scientific objectives associated with the entity. It SHOULD correspond - to scientific norms for objectives field in a structured abstract. - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - SIO:000337 - range: string - websites: - name: websites - description: A list of websites that are associated with the entity. - comments: - - DOIs should not be included as websites. Instead, use the associated_dois slot. - - A consortium's homepage website should be included in the homepage_website slot, - not in websites. - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: string - pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\/\/(?!.*[Dd][Oo][Ii]\.[Oo][Rr][Gg]).*$ - homepage_website: - name: homepage_website - description: The website address (URL) of an entity's homepage. - examples: - - value: https://www.neonscience.org/ - from_schema: https://w3id.org/nmdc/nmdc - is_a: websites - maximum_cardinality: 1 - highest_similarity_score: - name: highest_similarity_score - todos: - - Yuri to fill in description - from_schema: https://w3id.org/nmdc/nmdc - range: float - metabolite_quantified: - name: metabolite_quantified - description: the specific metabolite identifier - from_schema: https://w3id.org/nmdc/nmdc - domain: MetaboliteQuantification - range: ChemicalEntity - all_proteins: - name: all_proteins - description: the list of protein identifiers that are associated with the peptide - sequence - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: GeneProduct - best_protein: - name: best_protein - description: the specific protein identifier most correctly associated with the - peptide sequence - from_schema: https://w3id.org/nmdc/nmdc - range: GeneProduct - min_q_value: - name: min_q_value - description: smallest Q-Value associated with the peptide sequence as provided - by MSGFPlus tool - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - OBI:0001442 - range: float - peptide_sequence: - name: peptide_sequence - from_schema: https://w3id.org/nmdc/nmdc - range: string - peptide_spectral_count: - name: peptide_spectral_count - description: sum of filter passing MS2 spectra associated with the peptide sequence - within a given LC-MS/MS data file - from_schema: https://w3id.org/nmdc/nmdc - range: integer - peptide_sum_masic_abundance: - name: peptide_sum_masic_abundance - description: combined MS1 extracted ion chromatograms derived from MS2 spectra - associated with the peptide sequence from a given LC-MS/MS data file using the - MASIC tool - from_schema: https://w3id.org/nmdc/nmdc - range: integer - chemical_formula: - name: chemical_formula - description: A generic grouping for molecular formulae and empirical formulae - from_schema: https://w3id.org/nmdc/nmdc - range: string - inchi_key: - name: inchi_key - notes: - - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov - K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental - testing. J Cheminform. 4:12' - from_schema: https://w3id.org/nmdc/nmdc - range: string - inchi: - name: inchi - from_schema: https://w3id.org/nmdc/nmdc - range: string - peptide_sequence_count: - name: peptide_sequence_count - description: count of peptide sequences grouped to the best_protein - from_schema: https://w3id.org/nmdc/nmdc - range: integer - protein_spectral_count: - name: protein_spectral_count - description: sum of filter passing MS2 spectra associated with the best protein - within a given LC-MS/MS data file - from_schema: https://w3id.org/nmdc/nmdc - range: integer - protein_sum_masic_abundance: - name: protein_sum_masic_abundance - description: combined MS1 extracted ion chromatograms derived from MS2 spectra - associated with the best protein from a given LC-MS/MS data file using the MASIC - tool - from_schema: https://w3id.org/nmdc/nmdc - range: integer - smiles: - name: smiles - description: A string encoding of a molecular graph, no chiral or isotopic information. - There are usually a large number of valid SMILES which represent a given structure. - For example, CCO, OCC and C(O)C all specify the structure of ethanol. - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: string - has_part: - name: has_part - from_schema: https://w3id.org/nmdc/nmdc - domain: Pathway - multivalued: true - range: Reaction - chemical: - name: chemical - description: from reaction participant class - from_schema: https://w3id.org/nmdc/nmdc - domain: ReactionParticipant - range: ChemicalEntity - stoichiometry: - name: stoichiometry - description: from reaction participant class - from_schema: https://w3id.org/nmdc/nmdc - range: integer - subject: - name: subject - from_schema: https://w3id.org/nmdc/nmdc - domain: FunctionalAnnotation - range: GeneProduct - has_function: - name: has_function - notes: - - the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm, - - but is actually taking string arguments in MongoDB, - - and those are frequently fulltext, not CURIEs. MAM 2021-06-23 - from_schema: https://w3id.org/nmdc/nmdc - domain: FunctionalAnnotation - range: string - pattern: ^(KEGG_PATHWAY:\w{2,4}\d{5}|KEGG.REACTION:R\d+|RHEA:\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\d{1,2}(\.\d{0,3}){0,3}|GO:\d{7}|MetaNetX:(MNXR\d+|EMPTY)|SEED:\w+|KEGG\.ORTHOLOGY:K\d+|EGGNOG:\w+|PFAM:PF\d{5}|TIGRFAM:TIGR\d+|SUPFAM:\w+|CATH:[1-6]\.[0-9]+\.[0-9]+\.[0-9]+|PANTHER.FAMILY:PTHR\d{5}(\:SF\d{1,3})?)$ - has_participants: - name: has_participants - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - RO:0000057 - abstract: true - gff_coordinate: - name: gff_coordinate - description: A positive 1-based integer coordinate indicating start or end - comments: - - For features that cross the origin of a circular feature (e.g. most bacterial - genomes, plasmids, and some viral genomes), the requirement for start to be - less than or equal to end is satisfied by making end = the position of the end - + the length of the landmark feature. - from_schema: https://w3id.org/nmdc/nmdc - range: integer - minimum_value: 1 - seqid: - name: seqid - description: The ID of the landmark used to establish the coordinate system for - the current feature. - todos: - - change range from string to object - from_schema: https://w3id.org/nmdc/nmdc - range: string - strand: - name: strand - description: The strand on which a feature is located. Has a value of '+' (sense - strand or forward strand) or '-' (anti-sense strand or reverse strand). - todos: - - set the range to an enum? - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - biolink:strand - domain: GenomeFeature - direction: - name: direction - description: One of l->r, r->l, bidirectional, neutral - from_schema: https://w3id.org/nmdc/nmdc - domain: Reaction - range: string - encodes: - name: encodes - description: The gene product encoded by this feature. Typically this is used - for a CDS feature or gene feature which will encode a protein. It can also be - used by a nc transcript ot gene feature that encoded a ncRNA - from_schema: https://w3id.org/nmdc/nmdc - domain: GenomeFeature - range: GeneProduct - end: - name: end - description: The end of the feature in positive 1-based integer coordinates - comments: - - '- "constraint: end > start" - "For features that cross the origin of a circular - feature, end = the position of the end + the length of the landmark feature."' - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - biolink:end_interbase_coordinate - is_a: gff_coordinate - domain: GenomeFeature - range: integer - feature_type: - name: feature_type - description: 'TODO: Yuri to write' - from_schema: https://w3id.org/nmdc/nmdc - domain: GenomeFeature - range: string - is_balanced: - name: is_balanced - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - is_diastereoselective: - name: is_diastereoselective - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - is_fully_characterized: - name: is_fully_characterized - description: False if includes R-groups - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - is_stereo: - name: is_stereo - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - is_transport: - name: is_transport - from_schema: https://w3id.org/nmdc/nmdc - range: boolean - left_participants: - name: left_participants - from_schema: https://w3id.org/nmdc/nmdc - is_a: has_participants - domain: Reaction - multivalued: true - range: ReactionParticipant - phase: - name: phase - description: The phase for a coding sequence entity. For example, phase of a CDS - as represented in a GFF3 with a value of 0, 1 or 2. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - biolink:phase - domain: GenomeFeature - range: integer - minimum_value: 0 - maximum_value: 2 - right_participants: - name: right_participants - from_schema: https://w3id.org/nmdc/nmdc - is_a: has_participants - domain: Reaction - multivalued: true - range: ReactionParticipant - smarts_string: - name: smarts_string - from_schema: https://w3id.org/nmdc/nmdc - range: string - start: - name: start - description: The start of the feature in positive 1-based integer coordinates - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - biolink:start_interbase_coordinate - is_a: gff_coordinate - domain: GenomeFeature - abs_air_humidity: - name: abs_air_humidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram per gram, kilogram per kilogram, kilogram, pound - occurrence: - tag: occurrence - value: '1' - description: Actual mass of water vapor - mh20 - present in the air water vapor - mixture - title: absolute air humidity - examples: - - value: 9 gram per gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - absolute air humidity - is_a: core field - slot_uri: MIXS:0000122 - multivalued: false - range: QuantityValue - add_recov_method: - name: add_recov_method - annotations: - expected_value: - tag: expected_value - value: enumeration;timestamp - occurrence: - tag: occurrence - value: '1' - description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed - for increase of hydrocarbon recovery from resource and start date for each one - of them. If "other" is specified, please propose entry in "additional info" - field - title: secondary and tertiary recovery methods and start date - examples: - - value: Polymer Addition;2018-06-21T14:30Z - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - secondary and tertiary recovery methods and start date - is_a: core field - slot_uri: MIXS:0001009 - multivalued: false - range: TextValue - additional_info: - name: additional_info - annotations: - expected_value: - tag: expected_value - value: text - occurrence: - tag: occurrence - value: '1' - description: Information that doesn't fit anywhere else. Can also be used to propose - new entries for fields with controlled vocabulary - title: additional info - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - additional info - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000300 - multivalued: false - range: TextValue - address: - name: address - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The street name and building number where the sampling occurred. - title: address - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - address - is_a: core field - string_serialization: '{integer}{text}' - slot_uri: MIXS:0000218 - multivalued: false - range: TextValue - adj_room: - name: adj_room - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' - description: List of rooms (room number, room name) immediately adjacent to the - sampling room - title: adjacent rooms - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - adjacent rooms - is_a: core field - string_serialization: '{text};{integer}' - slot_uri: MIXS:0000219 - multivalued: false - range: TextValue - aero_struc: - name: aero_struc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Aerospace structures typically consist of thin plates with stiffeners - for the external surfaces, bulkheads and frames to support the shape and fasteners - such as welds, rivets, screws and bolts to hold the components together - title: aerospace structure - examples: - - value: plane - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - aerospace structure - is_a: core field - string_serialization: '[plane|glider]' - slot_uri: MIXS:0000773 - multivalued: false - range: TextValue - agrochem_addition: - name: agrochem_addition - annotations: - expected_value: - tag: expected_value - value: agrochemical name;agrochemical amount;timestamp - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Addition of fertilizers, pesticides, etc. - amount and time of applications - title: history/agrochemical additions - examples: - - value: roundup;5 milligram per liter;2018-06-21 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/agrochemical additions - is_a: core field - string_serialization: '{text};{float} {unit};{timestamp}' - slot_uri: MIXS:0000639 - multivalued: true - range: TextValue - air_PM_concen: - name: air_PM_concen - annotations: - expected_value: - tag: expected_value - value: particulate matter name;measurement value - preferred_unit: - tag: preferred_unit - value: micrograms per cubic meter - occurrence: - tag: occurrence - value: m - description: Concentration of substances that remain suspended in the air, and - comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can - report multiple PM's by entering numeric values preceded by name of PM - title: air particulate matter concentration - examples: - - value: PM2.5;10 microgram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - air particulate matter concentration - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000108 - multivalued: true - range: TextValue - air_temp: - name: air_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Temperature of the air at the time of sampling - title: air temperature - examples: - - value: 20 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - air temperature - is_a: core field - slot_uri: MIXS:0000124 - multivalued: false - range: QuantityValue - air_temp_regm: - name: air_temp_regm - annotations: - expected_value: - tag: expected_value - value: temperature value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving an exposure to varying temperatures; - should include the temperature, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include different temperature regimens - title: air temperature regimen - examples: - - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - air temperature regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000551 - multivalued: true - range: TextValue - al_sat: - name: al_sat - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: Aluminum saturation (esp. For tropical soils) - title: extreme_unusual_properties/Al saturation - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - extreme_unusual_properties/Al saturation - is_a: core field - slot_uri: MIXS:0000607 - multivalued: false - range: QuantityValue - al_sat_meth: - name: al_sat_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or URL - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining Al saturation - title: extreme_unusual_properties/Al saturation method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - extreme_unusual_properties/Al saturation method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000324 - multivalued: false - range: TextValue - alkalinity: - name: alkalinity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milliequivalent per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the - equivalence point of carbonate or bicarbonate - title: alkalinity - examples: - - value: 50 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - alkalinity - is_a: core field - slot_uri: MIXS:0000421 - multivalued: false - range: QuantityValue - alkalinity_method: - name: alkalinity_method - annotations: - expected_value: - tag: expected_value - value: description of method - occurrence: - tag: occurrence - value: '1' - description: Method used for alkalinity measurement - title: alkalinity method - examples: - - value: titration - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - alkalinity method - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000298 - multivalued: false - range: TextValue - alkyl_diethers: - name: alkyl_diethers - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of alkyl diethers - title: alkyl diethers - examples: - - value: 0.005 mole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - alkyl diethers - is_a: core field - slot_uri: MIXS:0000490 - multivalued: false - range: QuantityValue - alt: - name: alt - annotations: - expected_value: - tag: expected_value - value: measurement value - description: Altitude is a term used to identify heights of objects such as airplanes, - space shuttles, rockets, atmospheric balloons and heights of places such as - atmospheric layers and clouds. It is used to measure the height of an object - which is above the earth's surface. In this context, the altitude measurement - is the vertical distance between the earth's surface above sea level and the - sampled position in the air - title: altitude - examples: - - value: 100 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - altitude - is_a: environment field - slot_uri: MIXS:0000094 - multivalued: false - domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - range: QuantityValue - aminopept_act: - name: aminopept_act - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mole per liter per hour - occurrence: - tag: occurrence - value: '1' - description: Measurement of aminopeptidase activity - title: aminopeptidase activity - examples: - - value: 0.269 mole per liter per hour - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - aminopeptidase activity - is_a: core field - slot_uri: MIXS:0000172 - multivalued: false - range: QuantityValue - ammonium: - name: ammonium - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of ammonium in the sample - title: ammonium - examples: - - value: 1.5 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ammonium - is_a: core field - slot_uri: MIXS:0000427 - multivalued: false - range: QuantityValue - amount_light: - name: amount_light - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: lux, lumens per square meter - occurrence: - tag: occurrence - value: '1' - description: The unit of illuminance and luminous emittance, measuring luminous - flux per unit area - title: amount of light - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - amount of light - is_a: core field - slot_uri: MIXS:0000140 - multivalued: false - range: QuantityValue - ances_data: - name: ances_data - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: Information about either pedigree or other ancestral information - description (e.g. parental variety in case of mutant or selection), e.g. A/3*B - (meaning [(A x B) x B] x B) - title: ancestral data - examples: - - value: A/3*B - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ancestral data - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000247 - multivalued: false - range: TextValue - annual_precpt: - name: annual_precpt - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millimeter - occurrence: - tag: occurrence - value: '1' - description: The average of all annual precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps. - title: mean annual precipitation - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean annual precipitation - is_a: core field - slot_uri: MIXS:0000644 - multivalued: false - range: QuantityValue - annual_temp: - name: annual_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Mean annual temperature - title: mean annual temperature - examples: - - value: 12.5 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean annual temperature - is_a: core field - slot_uri: MIXS:0000642 - multivalued: false - range: QuantityValue - antibiotic_regm: - name: antibiotic_regm - annotations: - expected_value: - tag: expected_value - value: antibiotic name;antibiotic amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: milligram - occurrence: - tag: occurrence - value: m - description: Information about treatment involving antibiotic administration; - should include the name of antibiotic, amount administered, treatment regimen - including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - antibiotic regimens - title: antibiotic regimen - examples: - - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - antibiotic regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000553 - multivalued: true - range: TextValue - api: - name: api - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degrees API - occurrence: - tag: occurrence - value: '1' - description: 'API gravity is a measure of how heavy or light a petroleum liquid - is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. - 31.1¬∞ API)' - title: API gravity - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - API gravity - is_a: core field - slot_uri: MIXS:0000157 - multivalued: false - range: QuantityValue - arch_struc: - name: arch_struc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: An architectural structure is a human-made, free-standing, immobile - outdoor construction - title: architectural structure - examples: - - value: shed - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - architectural structure - is_a: core field - slot_uri: MIXS:0000774 - multivalued: false - range: arch_struc_enum - aromatics_pc: - name: aromatics_pc - annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis - method that divides¬†crude oil¬†components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: aromatics wt% - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - aromatics wt% - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000133 - multivalued: false - range: TextValue - asphaltenes_pc: - name: asphaltenes_pc - annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis - method that divides¬†crude oil¬†components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: asphaltenes wt% - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - asphaltenes wt% - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000135 - multivalued: false - range: TextValue - atmospheric_data: - name: atmospheric_data - annotations: - expected_value: - tag: expected_value - value: atmospheric data name;measurement value - occurrence: - tag: occurrence - value: m - description: Measurement of atmospheric data; can include multiple data - title: atmospheric data - examples: - - value: wind speed;9 knots - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - atmospheric data - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0001097 - multivalued: true - range: TextValue - avg_dew_point: - name: avg_dew_point - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The average of dew point measures taken at the beginning of every - hour over a 24 hour period on the sampling day - title: average dew point - examples: - - value: 25.5 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - average dew point - is_a: core field - slot_uri: MIXS:0000141 - multivalued: false - range: QuantityValue - avg_occup: - name: avg_occup - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: Daily average occupancy of room. Indicate the number of person(s) - daily occupying the sampling room. - title: average daily occupancy - examples: - - value: '2' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - average daily occupancy - is_a: core field - slot_uri: MIXS:0000775 - multivalued: false - range: TextValue - avg_temp: - name: avg_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The average of temperatures taken at the beginning of every hour - over a 24 hour period on the sampling day - title: average temperature - examples: - - value: 12.5 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - average temperature - is_a: core field - slot_uri: MIXS:0000142 - multivalued: false - range: QuantityValue - bac_prod: - name: bac_prod - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per cubic meter per day - occurrence: - tag: occurrence - value: '1' - description: Bacterial production in the water column measured by isotope uptake - title: bacterial production - examples: - - value: 5 milligram per cubic meter per day - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bacterial production - is_a: core field - slot_uri: MIXS:0000683 - multivalued: false - range: QuantityValue - bac_resp: - name: bac_resp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per cubic meter per day, micromole oxygen per liter per hour - occurrence: - tag: occurrence - value: '1' - description: Measurement of bacterial respiration in the water column - title: bacterial respiration - examples: - - value: 300 micromole oxygen per liter per hour - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bacterial respiration - is_a: core field - slot_uri: MIXS:0000684 - multivalued: false - range: QuantityValue - bacteria_carb_prod: - name: bacteria_carb_prod - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: nanogram per hour - occurrence: - tag: occurrence - value: '1' - description: Measurement of bacterial carbon production - title: bacterial carbon production - examples: - - value: 2.53 microgram per liter per hour - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bacterial carbon production - is_a: core field - slot_uri: MIXS:0000173 - multivalued: false - range: QuantityValue - barometric_press: - name: barometric_press - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millibar - occurrence: - tag: occurrence - value: '1' - description: Force per unit area exerted against a surface by the weight of air - above that surface - title: barometric pressure - examples: - - value: 5 millibar - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - barometric pressure - is_a: core field - slot_uri: MIXS:0000096 - multivalued: false - range: QuantityValue - basin: - name: basin - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Name of the basin (e.g. Campos) - title: basin name - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - basin name - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000290 - multivalued: false - range: TextValue - bathroom_count: - name: bathroom_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of bathrooms in the building - title: bathroom count - examples: - - value: '1' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bathroom count - is_a: core field - slot_uri: MIXS:0000776 - multivalued: false - range: TextValue - bedroom_count: - name: bedroom_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of bedrooms in the building - title: bedroom count - examples: - - value: '2' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bedroom count - is_a: core field - slot_uri: MIXS:0000777 - multivalued: false - range: TextValue - benzene: - name: benzene - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of benzene in the sample - title: benzene - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - benzene - is_a: core field - slot_uri: MIXS:0000153 - multivalued: false - range: QuantityValue - biochem_oxygen_dem: - name: biochem_oxygen_dem - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Amount of dissolved oxygen needed by aerobic biological organisms - in a body of water to break down organic material present in a given water sample - at certain temperature over a specific time period - title: biochemical oxygen demand - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biochemical oxygen demand - is_a: core field - slot_uri: MIXS:0000653 - multivalued: false - range: QuantityValue - biocide: - name: biocide - annotations: - expected_value: - tag: expected_value - value: name;name;timestamp - occurrence: - tag: occurrence - value: '1' - description: List of biocides (commercial name of product and supplier) and date - of administration - title: biocide administration - examples: - - value: ALPHA 1427;Baker Hughes;2008-01-23 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biocide administration - is_a: core field - string_serialization: '{text};{text};{timestamp}' - slot_uri: MIXS:0001011 - multivalued: false - range: TextValue - biocide_admin_method: - name: biocide_admin_method - annotations: - expected_value: - tag: expected_value - value: measurement value;frequency;duration;duration - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Method of biocide administration (dose, frequency, duration, time - elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 - days) - title: biocide administration method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biocide administration method - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' - slot_uri: MIXS:0000456 - multivalued: false - range: TextValue - biol_stat: - name: biol_stat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The level of genome modification. - title: biological status - examples: - - value: natural - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biological status - is_a: core field - slot_uri: MIXS:0000858 - multivalued: false - range: biol_stat_enum - biomass: - name: biomass - annotations: - expected_value: - tag: expected_value - value: biomass type;measurement value - preferred_unit: - tag: preferred_unit - value: ton, kilogram, gram - occurrence: - tag: occurrence - value: m - description: Amount of biomass; should include the name for the part of biomass - measured, e.g. Microbial, total. Can include multiple measurements - title: biomass - examples: - - value: total;20 gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biomass - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000174 - multivalued: true - range: TextValue - biotic_regm: - name: biotic_regm - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: Information about treatment(s) involving use of biotic factors, such - as bacteria, viruses or fungi. - title: biotic regimen - examples: - - value: sample inoculated with Rhizobium spp. Culture - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biotic regimen - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0001038 - multivalued: false - range: TextValue - biotic_relationship: - name: biotic_relationship - annotations: - expected_value: - tag: expected_value - value: enumeration - description: Description of relationship(s) between the subject organism and other - organism(s) it is associated with. E.g., parasite on species X; mutualist with - species Y. The target organism is the subject of the relationship, and the other - organism(s) is the object - title: observed biotic relationship - examples: - - value: free living - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - observed biotic relationship - is_a: nucleic acid sequence source field - slot_uri: MIXS:0000028 - multivalued: false - range: biotic_relationship_enum - bishomohopanol: - name: bishomohopanol - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, microgram per gram - occurrence: - tag: occurrence - value: '1' - description: Concentration of bishomohopanol - title: bishomohopanol - examples: - - value: 14 microgram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bishomohopanol - is_a: core field - slot_uri: MIXS:0000175 - multivalued: false - range: QuantityValue - blood_press_diast: - name: blood_press_diast - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millimeter mercury - occurrence: - tag: occurrence - value: '1' - description: Resting diastolic blood pressure, measured as mm mercury - title: host blood pressure diastolic - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host blood pressure diastolic - is_a: core field - slot_uri: MIXS:0000258 - multivalued: false - range: QuantityValue - blood_press_syst: - name: blood_press_syst - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millimeter mercury - occurrence: - tag: occurrence - value: '1' - description: Resting systolic blood pressure, measured as mm mercury - title: host blood pressure systolic - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host blood pressure systolic - is_a: core field - slot_uri: MIXS:0000259 - multivalued: false - range: QuantityValue - bromide: - name: bromide - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of bromide - title: bromide - examples: - - value: 0.05 parts per million - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - bromide - is_a: core field - slot_uri: MIXS:0000176 - multivalued: false - range: QuantityValue - build_docs: - name: build_docs - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The building design, construction and operation documents - title: design, construction, and operation documents - examples: - - value: maintenance plans - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - design, construction, and operation documents - is_a: core field - slot_uri: MIXS:0000787 - multivalued: false - range: build_docs_enum - build_occup_type: - name: build_occup_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: The primary function for which a building or discrete part of a building - is intended to be used - title: building occupancy type - examples: - - value: market - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - building occupancy type - is_a: core field - slot_uri: MIXS:0000761 - multivalued: true - range: build_occup_type_enum - building_setting: - name: building_setting - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: A location (geography) where a building is set - title: building setting - examples: - - value: rural - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - building setting - is_a: core field - slot_uri: MIXS:0000768 - multivalued: false - range: building_setting_enum - built_struc_age: - name: built_struc_age - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: year - occurrence: - tag: occurrence - value: '1' - description: The age of the built structure since construction - title: built structure age - examples: - - value: '15' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - built structure age - is_a: core field - slot_uri: MIXS:0000145 - multivalued: false - range: QuantityValue - built_struc_set: - name: built_struc_set - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The characterization of the location of the built structure as high - or low human density - title: built structure setting - examples: - - value: rural - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - built structure setting - is_a: core field - string_serialization: '[urban|rural]' - slot_uri: MIXS:0000778 - multivalued: false - range: TextValue - built_struc_type: - name: built_struc_type - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: A physical structure that is a body or assemblage of bodies in space - to form a system capable of supporting loads - title: built structure type - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - built structure type - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000721 - multivalued: false - range: TextValue - calcium: - name: calcium - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of calcium in the sample - title: calcium - examples: - - value: 0.2 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - calcium - is_a: core field - slot_uri: MIXS:0000432 - multivalued: false - range: QuantityValue - carb_dioxide: - name: carb_dioxide - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Carbon dioxide (gas) amount or concentration at the time of sampling - title: carbon dioxide - examples: - - value: 410 parts per million - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - carbon dioxide - is_a: core field - slot_uri: MIXS:0000097 - multivalued: false - range: QuantityValue - carb_monoxide: - name: carb_monoxide - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Carbon monoxide (gas) amount or concentration at the time of sampling - title: carbon monoxide - examples: - - value: 0.1 parts per million - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - carbon monoxide - is_a: core field - slot_uri: MIXS:0000098 - multivalued: false - range: QuantityValue - carb_nitro_ratio: - name: carb_nitro_ratio - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Ratio of amount or concentrations of carbon to nitrogen - title: carbon/nitrogen ratio - examples: - - value: '0.417361111' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - carbon/nitrogen ratio - is_a: core field - slot_uri: MIXS:0000310 - multivalued: false - range: QuantityValue - ceil_area: - name: ceil_area - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The area of the ceiling space within the room - title: ceiling area - examples: - - value: 25 square meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling area - is_a: core field - slot_uri: MIXS:0000148 - multivalued: false - range: QuantityValue - ceil_cond: - name: ceil_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The physical condition of the ceiling at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: ceiling condition - examples: - - value: damaged - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling condition - is_a: core field - slot_uri: MIXS:0000779 - multivalued: false - range: ceil_cond_enum - ceil_finish_mat: - name: ceil_finish_mat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of material used to finish a ceiling - title: ceiling finish material - examples: - - value: stucco - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling finish material - is_a: core field - slot_uri: MIXS:0000780 - multivalued: false - range: ceil_finish_mat_enum - ceil_struc: - name: ceil_struc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The construction format of the ceiling - title: ceiling structure - examples: - - value: concrete - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling structure - is_a: core field - string_serialization: '[wood frame|concrete]' - slot_uri: MIXS:0000782 - multivalued: false - range: TextValue - ceil_texture: - name: ceil_texture - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The feel, appearance, or consistency of a ceiling surface - title: ceiling texture - examples: - - value: popcorn - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling texture - is_a: core field - slot_uri: MIXS:0000783 - multivalued: false - range: ceil_texture_enum - ceil_thermal_mass: - name: ceil_thermal_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The ability of the ceiling to provide inertia against temperature - fluctuations. Generally this means concrete that is exposed. A metal deck that - supports a concrete slab will act thermally as long as it is exposed to room - air flow - title: ceiling thermal mass - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling thermal mass - is_a: core field - slot_uri: MIXS:0000143 - multivalued: false - range: QuantityValue - ceil_type: - name: ceil_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of ceiling according to the ceiling's appearance or construction - title: ceiling type - examples: - - value: coffered - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling type - is_a: core field - slot_uri: MIXS:0000784 - multivalued: false - range: ceil_type_enum - ceil_water_mold: - name: ceil_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on the ceiling - title: ceiling signs of water/mold - examples: - - value: presence of mold visible - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ceiling signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000781 - multivalued: false - range: TextValue - chem_administration: - name: chem_administration - annotations: - expected_value: - tag: expected_value - value: CHEBI;timestamp - occurrence: - tag: occurrence - value: m - description: List of chemical compounds administered to the host or site where - sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can - include multiple compounds. For chemical entities of biological interest ontology - (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - title: chemical administration - examples: - - value: agar [CHEBI:2509];2018-05-11T20:00Z - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chemical administration - is_a: core field - string_serialization: '{termLabel} {[termID]};{timestamp}' - slot_uri: MIXS:0000751 - multivalued: true - range: ControlledTermValue - chem_mutagen: - name: chem_mutagen - annotations: - expected_value: - tag: expected_value - value: mutagen name;mutagen amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: m - description: Treatment involving use of mutagens; should include the name of mutagen, - amount administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple mutagen regimens - title: chemical mutagen - examples: - - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chemical mutagen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000555 - multivalued: true - range: TextValue - chem_oxygen_dem: - name: chem_oxygen_dem - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: A measure of the capacity of water to consume oxygen during the decomposition - of organic matter and the oxidation of inorganic chemicals such as ammonia and - nitrite - title: chemical oxygen demand - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chemical oxygen demand - is_a: core field - slot_uri: MIXS:0000656 - multivalued: false - range: QuantityValue - chem_treat_method: - name: chem_treat_method - annotations: - expected_value: - tag: expected_value - value: measurement value;frequency;duration;duration - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Method of chemical administration(dose, frequency, duration, time - elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 - hr; 0 days) - title: chemical treatment method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chemical treatment method - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' - slot_uri: MIXS:0000457 - multivalued: false - range: string - chem_treatment: - name: chem_treatment - annotations: - expected_value: - tag: expected_value - value: name;name;timestamp - occurrence: - tag: occurrence - value: '1' - description: List of chemical compounds administered upstream the sampling location - where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, - demulsifiers, and other production chemicals etc.). The commercial name of the - product and name of the supplier should be provided. The date of administration - should also be included - title: chemical treatment - examples: - - value: ACCENT 1125;DOW;2010-11-17 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chemical treatment - is_a: core field - string_serialization: '{text};{text};{timestamp}' - slot_uri: MIXS:0001012 - multivalued: false - range: TextValue - chimera_check: - name: chimera_check - annotations: - expected_value: - tag: expected_value - value: name and version of software, parameters used - description: Tool(s) used for chimera checking, including version number and parameters, - to discover and remove chimeric sequences. A chimeric sequence is comprised - of two or more phylogenetically distinct parent sequences. - title: chimera check software - examples: - - value: uchime;v4.1;default parameters - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chimera check software - is_a: sequencing field - string_serialization: '{software};{version};{parameters}' - slot_uri: MIXS:0000052 - multivalued: false - range: TextValue - chloride: - name: chloride - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of chloride in the sample - title: chloride - examples: - - value: 5000 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chloride - is_a: core field - slot_uri: MIXS:0000429 - multivalued: false - range: QuantityValue - chlorophyll: - name: chlorophyll - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per cubic meter, microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of chlorophyll - title: chlorophyll - examples: - - value: 5 milligram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - chlorophyll - is_a: core field - slot_uri: MIXS:0000177 - multivalued: false - range: QuantityValue - climate_environment: - name: climate_environment - annotations: - expected_value: - tag: expected_value - value: climate name;treatment interval and duration - occurrence: - tag: occurrence - value: m - description: Treatment involving an exposure to a particular climate; treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - climates - title: climate environment - examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - climate environment - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001040 - multivalued: true - range: TextValue - collection_date: - name: collection_date - annotations: - expected_value: - tag: expected_value - value: date and time - description: 'The time of sampling, either as an instance (single point in time) - or interval. In case no exact time is available, the date/time can be right - truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; - 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' - title: collection date - examples: - - value: 2018-05-11T10:00:00+01:00; 2018-05-11 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - collection date - is_a: environment field - slot_uri: MIXS:0000011 - multivalued: false - range: TimestampValue - conduc: - name: conduc - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milliSiemens per centimeter - occurrence: - tag: occurrence - value: '1' - description: Electrical conductivity of water - title: conductivity - examples: - - value: 10 milliSiemens per centimeter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - conductivity - is_a: core field - slot_uri: MIXS:0000692 - multivalued: false - range: QuantityValue - cool_syst_id: - name: cool_syst_id - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' - description: The cooling system identifier - title: cooling system identifier - examples: - - value: '12345' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - cooling system identifier - is_a: core field - slot_uri: MIXS:0000785 - multivalued: false - range: TextValue - crop_rotation: - name: crop_rotation - annotations: - expected_value: - tag: expected_value - value: crop rotation status;schedule - occurrence: - tag: occurrence - value: '1' - description: Whether or not crop is rotated, and if yes, rotation schedule - title: history/crop rotation - examples: - - value: yes;R2/2017-01-01/2018-12-31/P6M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/crop rotation - is_a: core field - string_serialization: '{boolean};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000318 - multivalued: false - range: TextValue - cult_root_med: - name: cult_root_med - annotations: - expected_value: - tag: expected_value - value: name, PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Name or reference for the hydroponic or in vitro culture rooting - medium; can be the name of a commonly used medium or reference to a specific - medium, e.g. Murashige and Skoog medium. If the medium has not been formally - published, use the rooting medium descriptors. - title: culture rooting medium - examples: - - value: http://himedialabs.com/TD/PT158.pdf - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - culture rooting medium - is_a: core field - string_serialization: '{text}|{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0001041 - multivalued: false - range: TextValue - cur_land_use: - name: cur_land_use - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Present state of sample site - title: current land use - examples: - - value: conifers - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - current land use - is_a: core field - slot_uri: MIXS:0001080 - multivalued: false - range: cur_land_use_enum - cur_vegetation: - name: cur_vegetation - annotations: - expected_value: - tag: expected_value - value: current vegetation type - occurrence: - tag: occurrence - value: '1' - description: Vegetation classification from one or more standard classification - systems, or agricultural crop - title: current vegetation - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - current vegetation - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000312 - multivalued: false - range: TextValue - cur_vegetation_meth: - name: cur_vegetation_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in vegetation classification - title: current vegetation method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - current vegetation method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000314 - multivalued: false - range: TextValue - date_last_rain: - name: date_last_rain - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' - description: The date of the last time it rained - title: date last rain - examples: - - value: 2018-05-11:T14:30Z - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - date last rain - is_a: core field - slot_uri: MIXS:0000786 - multivalued: false - range: TimestampValue - density: - name: density - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram per cubic meter, gram per cubic centimeter - occurrence: - tag: occurrence - value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric - mass density) - title: density - examples: - - value: 1000 kilogram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - density - is_a: core field - slot_uri: MIXS:0000435 - multivalued: false - range: QuantityValue - depos_env: - name: depos_env - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). - If "other" is specified, please propose entry in "additional info" field - title: depositional environment - examples: - - value: Continental - Alluvial - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - depositional environment - is_a: core field - slot_uri: MIXS:0000992 - multivalued: false - range: depos_env_enum - depth: - name: depth - annotations: - expected_value: - tag: expected_value - value: measurement value - description: The vertical distance below local surface, e.g. for sediment or soil - samples depth is measured from sediment or soil surface, respectively. Depth - can be reported as an interval for subsurface samples. - title: depth - examples: - - value: 10 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - depth - is_a: environment field - slot_uri: MIXS:0000018 - multivalued: false - range: QuantityValue - dew_point: - name: dew_point - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The temperature to which a given parcel of humid air must be cooled, - at constant barometric pressure, for water vapor to condense into water. - title: dew point - examples: - - value: 22 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dew point - is_a: core field - slot_uri: MIXS:0000129 - multivalued: false - range: QuantityValue - diether_lipids: - name: diether_lipids - annotations: - expected_value: - tag: expected_value - value: diether lipid name;measurement value - preferred_unit: - tag: preferred_unit - value: nanogram per liter - occurrence: - tag: occurrence - value: m - description: Concentration of diether lipids; can include multiple types of diether - lipids - title: diether lipids - examples: - - value: 0.2 nanogram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - diether lipids - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000178 - multivalued: true - range: TextValue - diss_carb_dioxide: - name: diss_carb_dioxide - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid - portion of the sample - title: dissolved carbon dioxide - examples: - - value: 5 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved carbon dioxide - is_a: core field - slot_uri: MIXS:0000436 - multivalued: false - range: QuantityValue - diss_hydrogen: - name: diss_hydrogen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved hydrogen - title: dissolved hydrogen - examples: - - value: 0.3 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved hydrogen - is_a: core field - slot_uri: MIXS:0000179 - multivalued: false - range: QuantityValue - diss_inorg_carb: - name: diss_inorg_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Dissolved inorganic carbon concentration in the sample, typically - measured after filtering the sample using a 0.45 micrometer filter - title: dissolved inorganic carbon - examples: - - value: 2059 micromole per kilogram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved inorganic carbon - is_a: core field - slot_uri: MIXS:0000434 - multivalued: false - range: QuantityValue - diss_inorg_nitro: - name: diss_inorg_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved inorganic nitrogen - title: dissolved inorganic nitrogen - examples: - - value: 761 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved inorganic nitrogen - is_a: core field - slot_uri: MIXS:0000698 - multivalued: false - range: QuantityValue - diss_inorg_phosp: - name: diss_inorg_phosp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved inorganic phosphorus in the sample - title: dissolved inorganic phosphorus - examples: - - value: 56.5 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved inorganic phosphorus - is_a: core field - slot_uri: MIXS:0000106 - multivalued: false - range: QuantityValue - diss_iron: - name: diss_iron - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved iron in the sample - title: dissolved iron - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved iron - is_a: core field - slot_uri: MIXS:0000139 - multivalued: false - range: QuantityValue - diss_org_carb: - name: diss_org_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved organic carbon in the sample, liquid portion - of the sample, or aqueous phase of the fluid - title: dissolved organic carbon - examples: - - value: 197 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved organic carbon - is_a: core field - slot_uri: MIXS:0000433 - multivalued: false - range: QuantityValue - diss_org_nitro: - name: diss_org_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved - nitrogen - NH4 - NO3 - NO2 - title: dissolved organic nitrogen - examples: - - value: 0.05 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved organic nitrogen - is_a: core field - slot_uri: MIXS:0000162 - multivalued: false - range: QuantityValue - diss_oxygen: - name: diss_oxygen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per kilogram, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved oxygen - title: dissolved oxygen - examples: - - value: 175 micromole per kilogram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved oxygen - is_a: core field - slot_uri: MIXS:0000119 - multivalued: false - range: QuantityValue - diss_oxygen_fluid: - name: diss_oxygen_fluid - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per kilogram, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved oxygen in the oil field produced fluids - as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). - title: dissolved oxygen in fluids - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - dissolved oxygen in fluids - is_a: core field - slot_uri: MIXS:0000438 - multivalued: false - range: QuantityValue - door_comp_type: - name: door_comp_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The composite type of the door - title: door type, composite - examples: - - value: revolving - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door type, composite - is_a: core field - slot_uri: MIXS:0000795 - multivalued: false - range: door_comp_type_enum - door_cond: - name: door_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The phsical condition of the door - title: door condition - examples: - - value: new - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door condition - is_a: core field - slot_uri: MIXS:0000788 - multivalued: false - range: door_cond_enum - door_direct: - name: door_direct - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The direction the door opens - title: door direction of opening - examples: - - value: inward - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door direction of opening - is_a: core field - slot_uri: MIXS:0000789 - multivalued: false - range: door_direct_enum - door_loc: - name: door_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The relative location of the door in the room - title: door location - examples: - - value: north - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door location - is_a: core field - slot_uri: MIXS:0000790 - multivalued: false - range: door_loc_enum - door_mat: - name: door_mat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The material the door is composed of - title: door material - examples: - - value: wood - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door material - is_a: core field - slot_uri: MIXS:0000791 - multivalued: false - range: door_mat_enum - door_move: - name: door_move - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of movement of the door - title: door movement - examples: - - value: swinging - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door movement - is_a: core field - slot_uri: MIXS:0000792 - multivalued: false - range: door_move_enum - door_size: - name: door_size - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The size of the door - title: door area or size - examples: - - value: 2.5 square meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door area or size - is_a: core field - slot_uri: MIXS:0000158 - multivalued: false - range: QuantityValue - door_type: - name: door_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of door material - title: door type - examples: - - value: wooden - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door type - is_a: core field - slot_uri: MIXS:0000794 - multivalued: false - range: door_type_enum - door_type_metal: - name: door_type_metal - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of metal door - title: door type, metal - examples: - - value: hollow - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door type, metal - is_a: core field - slot_uri: MIXS:0000796 - multivalued: false - range: door_type_metal_enum - door_type_wood: - name: door_type_wood - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of wood door - title: door type, wood - examples: - - value: battened - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door type, wood - is_a: core field - slot_uri: MIXS:0000797 - multivalued: false - range: door_type_wood_enum - door_water_mold: - name: door_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on a door - title: door signs of water/mold - examples: - - value: presence of mold visible - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - door signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000793 - multivalued: false - range: TextValue - down_par: - name: down_par - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microEinstein per square meter per second, microEinstein per square - centimeter per second - occurrence: - tag: occurrence - value: '1' - description: Visible waveband radiance and irradiance measurements in the water - column - title: downward PAR - examples: - - value: 28.71 microEinstein per square meter per second - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - downward PAR - is_a: core field - slot_uri: MIXS:0000703 - multivalued: false - range: QuantityValue - drainage_class: - name: drainage_class - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Drainage classification from a standard system such as the USDA system - title: drainage classification - examples: - - value: well - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - drainage classification - is_a: core field - slot_uri: MIXS:0001085 - multivalued: false - range: drainage_class_enum - drawings: - name: drawings - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The buildings architectural drawings; if design is chosen, indicate - phase-conceptual, schematic, design development, and construction documents - title: drawings - examples: - - value: sketch - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - drawings - is_a: core field - slot_uri: MIXS:0000798 - multivalued: false - range: drawings_enum - efficiency_percent: - name: efficiency_percent - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Percentage of volatile solids removed from the anaerobic digestor - title: efficiency percent - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - efficiency percent - is_a: core field - slot_uri: MIXS:0000657 - multivalued: false - range: QuantityValue - elev: - name: elev - annotations: - expected_value: - tag: expected_value - value: measurement value - description: Elevation of the sampling site is its height above a fixed reference - point, most commonly the mean sea level. Elevation is mainly used when referring - to points on the earth's surface, while altitude is used for points above the - surface, such as an aircraft in flight or a spacecraft in orbit. - title: elevation - examples: - - value: 100 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - elevation - is_a: environment field - slot_uri: MIXS:0000093 - multivalued: false - range: float - elevator: - name: elevator - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of elevators within the built structure - title: elevator count - examples: - - value: '2' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - elevator count - is_a: core field - slot_uri: MIXS:0000799 - multivalued: false - range: TextValue - emulsions: - name: emulsions - annotations: - expected_value: - tag: expected_value - value: emulsion name;measurement value - preferred_unit: - tag: preferred_unit - value: gram per liter - occurrence: - tag: occurrence - value: m - description: Amount or concentration of substances such as paints, adhesives, - mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion - types - title: emulsions - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - emulsions - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000660 - multivalued: true - range: TextValue - env_broad_scale: - name: env_broad_scale - annotations: - expected_value: - tag: expected_value - value: The major environment type(s) where the sample was collected. Recommend - subclasses of biome [ENVO:00000428]. Multiple terms can be separated by - one or more pipes. - tooltip: - tag: tooltip - value: The biome or major environmental system where the sample or specimen - originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] - in the Environment Ontology (ENVO). For host-associated or plant-associated - samples, use terms from the UBERON or Plant Ontology to describe the broad - anatomical or morphological context - description: 'Report the major environmental system the sample or specimen came - from. The system(s) identified should have a coarse spatial grain, to provide - the general environmental context of where the sampling was done (e.g. in the - desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. - EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' - title: broad-scale environmental context - examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water - sample from the photic zone in middle of the Atlantic Ocean - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - broad-scale environmental context - is_a: environment field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000012 - multivalued: false - range: ControlledIdentifiedTermValue - env_local_scale: - name: env_local_scale - annotations: - expected_value: - tag: expected_value - value: Environmental entities having causal influences upon the entity at - time of sampling. - tooltip: - tag: tooltip - value: The specific environmental entities or features near the sample or - specimen that significantly influence its characteristics or composition. - These entities are typically smaller in scale than the broad environmental - context. Values for this field should be countable, material nouns and must - be chosen from subclasses of BFO:0000040 (material entity) that appear in - the Environment Ontology (ENVO). For host-associated or plant-associated - samples, use terms from the UBERON or Plant Ontology to describe specific - anatomical structures or plant parts. - description: 'Report the entity or entities which are in the sample or specimen’s - local vicinity and which you believe have significant causal influences on your - sample or specimen. We recommend using EnvO terms which are of smaller spatial - grain than your entry for env_broad_scale. Terms, such as anatomical sites, - from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) - are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.' - title: local environmental context - examples: - - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from - various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb - and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub - layer [ENVO:01000336].' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - local environmental context - is_a: environment field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000013 - multivalued: false - range: ControlledIdentifiedTermValue - env_medium: - name: env_medium - annotations: - expected_value: - tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend - subclasses of environmental material [ENVO:00010483]. - tooltip: - tag: tooltip - value: The predominant environmental material or substrate that directly surrounds - or hosts the sample or specimen at the time of sampling. Choose values from - subclasses of the 'environmental material' class [ENVO:00010483] in the - Environment Ontology (ENVO). Values for this field should be measurable - or mass material nouns, representing continuous environmental materials. - For host-associated or plant-associated samples, use terms from the UBERON - or Plant Ontology to indicate a tissue, organ, or plant structure - description: 'Report the environmental material(s) immediately surrounding the - sample or specimen at the time of sampling. We recommend using subclasses of - ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO - documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS - . Terms from other OBO ontologies are permissible as long as they reference - mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities - (e.g. a tree, a leaf, a table top).' - title: environmental medium - examples: - - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m - of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating - a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - environmental medium - is_a: environment field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000014 - multivalued: false - range: ControlledIdentifiedTermValue - escalator: - name: escalator - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of escalators within the built structure - title: escalator count - examples: - - value: '4' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - escalator count - is_a: core field - slot_uri: MIXS:0000800 - multivalued: false - range: TextValue - ethylbenzene: - name: ethylbenzene - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of ethylbenzene in the sample - title: ethylbenzene - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ethylbenzene - is_a: core field - slot_uri: MIXS:0000155 - multivalued: false - range: QuantityValue - exp_duct: - name: exp_duct - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The amount of exposed ductwork in the room - title: exposed ductwork - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - exposed ductwork - is_a: core field - slot_uri: MIXS:0000144 - multivalued: false - range: QuantityValue - exp_pipe: - name: exp_pipe - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The number of exposed pipes in the room - title: exposed pipes - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - exposed pipes - is_a: core field - slot_uri: MIXS:0000220 - multivalued: false - range: QuantityValue - experimental_factor: - name: experimental_factor - annotations: - expected_value: - tag: expected_value - value: text or EFO and/or OBI - description: Experimental factors are essentially the variable aspects of an experiment - design which can be used to describe an experiment, or set of experiments, in - an increasingly detailed manner. This field accepts ontology terms from Experimental - Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For - a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; - for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI - title: experimental factor - examples: - - value: time series design [EFO:EFO_0001779] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - experimental factor - is_a: investigation field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000008 - multivalued: false - range: ControlledTermValue - ext_door: - name: ext_door - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of exterior doors in the built structure - title: exterior door count - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - exterior door count - is_a: core field - slot_uri: MIXS:0000170 - multivalued: false - range: TextValue - ext_wall_orient: - name: ext_wall_orient - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The orientation of the exterior wall - title: orientations of exterior wall - examples: - - value: northwest - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - orientations of exterior wall - is_a: core field - slot_uri: MIXS:0000817 - multivalued: false - range: ext_wall_orient_enum - ext_window_orient: - name: ext_window_orient - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The compass direction the exterior window of the room is facing - title: orientations of exterior window - examples: - - value: southwest - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - orientations of exterior window - is_a: core field - slot_uri: MIXS:0000818 - multivalued: false - range: ext_window_orient_enum - extreme_event: - name: extreme_event - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' - description: Unusual physical events that may have affected microbial populations - title: history/extreme events - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/extreme events - is_a: core field - slot_uri: MIXS:0000320 - multivalued: false - range: string - fao_class: - name: fao_class - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Soil classification from the FAO World Reference Database for Soil - Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - title: soil_taxonomic/FAO classification - examples: - - value: Luvisols - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil_taxonomic/FAO classification - is_a: core field - slot_uri: MIXS:0001083 - multivalued: false - range: fao_class_enum - fertilizer_regm: - name: fertilizer_regm - annotations: - expected_value: - tag: expected_value - value: fertilizer name;fertilizer amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving the use of fertilizers; should - include the name of fertilizer, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple fertilizer - regimens - title: fertilizer regimen - examples: - - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - fertilizer regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000556 - multivalued: true - range: TextValue - field: - name: field - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Name of the hydrocarbon field (e.g. Albacora) - title: field name - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - field name - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000291 - multivalued: false - range: TextValue - filter_type: - name: filter_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: A device which removes solid particulates or airborne molecular contaminants - title: filter type - examples: - - value: HEPA - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - filter type - is_a: core field - slot_uri: MIXS:0000765 - multivalued: true - range: filter_type_enum - fire: - name: fire - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' - description: Historical and/or physical evidence of fire - title: history/fire - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/fire - is_a: core field - slot_uri: MIXS:0001086 - multivalued: false - range: string - fireplace_type: - name: fireplace_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: A firebox with chimney - title: fireplace type - examples: - - value: wood burning - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - fireplace type - is_a: core field - string_serialization: '[gas burning|wood burning]' - slot_uri: MIXS:0000802 - multivalued: false - range: TextValue - flooding: - name: flooding - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' - description: Historical and/or physical evidence of flooding - title: history/flooding - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/flooding - is_a: core field - slot_uri: MIXS:0000319 - multivalued: false - range: string - floor_age: - name: floor_age - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: years, weeks, days - occurrence: - tag: occurrence - value: '1' - description: The time period since installment of the carpet or flooring - title: floor age - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor age - is_a: core field - slot_uri: MIXS:0000164 - multivalued: false - range: QuantityValue - floor_area: - name: floor_area - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The area of the floor space within the room - title: floor area - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor area - is_a: core field - slot_uri: MIXS:0000165 - multivalued: false - range: QuantityValue - floor_cond: - name: floor_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The physical condition of the floor at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: floor condition - examples: - - value: new - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor condition - is_a: core field - slot_uri: MIXS:0000803 - multivalued: false - range: floor_cond_enum - floor_count: - name: floor_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of floors in the building, including basements and mechanical - penthouse - title: floor count - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor count - is_a: core field - slot_uri: MIXS:0000225 - multivalued: false - range: TextValue - floor_finish_mat: - name: floor_finish_mat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The floor covering type; the finished surface that is walked on - title: floor finish material - examples: - - value: carpet - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor finish material - is_a: core field - slot_uri: MIXS:0000804 - multivalued: false - range: floor_finish_mat_enum - floor_struc: - name: floor_struc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Refers to the structural elements and subfloor upon which the finish - flooring is installed - title: floor structure - examples: - - value: concrete - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor structure - is_a: core field - slot_uri: MIXS:0000806 - multivalued: false - range: floor_struc_enum - floor_thermal_mass: - name: floor_thermal_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The ability of the floor to provide inertia against temperature fluctuations - title: floor thermal mass - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor thermal mass - is_a: core field - slot_uri: MIXS:0000166 - multivalued: false - range: QuantityValue - floor_water_mold: - name: floor_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew in a room - title: floor signs of water/mold - examples: - - value: ceiling discoloration - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - floor signs of water/mold - is_a: core field - slot_uri: MIXS:0000805 - multivalued: false - range: floor_water_mold_enum - fluor: - name: fluor - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram chlorophyll a per cubic meter, volts - occurrence: - tag: occurrence - value: '1' - description: Raw or converted fluorescence of water - title: fluorescence - examples: - - value: 2.5 volts - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - fluorescence - is_a: core field - slot_uri: MIXS:0000704 - multivalued: false - range: QuantityValue - freq_clean: - name: freq_clean - annotations: - expected_value: - tag: expected_value - value: enumeration or {text} - occurrence: - tag: occurrence - value: '1' - description: The number of times the sample location is cleaned. Frequency of - cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually. - title: frequency of cleaning - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - frequency of cleaning - is_a: core field - slot_uri: MIXS:0000226 - multivalued: false - range: QuantityValue - freq_cook: - name: freq_cook - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The number of times a meal is cooked per week - title: frequency of cooking - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - frequency of cooking - is_a: core field - slot_uri: MIXS:0000227 - multivalued: false - range: QuantityValue - fungicide_regm: - name: fungicide_regm - annotations: - expected_value: - tag: expected_value - value: fungicide name;fungicide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of fungicides; should include - the name of fungicide, amount administered, treatment regimen including how - many times the treatment was repeated, how long each treatment lasted, and the - start and end time of the entire treatment; can include multiple fungicide regimens - title: fungicide regimen - examples: - - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - fungicide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000557 - multivalued: true - range: TextValue - furniture: - name: furniture - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The types of furniture present in the sampled room - title: furniture - examples: - - value: chair - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - furniture - is_a: core field - slot_uri: MIXS:0000807 - multivalued: false - range: furniture_enum - gaseous_environment: - name: gaseous_environment - annotations: - expected_value: - tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and - duration - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: m - description: Use of conditions with differing gaseous environments; should include - the name of gaseous compound, amount administered, treatment duration, interval - and total experimental duration; can include multiple gaseous environment regimens - title: gaseous environment - examples: - - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - gaseous environment - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000558 - multivalued: true - range: TextValue - gaseous_substances: - name: gaseous_substances - annotations: - expected_value: - tag: expected_value - value: gaseous substance name;measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: m - description: Amount or concentration of substances such as hydrogen sulfide, carbon - dioxide, methane, etc.; can include multiple substances - title: gaseous substances - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - gaseous substances - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000661 - multivalued: true - range: TextValue - gender_restroom: - name: gender_restroom - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The gender type of the restroom - title: gender of restroom - examples: - - value: male - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - gender of restroom - is_a: core field - slot_uri: MIXS:0000808 - multivalued: false - range: gender_restroom_enum - genetic_mod: - name: genetic_mod - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' - description: Genetic modifications of the genome of an organism, which may occur - naturally by spontaneous mutation, or be introduced by some experimental means, - e.g. specification of a transgene or the gene knocked-out or details of transient - transfection - title: genetic modification - examples: - - value: aox1A transgenic - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - genetic modification - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0000859 - multivalued: false - range: TextValue - geo_loc_name: - name: geo_loc_name - annotations: - expected_value: - tag: expected_value - value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location - name' - description: The geographical origin of the sample as defined by the country or - sea name followed by specific region name. Country or sea names should be chosen - from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology - (http://purl.bioontology.org/ontology/GAZ) - title: geographic location (country and/or sea,region) - examples: - - value: 'USA: Maryland, Bethesda' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - geographic location (country and/or sea,region) - is_a: environment field - string_serialization: '{term}: {term}, {text}' - slot_uri: MIXS:0000010 - multivalued: false - range: TextValue - glucosidase_act: - name: glucosidase_act - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mol per liter per hour - occurrence: - tag: occurrence - value: '1' - description: Measurement of glucosidase activity - title: glucosidase activity - examples: - - value: 5 mol per liter per hour - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - glucosidase activity - is_a: core field - slot_uri: MIXS:0000137 - multivalued: false - range: QuantityValue - gravidity: - name: gravidity - annotations: - expected_value: - tag: expected_value - value: gravidity status;timestamp - occurrence: - tag: occurrence - value: '1' - description: Whether or not subject is gravid, and if yes date due or date post-conception, - specifying which is used - title: gravidity - examples: - - value: yes;due date:2018-05-11 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - gravidity - is_a: core field - string_serialization: '{boolean};{timestamp}' - slot_uri: MIXS:0000875 - multivalued: false - range: TextValue - gravity: - name: gravity - annotations: - expected_value: - tag: expected_value - value: gravity factor value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: meter per square second, g - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of gravity factor to study - various types of responses in presence, absence or modified levels of gravity; - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple treatments - title: gravity - examples: - - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - gravity - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000559 - multivalued: true - range: TextValue - growth_facil: - name: growth_facil - annotations: - expected_value: - tag: expected_value - value: free text or CO - occurrence: - tag: occurrence - value: '1' - description: 'Type of facility where the sampled plant was grown; controlled vocabulary: - growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively - use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' - title: growth facility - examples: - - value: Growth chamber [CO_715:0000189] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - growth facility - is_a: core field - string_serialization: '{text}|{termLabel} {[termID]}' - slot_uri: MIXS:0001043 - multivalued: false - range: ControlledTermValue - growth_habit: - name: growth_habit - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Characteristic shape, appearance or growth form of a plant species - title: growth habit - examples: - - value: spreading - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - growth habit - is_a: core field - slot_uri: MIXS:0001044 - multivalued: false - range: growth_habit_enum - growth_hormone_regm: - name: growth_hormone_regm - annotations: - expected_value: - tag: expected_value - value: growth hormone name;growth hormone amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of growth hormones; should - include the name of growth hormone, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple growth - hormone regimens - title: growth hormone regimen - examples: - - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - growth hormone regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000560 - multivalued: true - range: TextValue - hall_count: - name: hall_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The total count of hallways and cooridors in the built structure - title: hallway/corridor count - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hallway/corridor count - is_a: core field - slot_uri: MIXS:0000228 - multivalued: false - range: TextValue - handidness: - name: handidness - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The handidness of the individual sampled - title: handidness - examples: - - value: right handedness - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - handidness - is_a: core field - slot_uri: MIXS:0000809 - multivalued: false - range: handidness_enum - hc_produced: - name: hc_produced - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, - etc). If "other" is specified, please propose entry in "additional info" field - title: hydrocarbon type produced - examples: - - value: Gas - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hydrocarbon type produced - is_a: core field - slot_uri: MIXS:0000989 - multivalued: false - range: hc_produced_enum - hcr: - name: hcr - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR - defined as a natural environmental feature containing large amounts of hydrocarbons - at high concentrations potentially suitable for commercial exploitation. This - term should not be confused with the Hydrocarbon Occurrence term which also - includes hydrocarbon-rich environments with currently limited commercial interest - such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose - entry in "additional info" field - title: hydrocarbon resource type - examples: - - value: Oil Sand - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hydrocarbon resource type - is_a: core field - slot_uri: MIXS:0000988 - multivalued: false - range: hcr_enum - hcr_fw_salinity: - name: hcr_fw_salinity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Original formation water salinity (prior to secondary recovery e.g. - Waterflooding) expressed as TDS - title: formation water salinity - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - formation water salinity - is_a: core field - slot_uri: MIXS:0000406 - multivalued: false - range: QuantityValue - hcr_geol_age: - name: hcr_geol_age - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - title: hydrocarbon resource geological age - examples: - - value: Silurian - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hydrocarbon resource geological age - is_a: core field - slot_uri: MIXS:0000993 - multivalued: false - range: hcr_geol_age_enum - hcr_pressure: - name: hcr_pressure - annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit - value: atmosphere, kilopascal - occurrence: - tag: occurrence - value: '1' - description: Original pressure of the hydrocarbon resource - title: hydrocarbon resource original pressure - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hydrocarbon resource original pressure - is_a: core field - string_serialization: '{float} - {float} {unit}' - slot_uri: MIXS:0000395 - multivalued: false - range: TextValue - hcr_temp: - name: hcr_temp - annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Original temperature of the hydrocarbon resource - title: hydrocarbon resource original temperature - examples: - - value: 150-295 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - hydrocarbon resource original temperature - is_a: core field - string_serialization: '{float} - {float} {unit}' - slot_uri: MIXS:0000393 - multivalued: false - range: TextValue - heat_cool_type: - name: heat_cool_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: Methods of conditioning or heating a room or building - title: heating and cooling system type - examples: - - value: heat pump - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - heating and cooling system type - is_a: core field - slot_uri: MIXS:0000766 - multivalued: true - range: heat_cool_type_enum - heat_deliv_loc: - name: heat_deliv_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The location of heat delivery within the room - title: heating delivery locations - examples: - - value: north - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - heating delivery locations - is_a: core field - slot_uri: MIXS:0000810 - multivalued: false - range: heat_deliv_loc_enum - heat_sys_deliv_meth: - name: heat_sys_deliv_meth - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The method by which the heat is delivered through the system - title: heating system delivery method - examples: - - value: radiant - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - heating system delivery method - is_a: core field - string_serialization: '[conductive|radiant]' - slot_uri: MIXS:0000812 - multivalued: false - range: string - heat_system_id: - name: heat_system_id - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' - description: The heating system identifier - title: heating system identifier - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - heating system identifier - is_a: core field - slot_uri: MIXS:0000833 - multivalued: false - range: TextValue - heavy_metals: - name: heavy_metals - annotations: - expected_value: - tag: expected_value - value: heavy metal name;measurement value unit - preferred_unit: - tag: preferred_unit - value: microgram per gram - occurrence: - tag: occurrence - value: m - description: Heavy metals present in the sequenced sample and their concentrations. - For multiple heavy metals and concentrations, add multiple copies of this field. - title: extreme_unusual_properties/heavy metals - examples: - - value: mercury;0.09 micrograms per gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - extreme_unusual_properties/heavy metals - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000652 - multivalued: true - range: TextValue - heavy_metals_meth: - name: heavy_metals_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining heavy metals - title: extreme_unusual_properties/heavy metals method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - extreme_unusual_properties/heavy metals method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000343 - multivalued: false - range: TextValue - height_carper_fiber: - name: height_carper_fiber - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: centimeter - occurrence: - tag: occurrence - value: '1' - description: The average carpet fiber height in the indoor environment - title: height carpet fiber mat - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - height carpet fiber mat - is_a: core field - slot_uri: MIXS:0000167 - multivalued: false - range: QuantityValue - herbicide_regm: - name: herbicide_regm - annotations: - expected_value: - tag: expected_value - value: herbicide name;herbicide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of herbicides; information - about treatment involving use of growth hormones; should include the name of - herbicide, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple regimens - title: herbicide regimen - examples: - - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - herbicide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000561 - multivalued: true - range: TextValue - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: soil horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - range: TextValue - host_age: - name: host_age - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: year, day, hour - occurrence: - tag: occurrence - value: '1' - description: Age of host at the time of sampling; relevant scale depends on species - and study, e.g. Could be seconds for amoebae or centuries for trees - title: host age - examples: - - value: 10 days - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host age - is_a: core field - slot_uri: MIXS:0000255 - multivalued: false - range: QuantityValue - host_body_habitat: - name: host_body_habitat - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: Original body habitat where the sample was obtained from - title: host body habitat - examples: - - value: nasopharynx - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host body habitat - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000866 - multivalued: false - range: TextValue - host_body_product: - name: host_body_product - annotations: - expected_value: - tag: expected_value - value: FMA or UBERON - occurrence: - tag: occurrence - value: '1' - description: Substance produced by the body, e.g. Stool, mucus, where the sample - was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy - ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma - or https://www.ebi.ac.uk/ols/ontologies/uberon - title: host body product - examples: - - value: Portion of mucus [fma66938] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host body product - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000888 - multivalued: false - range: ControlledTermValue - host_body_site: - name: host_body_site - annotations: - expected_value: - tag: expected_value - value: FMA or UBERON - occurrence: - tag: occurrence - value: '1' - description: Name of body site where the sample was obtained from, such as a specific - organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology - (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, - please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON - title: host body site - examples: - - value: gill [UBERON:0002535] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host body site - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000867 - multivalued: false - range: ControlledTermValue - host_body_temp: - name: host_body_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Core body temperature of the host when sample was collected - title: host body temperature - examples: - - value: 15 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host body temperature - is_a: core field - slot_uri: MIXS:0000274 - multivalued: false - range: QuantityValue - host_color: - name: host_color - annotations: - expected_value: - tag: expected_value - value: color - occurrence: - tag: occurrence - value: '1' - description: The color of host - title: host color - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host color - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000260 - multivalued: false - range: TextValue - host_common_name: - name: host_common_name - annotations: - expected_value: - tag: expected_value - value: common name - occurrence: - tag: occurrence - value: '1' - description: Common name of the host. - title: host common name - examples: - - value: human - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host common name - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000248 - multivalued: false - range: TextValue - host_diet: - name: host_diet - annotations: - expected_value: - tag: expected_value - value: diet type - occurrence: - tag: occurrence - value: m - description: Type of diet depending on the host, for animals omnivore, herbivore - etc., for humans high-fat, meditteranean etc.; can include multiple diet types - title: host diet - examples: - - value: herbivore - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host diet - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000869 - multivalued: true - range: TextValue - host_disease_stat: - name: host_disease_stat - annotations: - expected_value: - tag: expected_value - value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include - multiple diagnoses. The value of the field depends on host; for humans the terms - should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, - non-human host diseases are free text - title: host disease status - examples: - - value: rabies [DOID:11260] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host disease status - is_a: nucleic acid sequence source field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000031 - multivalued: false - range: TextValue - host_dry_mass: - name: host_dry_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: kilogram, gram - occurrence: - tag: occurrence - value: '1' - description: Measurement of dry mass - title: host dry mass - examples: - - value: 500 gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host dry mass - is_a: core field - slot_uri: MIXS:0000257 - multivalued: false - range: QuantityValue - host_family_relation: - name: host_family_relation - annotations: - expected_value: - tag: expected_value - value: relationship type;arbitrary identifier - occurrence: - tag: occurrence - value: m - description: Familial relationships to other hosts in the same study; can include - multiple relationships - title: host family relationship - examples: - - value: offspring;Mussel25 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host family relationship - is_a: core field - string_serialization: '{text};{text}' - slot_uri: MIXS:0000872 - multivalued: true - range: string - host_genotype: - name: host_genotype - annotations: - expected_value: - tag: expected_value - value: genotype - occurrence: - tag: occurrence - value: '1' - description: Observed genotype - title: host genotype - examples: - - value: C57BL/6 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host genotype - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000365 - multivalued: false - range: TextValue - host_growth_cond: - name: host_growth_cond - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' - description: Literature reference giving growth conditions of the host - title: host growth conditions - examples: - - value: https://academic.oup.com/icesjms/article/68/2/349/617247 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host growth conditions - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0000871 - multivalued: false - range: TextValue - host_height: - name: host_height - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: centimeter, millimeter, meter - occurrence: - tag: occurrence - value: '1' - description: The height of subject - title: host height - examples: - - value: 0.1 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host height - is_a: core field - slot_uri: MIXS:0000264 - multivalued: false - range: QuantityValue - host_last_meal: - name: host_last_meal - annotations: - expected_value: - tag: expected_value - value: content;duration - occurrence: - tag: occurrence - value: m - description: Content of last meal and time since feeding; can include multiple - values - title: host last meal - examples: - - value: corn feed;P2H - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host last meal - is_a: core field - string_serialization: '{text};{duration}' - slot_uri: MIXS:0000870 - multivalued: true - range: TextValue - host_length: - name: host_length - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: centimeter, millimeter, meter - occurrence: - tag: occurrence - value: '1' - description: The length of subject - title: host length - examples: - - value: 1 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host length - is_a: core field - slot_uri: MIXS:0000256 - multivalued: false - range: QuantityValue - host_life_stage: - name: host_life_stage - annotations: - expected_value: - tag: expected_value - value: stage - occurrence: - tag: occurrence - value: '1' - description: Description of life stage of host - title: host life stage - examples: - - value: adult - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host life stage - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000251 - multivalued: false - range: TextValue - host_phenotype: - name: host_phenotype - annotations: - expected_value: - tag: expected_value - value: PATO or HP - occurrence: - tag: occurrence - value: '1' - description: Phenotype of human or other host. For phenotypic quality ontology - (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. - For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP - title: host phenotype - examples: - - value: elongated [PATO:0001154] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host phenotype - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000874 - multivalued: false - range: ControlledTermValue - host_sex: - name: host_sex - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Gender or physical sex of the host. - title: host sex - examples: - - value: non-binary - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host sex - is_a: core field - slot_uri: MIXS:0000811 - multivalued: false - range: host_sex_enum - host_shape: - name: host_shape - annotations: - expected_value: - tag: expected_value - value: shape - occurrence: - tag: occurrence - value: '1' - description: Morphological shape of host - title: host shape - examples: - - value: round - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host shape - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000261 - multivalued: false - range: TextValue - host_subject_id: - name: host_subject_id - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' - description: A unique identifier by which each subject can be referred to, de-identified. - title: host subject id - examples: - - value: MPI123 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host subject id - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000861 - multivalued: false - range: TextValue - host_subspecf_genlin: - name: host_subspecf_genlin - annotations: - expected_value: - tag: expected_value - value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, - e.g. serovar, biotype, ecotype, variety, cultivar. - occurrence: - tag: occurrence - value: m - description: Information about the genetic distinctness of the host organism below - the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, - or any relevant genetic typing schemes like Group I plasmid. Subspecies should - not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage - name and the lineage rank separated by a colon, e.g., biovar:abc123. - title: host subspecific genetic lineage - examples: - - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host subspecific genetic lineage - is_a: core field - string_serialization: '{rank name}:{text}' - slot_uri: MIXS:0001318 - multivalued: true - range: string - host_substrate: - name: host_substrate - annotations: - expected_value: - tag: expected_value - value: substrate name - occurrence: - tag: occurrence - value: '1' - description: The growth substrate of the host. - title: host substrate - examples: - - value: rock - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host substrate - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000252 - multivalued: false - range: TextValue - host_symbiont: - name: host_symbiont - annotations: - expected_value: - tag: expected_value - value: species name or common name - occurrence: - tag: occurrence - value: m - description: The taxonomic name of the organism(s) found living in mutualistic, - commensalistic, or parasitic symbiosis with the specific host. - title: observed host symbionts - examples: - - value: flukeworms - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - observed host symbionts - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0001298 - multivalued: true - range: string - host_taxid: - name: host_taxid - annotations: - expected_value: - tag: expected_value - value: NCBI taxon identifier - occurrence: - tag: occurrence - value: '1' - description: NCBI taxon id of the host, e.g. 9606 - title: host taxid - comments: - - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host taxid - is_a: core field - slot_uri: MIXS:0000250 - multivalued: false - range: ControlledIdentifiedTermValue - host_tot_mass: - name: host_tot_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: kilogram, gram - occurrence: - tag: occurrence - value: '1' - description: Total mass of the host at collection, the unit depends on host - title: host total mass - examples: - - value: 2500 gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host total mass - is_a: core field - slot_uri: MIXS:0000263 - multivalued: false - range: QuantityValue - host_wet_mass: - name: host_wet_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: kilogram, gram - occurrence: - tag: occurrence - value: '1' - description: Measurement of wet mass - title: host wet mass - examples: - - value: 1500 gram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - host wet mass - is_a: core field - slot_uri: MIXS:0000567 - multivalued: false - range: QuantityValue - humidity: - name: humidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram per cubic meter - occurrence: - tag: occurrence - value: '1' - description: Amount of water vapour in the air, at the time of sampling - title: humidity - examples: - - value: 25 gram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - humidity - is_a: core field - slot_uri: MIXS:0000100 - multivalued: false - range: QuantityValue - humidity_regm: - name: humidity_regm - annotations: - expected_value: - tag: expected_value - value: humidity value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram per cubic meter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving an exposure to varying degree - of humidity; information about treatment involving use of growth hormones; should - include amount of humidity administered, treatment regimen including how many - times the treatment was repeated, how long each treatment lasted, and the start - and end time of the entire treatment; can include multiple regimens - title: humidity regimen - examples: - - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - humidity regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000568 - multivalued: true - range: TextValue - indoor_space: - name: indoor_space - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: A distinguishable space within a structure, the purpose for which - discrete areas of a building is used - title: indoor space - examples: - - value: foyer - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - indoor space - is_a: core field - slot_uri: MIXS:0000763 - multivalued: false - range: indoor_space_enum - indoor_surf: - name: indoor_surf - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Type of indoor surface - title: indoor surface - examples: - - value: wall - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - indoor surface - is_a: core field - slot_uri: MIXS:0000764 - multivalued: false - range: indoor_surf_enum - indust_eff_percent: - name: indust_eff_percent - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: Percentage of industrial effluents received by wastewater treatment - plant - title: industrial effluent percent - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - industrial effluent percent - is_a: core field - slot_uri: MIXS:0000662 - multivalued: false - range: QuantityValue - inorg_particles: - name: inorg_particles - annotations: - expected_value: - tag: expected_value - value: inorganic particle name;measurement value - preferred_unit: - tag: preferred_unit - value: mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Concentration of particles such as sand, grit, metal particles, ceramics, - etc.; can include multiple particles - title: inorganic particles - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - inorganic particles - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000664 - multivalued: true - range: TextValue - inside_lux: - name: inside_lux - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: kilowatt per square metre - occurrence: - tag: occurrence - value: '1' - description: The recorded value at sampling time (power density) - title: inside lux light - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - inside lux light - is_a: core field - slot_uri: MIXS:0000168 - multivalued: false - range: QuantityValue - int_wall_cond: - name: int_wall_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The physical condition of the wall at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: interior wall condition - examples: - - value: damaged - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - interior wall condition - is_a: core field - slot_uri: MIXS:0000813 - multivalued: false - range: int_wall_cond_enum - iw_bt_date_well: - name: iw_bt_date_well - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' - description: Injection water breakthrough date per well following a secondary - and/or tertiary recovery - title: injection water breakthrough date of specific well - examples: - - value: '2018-05-11' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - injection water breakthrough date of specific well - is_a: core field - slot_uri: MIXS:0001010 - multivalued: false - range: TimestampValue - iwf: - name: iwf - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: Proportion of the produced fluids derived from injected water at - the time of sampling. (e.g. 87%) - title: injection water fraction - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - injection water fraction - is_a: core field - slot_uri: MIXS:0000455 - multivalued: false - range: QuantityValue - last_clean: - name: last_clean - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' - description: The last time the floor was cleaned (swept, mopped, vacuumed) - title: last time swept/mopped/vacuumed - examples: - - value: 2018-05-11:T14:30Z - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - last time swept/mopped/vacuumed - is_a: core field - slot_uri: MIXS:0000814 - multivalued: false - range: TimestampValue - lat_lon: - name: lat_lon - annotations: - expected_value: - tag: expected_value - value: decimal degrees, limit to 8 decimal points - description: The geographical origin of the sample as defined by latitude and - longitude. The values should be reported in decimal degrees and in WGS84 system - title: geographic location (latitude and longitude) - examples: - - value: 50.586825 6.408977 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - geographic location (latitude and longitude) - is_a: environment field - string_serialization: '{float} {float}' - slot_uri: MIXS:0000009 - multivalued: false - range: GeolocationValue - light_intensity: - name: light_intensity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: lux - occurrence: - tag: occurrence - value: '1' - description: Measurement of light intensity - title: light intensity - examples: - - value: 0.3 lux - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - light intensity - is_a: core field - slot_uri: MIXS:0000706 - multivalued: false - range: QuantityValue - light_regm: - name: light_regm - annotations: - expected_value: - tag: expected_value - value: exposure type;light intensity;light quality - preferred_unit: - tag: preferred_unit - value: lux; micrometer, nanometer, angstrom - occurrence: - tag: occurrence - value: '1' - description: Information about treatment(s) involving exposure to light, including - both light intensity and quality. - title: light regimen - examples: - - value: incandescant light;10 lux;450 nanometer - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - light regimen - is_a: core field - string_serialization: '{text};{float} {unit};{float} {unit}' - slot_uri: MIXS:0000569 - multivalued: false - range: TextValue - light_type: - name: light_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: Application of light to achieve some practical or aesthetic effect. - Lighting includes the use of both artificial light sources such as lamps and - light fixtures, as well as natural illumination by capturing daylight. Can also - include absence of light - title: light type - examples: - - value: desk lamp - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - light type - is_a: core field - slot_uri: MIXS:0000769 - multivalued: true - range: light_type_enum - link_addit_analys: - name: link_addit_analys - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Link to additional analysis results performed on the sample - title: links to additional analysis - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - links to additional analysis - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000340 - multivalued: false - range: TextValue - link_class_info: - name: link_class_info - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Link to digitized soil maps or other soil classification information - title: link to classification information - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - link to classification information - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000329 - multivalued: false - range: TextValue - link_climate_info: - name: link_climate_info - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Link to climate resource - title: link to climate information - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - link to climate information - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000328 - multivalued: false - range: TextValue - lithology: - name: lithology - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). - If "other" is specified, please propose entry in "additional info" field' - title: lithology - examples: - - value: Volcanic - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - lithology - is_a: core field - slot_uri: MIXS:0000990 - multivalued: false - range: lithology_enum - local_class: - name: local_class - annotations: - expected_value: - tag: expected_value - value: local classification name - occurrence: - tag: occurrence - value: '1' - description: Soil classification based on local soil classification system - title: soil_taxonomic/local classification - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil_taxonomic/local classification - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000330 - multivalued: false - range: TextValue - local_class_meth: - name: local_class_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the local soil classification - title: soil_taxonomic/local classification method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil_taxonomic/local classification method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000331 - multivalued: false - range: TextValue - magnesium: - name: magnesium - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per - kilogram - occurrence: - tag: occurrence - value: '1' - description: Concentration of magnesium in the sample - title: magnesium - examples: - - value: 52.8 micromole per kilogram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - magnesium - is_a: core field - slot_uri: MIXS:0000431 - multivalued: false - range: QuantityValue - max_occup: - name: max_occup - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The maximum amount of people allowed in the indoor environment - title: maximum occupancy - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - maximum occupancy - is_a: core field - slot_uri: MIXS:0000229 - multivalued: false - range: QuantityValue - mean_frict_vel: - name: mean_frict_vel - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter per second - occurrence: - tag: occurrence - value: '1' - description: Measurement of mean friction velocity - title: mean friction velocity - examples: - - value: 0.5 meter per second - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean friction velocity - is_a: core field - slot_uri: MIXS:0000498 - multivalued: false - range: QuantityValue - mean_peak_frict_vel: - name: mean_peak_frict_vel - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter per second - occurrence: - tag: occurrence - value: '1' - description: Measurement of mean peak friction velocity - title: mean peak friction velocity - examples: - - value: 1 meter per second - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean peak friction velocity - is_a: core field - slot_uri: MIXS:0000502 - multivalued: false - range: QuantityValue - mech_struc: - name: mech_struc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'mechanical structure: a moving structure' - title: mechanical structure - examples: - - value: elevator - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mechanical structure - is_a: core field - slot_uri: MIXS:0000815 - multivalued: false - range: mech_struc_enum - mechanical_damage: - name: mechanical_damage - annotations: - expected_value: - tag: expected_value - value: damage type;body site - occurrence: - tag: occurrence - value: m - description: Information about any mechanical damage exerted on the plant; can - include multiple damages and sites - title: mechanical damage - examples: - - value: pruning;bark - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mechanical damage - is_a: core field - string_serialization: '{text};{text}' - slot_uri: MIXS:0001052 - multivalued: true - range: TextValue - methane: - name: methane - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, parts per billion, parts per million - occurrence: - tag: occurrence - value: '1' - description: Methane (gas) amount or concentration at the time of sampling - title: methane - examples: - - value: 1800 parts per billion - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - methane - is_a: core field - slot_uri: MIXS:0000101 - multivalued: false - range: QuantityValue - micro_biomass_meth: - name: micro_biomass_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining microbial biomass - title: microbial biomass method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - microbial biomass method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000339 - multivalued: false - range: string - microbial_biomass: - name: microbial_biomass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: ton, kilogram, gram per kilogram soil - occurrence: - tag: occurrence - value: '1' - description: The part of the organic matter in the soil that constitutes living - microorganisms smaller than 5-10 micrometer. If you keep this, you would need - to have correction factors used for conversion to the final units - title: microbial biomass - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - microbial biomass - is_a: core field - slot_uri: MIXS:0000650 - multivalued: false - range: QuantityValue - mineral_nutr_regm: - name: mineral_nutr_regm - annotations: - expected_value: - tag: expected_value - value: mineral nutrient name;mineral nutrient amount;treatment interval and - duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving the use of mineral supplements; - should include the name of mineral nutrient, amount administered, treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - mineral nutrient regimens - title: mineral nutrient regimen - examples: - - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mineral nutrient regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000570 - multivalued: true - range: TextValue - misc_param: - name: misc_param - annotations: - expected_value: - tag: expected_value - value: parameter name;measurement value - occurrence: - tag: occurrence - value: m - description: Any other measurement performed or parameter collected, that is not - listed here - title: miscellaneous parameter - examples: - - value: Bicarbonate ion concentration;2075 micromole per kilogram - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - miscellaneous parameter - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000752 - multivalued: true - range: TextValue - n_alkanes: - name: n_alkanes - annotations: - expected_value: - tag: expected_value - value: n-alkane name;measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: m - description: Concentration of n-alkanes; can include multiple n-alkanes - title: n-alkanes - examples: - - value: n-hexadecane;100 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - n-alkanes - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000503 - multivalued: true - range: TextValue - nitrate: - name: nitrate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of nitrate in the sample - title: nitrate - examples: - - value: 65 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - nitrate - is_a: core field - slot_uri: MIXS:0000425 - multivalued: false - range: QuantityValue - nitrite: - name: nitrite - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of nitrite in the sample - title: nitrite - examples: - - value: 0.5 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - nitrite - is_a: core field - slot_uri: MIXS:0000426 - multivalued: false - range: QuantityValue - nitro: - name: nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of nitrogen (total) - title: nitrogen - examples: - - value: 4.2 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - nitrogen - is_a: core field - slot_uri: MIXS:0000504 - multivalued: false - range: QuantityValue - non_min_nutr_regm: - name: non_min_nutr_regm - annotations: - expected_value: - tag: expected_value - value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval - and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving the exposure of plant to non-mineral - nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral - nutrient, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple non-mineral nutrient regimens - title: non-mineral nutrient regimen - examples: - - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - non-mineral nutrient regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000571 - multivalued: true - range: string - nucl_acid_amp: - name: nucl_acid_amp - annotations: - expected_value: - tag: expected_value - value: PMID, DOI or URL - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the enzymatic amplification (PCR, - TMA, NASBA) of specific nucleic acids - title: nucleic acid amplification - examples: - - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - nucleic acid amplification - is_a: sequencing field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000038 - multivalued: false - range: TextValue - nucl_acid_ext: - name: nucl_acid_ext - annotations: - expected_value: - tag: expected_value - value: PMID, DOI or URL - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the material separation to recover - the nucleic acid fraction from a sample - title: nucleic acid extraction - examples: - - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - nucleic acid extraction - is_a: sequencing field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000037 - multivalued: false - range: TextValue - number_pets: - name: number_pets - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The number of pets residing in the sampled space - title: number of pets - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - number of pets - is_a: core field - slot_uri: MIXS:0000231 - multivalued: false - range: QuantityValue - number_plants: - name: number_plants - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The number of plant(s) in the sampling space - title: number of houseplants - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - number of houseplants - is_a: core field - slot_uri: MIXS:0000230 - multivalued: false - range: QuantityValue - number_resident: - name: number_resident - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The number of individuals currently occupying in the sampling location - title: number of residents - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - number of residents - is_a: core field - slot_uri: MIXS:0000232 - multivalued: false - range: QuantityValue - occup_density_samp: - name: occup_density_samp - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Average number of occupants at time of sampling per square footage - title: occupant density at sampling - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - occupant density at sampling - is_a: core field - slot_uri: MIXS:0000217 - multivalued: false - range: QuantityValue - occup_document: - name: occup_document - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of documentation of occupancy - title: occupancy documentation - examples: - - value: estimate - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - occupancy documentation - is_a: core field - slot_uri: MIXS:0000816 - multivalued: false - range: occup_document_enum - occup_samp: - name: occup_samp - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Number of occupants present at time of sample within the given space - title: occupancy at sampling - examples: - - value: '10' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - occupancy at sampling - is_a: core field - slot_uri: MIXS:0000772 - multivalued: false - range: QuantityValue - org_carb: - name: org_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of organic carbon - title: organic carbon - examples: - - value: 1.5 microgram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organic carbon - is_a: core field - slot_uri: MIXS:0000508 - multivalued: false - range: QuantityValue - org_count_qpcr_info: - name: org_count_qpcr_info - annotations: - expected_value: - tag: expected_value - value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial - denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles - preferred_unit: - tag: preferred_unit - value: number of cells per gram (or ml or cm^2) - occurrence: - tag: occurrence - value: '1' - description: 'If qpcr was used for the cell count, the target gene name, the primer - sequence and the cycling conditions should also be provided. (Example: 16S rrna; - FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; - annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; - 30 cycles)' - title: organism count qPCR information - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organism count qPCR information - is_a: core field - string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles' - slot_uri: MIXS:0000099 - multivalued: false - range: string - org_matter: - name: org_matter - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of organic matter - title: organic matter - examples: - - value: 1.75 milligram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organic matter - is_a: core field - slot_uri: MIXS:0000204 - multivalued: false - range: QuantityValue - org_nitro: - name: org_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of organic nitrogen - title: organic nitrogen - examples: - - value: 4 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organic nitrogen - is_a: core field - slot_uri: MIXS:0000205 - multivalued: false - range: QuantityValue - org_particles: - name: org_particles - annotations: - expected_value: - tag: expected_value - value: particle name;measurement value - preferred_unit: - tag: preferred_unit - value: gram per liter - occurrence: - tag: occurrence - value: m - description: Concentration of particles such as faeces, hairs, food, vomit, paper - fibers, plant material, humus, etc. - title: organic particles - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organic particles - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000665 - multivalued: true - range: TextValue - organism_count: - name: organism_count - annotations: - expected_value: - tag: expected_value - value: organism name;measurement value;enumeration - preferred_unit: - tag: preferred_unit - value: number of cells per cubic meter, number of cells per milliliter, number - of cells per cubic centimeter - occurrence: - tag: occurrence - value: m - description: 'Total cell count of any organism (or group of organisms) per gram, - volume or area of sample, should include name of organism followed by count. - The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should - also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' - title: organism count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - organism count - is_a: core field - slot_uri: MIXS:0000103 - multivalued: true - range: QuantityValue - owc_tvdss: - name: owc_tvdss - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - title: oil water contact depth - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - oil water contact depth - is_a: core field - slot_uri: MIXS:0000405 - multivalued: false - range: QuantityValue - oxy_stat_samp: - name: oxy_stat_samp - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Oxygenation status of sample - title: oxygenation status of sample - examples: - - value: aerobic - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - oxygenation status of sample - is_a: core field - slot_uri: MIXS:0000753 - multivalued: false - range: oxy_stat_samp_enum - oxygen: - name: oxygen - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Oxygen (gas) amount or concentration at the time of sampling - title: oxygen - examples: - - value: 600 parts per million - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - oxygen - is_a: core field - slot_uri: MIXS:0000104 - multivalued: false - range: QuantityValue - part_org_carb: - name: part_org_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of particulate organic carbon - title: particulate organic carbon - examples: - - value: 1.92 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - particulate organic carbon - is_a: core field - slot_uri: MIXS:0000515 - multivalued: false - range: QuantityValue - part_org_nitro: - name: part_org_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of particulate organic nitrogen - title: particulate organic nitrogen - examples: - - value: 0.3 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - particulate organic nitrogen - is_a: core field - slot_uri: MIXS:0000719 - multivalued: false - range: QuantityValue - particle_class: - name: particle_class - annotations: - expected_value: - tag: expected_value - value: particle name;measurement value - preferred_unit: - tag: preferred_unit - value: micrometer - occurrence: - tag: occurrence - value: m - description: Particles are classified, based on their size, into six general categories:clay, - silt, sand, gravel, cobbles, and boulders; should include amount of particle - preceded by the name of the particle type; can include multiple values - title: particle classification - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - particle classification - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000206 - multivalued: true - range: TextValue - pcr_cond: - name: pcr_cond - annotations: - expected_value: - tag: expected_value - value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles - description: Description of reaction conditions and components of PCR in the form - of 'initial denaturation:94degC_1.5min; annealing=...' - title: pcr conditions - examples: - - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pcr conditions - is_a: sequencing field - string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles - slot_uri: MIXS:0000049 - multivalued: false - range: TextValue - pcr_primers: - name: pcr_primers - annotations: - expected_value: - tag: expected_value - value: 'FWD: forward primer sequence;REV:reverse primer sequence' - description: PCR primers that were used to amplify the sequence of the targeted - gene, locus or subfragment. This field should contain all the primers used for - a single PCR reaction if multiple forward or reverse primers are present in - a single PCR reaction. The primer sequence should be reported in uppercase letters - title: pcr primers - examples: - - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pcr primers - is_a: sequencing field - string_serialization: FWD:{dna};REV:{dna} - slot_uri: MIXS:0000046 - multivalued: false - range: TextValue - permeability: - name: permeability - annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit - value: mD - occurrence: - tag: occurrence - value: '1' - description: 'Measure of the ability of a hydrocarbon resource to allow fluids - to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' - title: permeability - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - permeability - is_a: core field - string_serialization: '{integer} - {integer} {unit}' - slot_uri: MIXS:0000404 - multivalued: false - range: TextValue - perturbation: - name: perturbation - annotations: - expected_value: - tag: expected_value - value: perturbation type name;perturbation interval and duration - occurrence: - tag: occurrence - value: m - description: Type of perturbation, e.g. chemical administration, physical disturbance, - etc., coupled with perturbation regimen including how many times the perturbation - was repeated, how long each perturbation lasted, and the start and end time - of the entire perturbation period; can include multiple perturbation types - title: perturbation - examples: - - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - perturbation - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000754 - multivalued: true - range: TextValue - pesticide_regm: - name: pesticide_regm - annotations: - expected_value: - tag: expected_value - value: pesticide name;pesticide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of insecticides; should - include the name of pesticide, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple pesticide - regimens - title: pesticide regimen - examples: - - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pesticide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000573 - multivalued: true - range: TextValue - petroleum_hydrocarb: - name: petroleum_hydrocarb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of petroleum hydrocarbon - title: petroleum hydrocarbon - examples: - - value: 0.05 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - petroleum hydrocarbon - is_a: core field - slot_uri: MIXS:0000516 - multivalued: false - range: QuantityValue - ph: - name: ph - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Ph measurement of the sample, or liquid portion of sample, or aqueous - phase of the fluid - title: pH - examples: - - value: '7.2' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pH - is_a: core field - slot_uri: MIXS:0001001 - multivalued: false - range: double - ph_meth: - name: ph_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining ph - title: pH method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pH method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0001106 - multivalued: false - range: TextValue - ph_regm: - name: ph_regm - annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - occurrence: - tag: occurrence - value: m - description: Information about treatment involving exposure of plants to varying - levels of ph of the growth media, treatment regimen including how many times - the treatment was repeated, how long each treatment lasted, and the start and - end time of the entire treatment; can include multiple regimen - title: pH regimen - examples: - - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pH regimen - is_a: core field - string_serialization: '{float};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001056 - multivalued: true - range: TextValue - phaeopigments: - name: phaeopigments - annotations: - expected_value: - tag: expected_value - value: phaeopigment name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per cubic meter - occurrence: - tag: occurrence - value: m - description: Concentration of phaeopigments; can include multiple phaeopigments - title: phaeopigments - examples: - - value: 2.5 milligram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - phaeopigments - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000180 - multivalued: true - range: TextValue - phosphate: - name: phosphate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of phosphate - title: phosphate - examples: - - value: 0.7 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - phosphate - is_a: core field - slot_uri: MIXS:0000505 - multivalued: false - range: QuantityValue - phosplipid_fatt_acid: - name: phosplipid_fatt_acid - annotations: - expected_value: - tag: expected_value - value: phospholipid fatty acid name;measurement value - preferred_unit: - tag: preferred_unit - value: mole per gram, mole per liter - occurrence: - tag: occurrence - value: m - description: Concentration of phospholipid fatty acids; can include multiple values - title: phospholipid fatty acid - examples: - - value: 2.98 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - phospholipid fatty acid - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000181 - multivalued: true - range: TextValue - photon_flux: - name: photon_flux - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: number of photons per second per unit area - occurrence: - tag: occurrence - value: '1' - description: Measurement of photon flux - title: photon flux - examples: - - value: 3.926 micromole photons per second per square meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - photon flux - is_a: core field - slot_uri: MIXS:0000725 - multivalued: false - range: QuantityValue - plant_growth_med: - name: plant_growth_med - annotations: - expected_value: - tag: expected_value - value: EO or enumeration - occurrence: - tag: occurrence - value: '1' - description: Specification of the media for growing the plants or tissue cultured - samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in - vitro liquid culture medium. Recommended value is a specific value from EO:plant - growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) - or other controlled vocabulary - title: plant growth medium - examples: - - value: hydroponic plant culture media [EO:0007067] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - plant growth medium - is_a: core field - slot_uri: MIXS:0001057 - multivalued: false - range: ControlledTermValue - plant_product: - name: plant_product - annotations: - expected_value: - tag: expected_value - value: product name - occurrence: - tag: occurrence - value: '1' - description: Substance produced by the plant, where the sample was obtained from - title: plant product - examples: - - value: xylem sap [PO:0025539] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - plant product - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0001058 - multivalued: false - range: TextValue - plant_sex: - name: plant_sex - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, - staminate, monoecieous, hermaphrodite. - title: plant sex - examples: - - value: Hermaphroditic - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - plant sex - is_a: core field - slot_uri: MIXS:0001059 - multivalued: false - range: plant_sex_enum - plant_struc: - name: plant_struc - annotations: - expected_value: - tag: expected_value - value: PO - occurrence: - tag: occurrence - value: '1' - description: Name of plant structure the sample was obtained from; for Plant Ontology - (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, - e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the - sex of it can be recorded here. - title: plant structure - examples: - - value: epidermis [PO:0005679] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - plant structure - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0001060 - multivalued: false - range: ControlledTermValue - pollutants: - name: pollutants - annotations: - expected_value: - tag: expected_value - value: pollutant name;measurement value - preferred_unit: - tag: preferred_unit - value: gram, mole per liter, milligram per liter, microgram per cubic meter - occurrence: - tag: occurrence - value: m - description: Pollutant types and, amount or concentrations measured at the time - of sampling; can report multiple pollutants by entering numeric values preceded - by name of pollutant - title: pollutants - examples: - - value: lead;0.15 microgram per cubic meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pollutants - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000107 - multivalued: true - range: TextValue - pool_dna_extracts: - name: pool_dna_extracts - annotations: - expected_value: - tag: expected_value - value: pooling status;number of pooled extracts - occurrence: - tag: occurrence - value: '1' - description: Indicate whether multiple DNA extractions were mixed. If the answer - yes, the number of extracts that were pooled should be given - title: pooling of DNA extracts (if done) - examples: - - value: yes;5 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pooling of DNA extracts (if done) - is_a: core field - string_serialization: '{boolean};{integer}' - slot_uri: MIXS:0000325 - multivalued: false - range: TextValue - porosity: - name: porosity - annotations: - expected_value: - tag: expected_value - value: measurement value or range - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: Porosity of deposited sediment is volume of voids divided by the - total volume of sample - title: porosity - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - porosity - is_a: core field - string_serialization: '{float} - {float} {unit}' - slot_uri: MIXS:0000211 - multivalued: false - range: TextValue - potassium: - name: potassium - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of potassium in the sample - title: potassium - examples: - - value: 463 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - potassium - is_a: core field - slot_uri: MIXS:0000430 - multivalued: false - range: QuantityValue - pour_point: - name: pour_point - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: 'Temperature at which a liquid becomes semi solid and loses its flow - characteristics. In crude oil a high¬†pour point¬†is generally associated with - a high paraffin content, typically found in crude deriving from a larger proportion - of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' - title: pour point - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pour point - is_a: core field - slot_uri: MIXS:0000127 - multivalued: false - range: QuantityValue - pre_treatment: - name: pre_treatment - annotations: - expected_value: - tag: expected_value - value: pre-treatment type - occurrence: - tag: occurrence - value: '1' - description: The process of pre-treatment removes materials that can be easily - collected from the raw wastewater - title: pre-treatment - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pre-treatment - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000348 - multivalued: false - range: TextValue - pres_animal_insect: - name: pres_animal_insect - annotations: - expected_value: - tag: expected_value - value: enumeration;count - occurrence: - tag: occurrence - value: '1' - description: The type and number of animals or insects present in the sampling - space. - title: presence of pets, animals, or insects - examples: - - value: cat;5 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - presence of pets, animals, or insects - is_a: core field - slot_uri: MIXS:0000819 - multivalued: false - range: string - pattern: ^(cat|dog|rodent|snake|other);\d+$ - pressure: - name: pressure - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: atmosphere - occurrence: - tag: occurrence - value: '1' - description: Pressure to which the sample is subject to, in atmospheres - title: pressure - examples: - - value: 50 atmosphere - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - pressure - is_a: core field - slot_uri: MIXS:0000412 - multivalued: false - range: QuantityValue - prev_land_use_meth: - name: prev_land_use_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining previous land use and dates - title: history/previous land use method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/previous land use method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000316 - multivalued: false - range: string - previous_land_use: - name: previous_land_use - annotations: - expected_value: - tag: expected_value - value: land use name;date - occurrence: - tag: occurrence - value: '1' - description: Previous land use and dates - title: history/previous land use - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/previous land use - is_a: core field - string_serialization: '{text};{timestamp}' - slot_uri: MIXS:0000315 - multivalued: false - range: TextValue - primary_prod: - name: primary_prod - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per cubic meter per day, gram per square meter per day - occurrence: - tag: occurrence - value: '1' - description: Measurement of primary production, generally measured as isotope - uptake - title: primary production - examples: - - value: 100 milligram per cubic meter per day - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - primary production - is_a: core field - slot_uri: MIXS:0000728 - multivalued: false - range: QuantityValue - primary_treatment: - name: primary_treatment - annotations: - expected_value: - tag: expected_value - value: primary treatment type - occurrence: - tag: occurrence - value: '1' - description: The process to produce both a generally homogeneous liquid capable - of being treated biologically and a sludge that can be separately treated or - processed - title: primary treatment - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - primary treatment - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000349 - multivalued: false - range: TextValue - prod_rate: - name: prod_rate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: cubic meter per day - occurrence: - tag: occurrence - value: '1' - description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - title: production rate - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - production rate - is_a: core field - slot_uri: MIXS:0000452 - multivalued: false - range: QuantityValue - prod_start_date: - name: prod_start_date - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' - description: Date of field's first production - title: production start date - examples: - - value: '2018-05-11' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - production start date - is_a: core field - slot_uri: MIXS:0001008 - multivalued: false - range: TimestampValue - profile_position: - name: profile_position - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Cross-sectional position in the hillslope where sample was collected.sample - area position in relation to surrounding areas - title: profile position - examples: - - value: summit - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - profile position - is_a: core field - slot_uri: MIXS:0001084 - multivalued: false - range: profile_position_enum - quad_pos: - name: quad_pos - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The quadrant position of the sampling room within the building - title: quadrant position - examples: - - value: West side - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - quadrant position - is_a: core field - slot_uri: MIXS:0000820 - multivalued: false - range: quad_pos_enum - radiation_regm: - name: radiation_regm - annotations: - expected_value: - tag: expected_value - value: radiation type name;radiation amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: rad, gray - occurrence: - tag: occurrence - value: m - description: Information about treatment involving exposure of plant or a plant - part to a particular radiation regimen; should include the radiation type, amount - or intensity administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple radiation regimens - title: radiation regimen - examples: - - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - radiation regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000575 - multivalued: true - range: TextValue - rainfall_regm: - name: rainfall_regm - annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: millimeter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving an exposure to a given amount - of rainfall, treatment regimen including how many times the treatment was repeated, - how long each treatment lasted, and the start and end time of the entire treatment; - can include multiple regimens - title: rainfall regimen - examples: - - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rainfall regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000576 - multivalued: true - range: TextValue - reactor_type: - name: reactor_type - annotations: - expected_value: - tag: expected_value - value: reactor type name - occurrence: - tag: occurrence - value: '1' - description: Anaerobic digesters can be designed and engineered to operate using - a number of different process configurations, as batch or continuous, mesophilic, - high solid or low solid, and single stage or multistage - title: reactor type - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - reactor type - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000350 - multivalued: false - range: TextValue - redox_potential: - name: redox_potential - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millivolt - occurrence: - tag: occurrence - value: '1' - description: Redox potential, measured relative to a hydrogen cell, indicating - oxidation or reduction potential - title: redox potential - examples: - - value: 300 millivolt - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - redox potential - is_a: core field - slot_uri: MIXS:0000182 - multivalued: false - range: QuantityValue - rel_air_humidity: - name: rel_air_humidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: Partial vapor and air pressure, density of the vapor and air, or - by the actual mass of the vapor and air - title: relative air humidity - examples: - - value: 80% - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - relative air humidity - is_a: core field - slot_uri: MIXS:0000121 - multivalued: false - range: QuantityValue - rel_humidity_out: - name: rel_humidity_out - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram of air, kilogram of air - occurrence: - tag: occurrence - value: '1' - description: The recorded outside relative humidity value at the time of sampling - title: outside relative humidity - examples: - - value: 12 per kilogram of air - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - outside relative humidity - is_a: core field - slot_uri: MIXS:0000188 - multivalued: false - range: QuantityValue - rel_samp_loc: - name: rel_samp_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The sampling location within the train car - title: relative sampling location - examples: - - value: center of car - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - relative sampling location - is_a: core field - slot_uri: MIXS:0000821 - multivalued: false - range: rel_samp_loc_enum - reservoir: - name: reservoir - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Name of the reservoir (e.g. Carapebus) - title: reservoir name - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - reservoir name - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000303 - multivalued: false - range: TextValue - resins_pc: - name: resins_pc - annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis - method that divides¬†crude oil¬†components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: resins wt% - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - resins wt% - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000134 - multivalued: false - range: TextValue - room_air_exch_rate: - name: room_air_exch_rate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: liter per hour - occurrence: - tag: occurrence - value: '1' - description: The rate at which outside air replaces indoor air in a given space - title: room air exchange rate - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room air exchange rate - is_a: core field - slot_uri: MIXS:0000169 - multivalued: false - range: QuantityValue - room_architec_elem: - name: room_architec_elem - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: The unique details and component parts that, together, form the architecture - of a distinguisahable space within a built structure - title: room architectural elements - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room architectural elements - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000233 - multivalued: false - range: string - room_condt: - name: room_condt - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The condition of the room at the time of sampling - title: room condition - examples: - - value: new - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room condition - is_a: core field - slot_uri: MIXS:0000822 - multivalued: false - range: room_condt_enum - room_connected: - name: room_connected - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: List of rooms connected to the sampling room by a doorway - title: rooms connected by a doorway - examples: - - value: office - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooms connected by a doorway - is_a: core field - slot_uri: MIXS:0000826 - multivalued: false - range: room_connected_enum - room_count: - name: room_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The total count of rooms in the built structure including all room - types - title: room count - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room count - is_a: core field - slot_uri: MIXS:0000234 - multivalued: false - range: TextValue - room_dim: - name: room_dim - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: The length, width and height of sampling room - title: room dimensions - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room dimensions - is_a: core field - string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' - slot_uri: MIXS:0000192 - multivalued: false - range: TextValue - room_door_dist: - name: room_door_dist - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: Distance between doors (meters) in the hallway between the sampling - room and adjacent rooms - title: room door distance - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room door distance - is_a: core field - string_serialization: '{integer} {unit}' - slot_uri: MIXS:0000193 - multivalued: false - range: TextValue - room_door_share: - name: room_door_share - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' - description: List of room(s) (room number, room name) sharing a door with the - sampling room - title: rooms that share a door with sampling room - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooms that share a door with sampling room - is_a: core field - string_serialization: '{text};{integer}' - slot_uri: MIXS:0000242 - multivalued: false - range: TextValue - room_hallway: - name: room_hallway - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' - description: List of room(s) (room number, room name) located in the same hallway - as sampling room - title: rooms that are on the same hallway - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooms that are on the same hallway - is_a: core field - string_serialization: '{text};{integer}' - slot_uri: MIXS:0000238 - multivalued: false - range: TextValue - room_loc: - name: room_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The position of the room within the building - title: room location in building - examples: - - value: interior room - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room location in building - is_a: core field - slot_uri: MIXS:0000823 - multivalued: false - range: room_loc_enum - room_moist_dam_hist: - name: room_moist_dam_hist - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The history of moisture damage or mold in the past 12 months. Number - of events of moisture damage or mold observed - title: room moisture damage or mold history - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room moisture damage or mold history - is_a: core field - slot_uri: MIXS:0000235 - multivalued: false - range: integer - room_net_area: - name: room_net_area - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square feet, square meter - occurrence: - tag: occurrence - value: '1' - description: The net floor area of sampling room. Net area excludes wall thicknesses - title: room net area - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room net area - is_a: core field - string_serialization: '{integer} {unit}' - slot_uri: MIXS:0000194 - multivalued: false - range: TextValue - room_occup: - name: room_occup - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Count of room occupancy at time of sampling - title: room occupancy - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room occupancy - is_a: core field - slot_uri: MIXS:0000236 - multivalued: false - range: QuantityValue - room_samp_pos: - name: room_samp_pos - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The horizontal sampling position in the room relative to architectural - elements - title: room sampling position - examples: - - value: south corner - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room sampling position - is_a: core field - slot_uri: MIXS:0000824 - multivalued: false - range: room_samp_pos_enum - room_type: - name: room_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The main purpose or activity of the sampling room. A room is any - distinguishable space within a structure - title: room type - examples: - - value: bathroom - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room type - is_a: core field - slot_uri: MIXS:0000825 - multivalued: false - range: room_type_enum - room_vol: - name: room_vol - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: cubic feet, cubic meter - occurrence: - tag: occurrence - value: '1' - description: Volume of sampling room - title: room volume - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room volume - is_a: core field - string_serialization: '{integer} {unit}' - slot_uri: MIXS:0000195 - multivalued: false - range: TextValue - room_wall_share: - name: room_wall_share - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' - description: List of room(s) (room number, room name) sharing a wall with the - sampling room - title: rooms that share a wall with sampling room - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooms that share a wall with sampling room - is_a: core field - string_serialization: '{text};{integer}' - slot_uri: MIXS:0000243 - multivalued: false - range: TextValue - room_window_count: - name: room_window_count - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: Number of windows in the room - title: room window count - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - room window count - is_a: core field - slot_uri: MIXS:0000237 - multivalued: false - range: integer - root_cond: - name: root_cond - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' - description: Relevant rooting conditions such as field plot size, sowing density, - container dimensions, number of plants per container. - title: rooting conditions - examples: - - value: http://himedialabs.com/TD/PT158.pdf - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting conditions - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001061 - multivalued: false - range: TextValue - root_med_carbon: - name: root_med_carbon - annotations: - expected_value: - tag: expected_value - value: carbon source name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Source of organic carbon in the culture rooting medium; e.g. sucrose. - title: rooting medium carbon - examples: - - value: sucrose - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium carbon - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000577 - multivalued: false - range: TextValue - root_med_macronutr: - name: root_med_macronutr - annotations: - expected_value: - tag: expected_value - value: macronutrient name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Measurement of the culture rooting medium macronutrients (N,P, K, - Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). - title: rooting medium macronutrients - examples: - - value: KH2PO4;170¬†milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium macronutrients - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000578 - multivalued: false - range: TextValue - root_med_micronutr: - name: root_med_micronutr - annotations: - expected_value: - tag: expected_value - value: micronutrient name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Measurement of the culture rooting medium micronutrients (Fe, Mn, - Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). - title: rooting medium micronutrients - examples: - - value: H3BO3;6.2¬†milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium micronutrients - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000579 - multivalued: false - range: TextValue - root_med_ph: - name: root_med_ph - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: pH measurement of the culture rooting medium; e.g. 5.5. - title: rooting medium pH - examples: - - value: '7.5' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium pH - is_a: core field - slot_uri: MIXS:0001062 - multivalued: false - range: QuantityValue - root_med_regl: - name: root_med_regl - annotations: - expected_value: - tag: expected_value - value: regulator name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Growth regulators in the culture rooting medium such as cytokinins, - auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. - title: rooting medium regulators - examples: - - value: abscisic acid;0.75 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium regulators - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000581 - multivalued: false - range: TextValue - root_med_solid: - name: root_med_solid - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Specification of the solidifying agent in the culture rooting medium; - e.g. agar. - title: rooting medium solidifier - examples: - - value: agar - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium solidifier - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0001063 - multivalued: false - range: TextValue - root_med_suppl: - name: root_med_suppl - annotations: - expected_value: - tag: expected_value - value: supplement name;measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Organic supplements of the culture rooting medium, such as vitamins, - amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid - (0.5¬†mg/L). - title: rooting medium organic supplements - examples: - - value: nicotinic acid;0.5 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - rooting medium organic supplements - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000580 - multivalued: false - range: TextValue - salinity: - name: salinity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: practical salinity unit, percentage - occurrence: - tag: occurrence - value: '1' - description: The total concentration of all dissolved salts in a liquid or solid - sample. While salinity can be measured by a complete chemical analysis, this - method is difficult and time consuming. More often, it is instead derived from - the conductivity measurement. This is known as practical salinity. These derivations - compare the specific conductance of the sample to a salinity standard such as - seawater. - title: salinity - examples: - - value: 25 practical salinity unit - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - salinity - is_a: core field - slot_uri: MIXS:0000183 - multivalued: false - range: QuantityValue - salinity_meth: - name: salinity_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining salinity - title: salinity method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - salinity method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000341 - multivalued: false - range: TextValue - salt_regm: - name: salt_regm - annotations: - expected_value: - tag: expected_value - value: salt name;salt amount;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: gram, microgram, mole per liter, gram per liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving use of salts as supplement - to liquid and soil growth media; should include the name of salt, amount administered, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple salt regimens - title: salt regimen - examples: - - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - salt regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000582 - multivalued: true - range: TextValue - samp_capt_status: - name: samp_capt_status - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Reason for the sample - title: sample capture status - examples: - - value: farm sample - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample capture status - is_a: core field - slot_uri: MIXS:0000860 - multivalued: false - range: samp_capt_status_enum - samp_collec_device: - name: samp_collec_device - annotations: - expected_value: - tag: expected_value - value: device name - description: The device used to collect an environmental sample. This field accepts - terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). - This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). - title: sample collection device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample collection device - is_a: nucleic acid sequence source field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000002 - multivalued: false - range: string - samp_collec_method: - name: samp_collec_method - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url , or text - description: The method employed for collecting the sample. - title: sample collection method - examples: - - value: swabbing - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample collection method - is_a: nucleic acid sequence source field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001225 - multivalued: false - range: string - samp_collect_point: - name: samp_collect_point - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Sampling point on the asset were sample was collected (e.g. Wellhead, - storage tank, separator, etc). If "other" is specified, please propose entry - in "additional info" field - title: sample collection point - examples: - - value: well - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample collection point - is_a: core field - slot_uri: MIXS:0001015 - multivalued: false - range: samp_collect_point_enum - samp_dis_stage: - name: samp_dis_stage - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Stage of the disease at the time of sample collection, e.g. inoculation, - penetration, infection, growth and reproduction, dissemination of pathogen. - title: sample disease stage - examples: - - value: infection - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample disease stage - is_a: core field - slot_uri: MIXS:0000249 - multivalued: false - range: samp_dis_stage_enum - samp_floor: - name: samp_floor - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The floor of the building, where the sampling room is located - title: sampling floor - examples: - - value: 4th floor - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sampling floor - is_a: core field - slot_uri: MIXS:0000828 - multivalued: false - range: samp_floor_enum - samp_loc_corr_rate: - name: samp_loc_corr_rate - annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit - value: millimeter per year - occurrence: - tag: occurrence - value: '1' - description: Metal corrosion rate is the speed of metal deterioration due to environmental - conditions. As environmental conditions change corrosion rates change accordingly. - Therefore, long term corrosion rates are generally more informative than short - term rates and for that reason they are preferred during reporting. In the case - of suspected MIC, corrosion rate measurements at the time of sampling might - provide insights into the involvement of certain microbial community members - in MIC as well as potential microbial interplays - title: corrosion rate at sample location - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - corrosion rate at sample location - is_a: core field - string_serialization: '{float} - {float} {unit}' - slot_uri: MIXS:0000136 - multivalued: false - range: TextValue - samp_mat_process: - name: samp_mat_process - annotations: - expected_value: - tag: expected_value - value: text - description: A brief description of any processing applied to the sample during - or after retrieving the sample from environment, or a link to the relevant protocol(s) - performed. - title: sample material processing - examples: - - value: filtering of seawater, storing samples in ethanol - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample material processing - is_a: nucleic acid sequence source field - string_serialization: '{text}' - slot_uri: MIXS:0000016 - multivalued: false - range: ControlledTermValue - samp_md: - name: samp_md - annotations: - expected_value: - tag: expected_value - value: measurement value;enumeration - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: In non deviated well, measured depth is equal to the true vertical - depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated - wells, the MD is the length of trajectory of the borehole measured from the - same reference or datum. Common datums used are ground level (GL), drilling - rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). - If "other" is specified, please propose entry in "additional info" field - title: sample measured depth - examples: - - value: 1534 meter;MSL - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample measured depth - is_a: core field - slot_uri: MIXS:0000413 - multivalued: false - range: QuantityValue - samp_name: - name: samp_name - annotations: - expected_value: - tag: expected_value - value: text - description: A local identifier or name that for the material sample used for - extracting nucleic acids, and subsequent sequencing. It can refer either to - the original material collected or to any derived sub-samples. It can have any - format, but we suggest that you make it concise, unique and consistent within - your lab, and as informative as possible. INSDC requires every sample name from - a single Submitter to be unique. Use of a globally unique identifier for the - field source_mat_id is recommended in addition to sample_name. - title: sample name - examples: - - value: ISDsoil1 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample name - is_a: investigation field - string_serialization: '{text}' - slot_uri: MIXS:0001107 - multivalued: false - range: string - samp_preserv: - name: samp_preserv - annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit - value: milliliter - occurrence: - tag: occurrence - value: '1' - description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, - etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - title: preservative added to sample - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - preservative added to sample - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000463 - multivalued: false - range: TextValue - samp_room_id: - name: samp_room_id - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: Sampling room number. This ID should be consistent with the designations - on the building floor plans - title: sampling room ID or name - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sampling room ID or name - is_a: core field - slot_uri: MIXS:0000244 - multivalued: false - range: TextValue - samp_size: - name: samp_size - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millliter, gram, milligram, liter - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of - sample collected. - title: amount or size of sample collected - examples: - - value: 5 liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - amount or size of sample collected - is_a: nucleic acid sequence source field - slot_uri: MIXS:0000001 - multivalued: false - range: QuantityValue - samp_sort_meth: - name: samp_sort_meth - annotations: - expected_value: - tag: expected_value - value: description of method - occurrence: - tag: occurrence - value: m - description: Method by which samples are sorted; open face filter collecting total - suspended particles, prefilter to remove particles larger than X micrometers - in diameter, where common values of X would be 10 and 2.5 full size sorting - in a cascade impactor. - title: sample size sorting method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample size sorting method - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000216 - multivalued: true - range: TextValue - samp_store_dur: - name: samp_store_dur - annotations: - expected_value: - tag: expected_value - value: duration - occurrence: - tag: occurrence - value: '1' - description: Duration for which the sample was stored - title: sample storage duration - examples: - - value: P1Y6M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample storage duration - is_a: core field - string_serialization: '{duration}' - slot_uri: MIXS:0000116 - multivalued: false - range: TextValue - samp_store_loc: - name: samp_store_loc - annotations: - expected_value: - tag: expected_value - value: location name - occurrence: - tag: occurrence - value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room - title: sample storage location - examples: - - value: Freezer no:5 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample storage location - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000755 - multivalued: false - range: TextValue - samp_store_temp: - name: samp_store_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Temperature at which sample was stored, e.g. -80 degree Celsius - title: sample storage temperature - examples: - - value: -80 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample storage temperature - is_a: core field - slot_uri: MIXS:0000110 - multivalued: false - range: QuantityValue - samp_subtype: - name: samp_subtype - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Name of sample sub-type. For example if "sample type" is "Produced - Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, - please propose entry in "additional info" field - title: sample subtype - examples: - - value: biofilm - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample subtype - is_a: core field - slot_uri: MIXS:0000999 - multivalued: false - range: samp_subtype_enum - samp_taxon_id: - name: samp_taxon_id - annotations: - expected_value: - tag: expected_value - value: Taxonomy ID - description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa - sample. Use 'synthetic metagenome’ for mock community/positive controls, or - 'blank sample' for negative controls. - title: Taxonomy ID of DNA sample - comments: - - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Taxonomy ID of DNA sample - is_a: investigation field - slot_uri: MIXS:0001320 - multivalued: false - range: ControlledIdentifiedTermValue - samp_time_out: - name: samp_time_out - annotations: - expected_value: - tag: expected_value - value: time - preferred_unit: - tag: preferred_unit - value: hour - occurrence: - tag: occurrence - value: '1' - description: The recent and long term history of outside sampling - title: sampling time outside - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sampling time outside - is_a: core field - slot_uri: MIXS:0000196 - multivalued: false - range: TextValue - samp_transport_cond: - name: samp_transport_cond - annotations: - expected_value: - tag: expected_value - value: measurement value;measurement value - preferred_unit: - tag: preferred_unit - value: days;degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Sample transport duration (in days or hrs) and temperature the sample - was exposed to (e.g. 5.5 days; 20 ¬∞C) - title: sample transport conditions - examples: - - value: 5 days;-20 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample transport conditions - is_a: core field - string_serialization: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000410 - multivalued: false - range: TextValue - samp_tvdss: - name: samp_tvdss - annotations: - expected_value: - tag: expected_value - value: measurement value or measurement value range - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: Depth of the sample i.e. The vertical distance between the sea level - and the sampled position in the subsurface. Depth can be reported as an interval - for subsurface samples e.g. 1325.75-1362.25 m - title: sample true vertical depth subsea - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample true vertical depth subsea - is_a: core field - string_serialization: '{float}-{float} {unit}' - slot_uri: MIXS:0000409 - multivalued: false - range: TextValue - samp_type: - name: samp_type - annotations: - expected_value: - tag: expected_value - value: GENEPIO:0001246 - occurrence: - tag: occurrence - value: '1' - description: The type of material from which the sample was obtained. For the - Hydrocarbon package, samples include types like core, rock trimmings, drill - cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, - produced water, injected water, swabs, etc. For the Food Package, samples are - usually categorized as food, body products or tissues, or environmental material. - This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246). - title: sample type - examples: - - value: built environment sample [GENEPIO:0001248] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample type - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000998 - multivalued: false - range: TextValue - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millliter, gram, milligram, square centimeter - description: 'Volume (ml) or mass (g) of total collected sample processed for - DNA extraction. Note: total sample collected should be entered under the term - Sample Size (MIXS:0000001).' - title: sample volume or weight for DNA extraction - examples: - - value: 1500 milliliter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample volume or weight for DNA extraction - is_a: nucleic acid sequence source field - slot_uri: MIXS:0000111 - multivalued: false - range: QuantityValue - samp_weather: - name: samp_weather - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The weather on the sampling day - title: sampling day weather - examples: - - value: foggy - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sampling day weather - is_a: core field - slot_uri: MIXS:0000827 - multivalued: false - range: samp_weather_enum - samp_well_name: - name: samp_well_name - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Name of the well (e.g. BXA1123) where sample was taken - title: sample well name - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample well name - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000296 - multivalued: false - range: TextValue - saturates_pc: - name: saturates_pc - annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis - method that divides¬†crude oil¬†components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: saturates wt% - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - saturates wt% - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000131 - multivalued: false - range: TextValue - season: - name: season - annotations: - expected_value: - tag: expected_value - value: NCIT:C94729 - occurrence: - tag: occurrence - value: '1' - description: The season when sampling occurred. Any of the four periods into which - the year is divided by the equinoxes and solstices. This field accepts terms - listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). - title: season - examples: - - value: autumn [NCIT:C94733] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - season - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000829 - multivalued: false - range: TextValue - season_environment: - name: season_environment - annotations: - expected_value: - tag: expected_value - value: seasonal environment name;treatment interval and duration - occurrence: - tag: occurrence - value: m - description: Treatment involving an exposure to a particular season (e.g. Winter, - summer, rabi, rainy etc.), treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment - title: seasonal environment - examples: - - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - seasonal environment - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001068 - multivalued: true - range: TextValue - season_precpt: - name: season_precpt - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millimeter - occurrence: - tag: occurrence - value: '1' - description: The average of all seasonal precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps. - title: mean seasonal precipitation - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean seasonal precipitation - is_a: core field - slot_uri: MIXS:0000645 - multivalued: false - range: QuantityValue - season_temp: - name: season_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Mean seasonal temperature - title: mean seasonal temperature - examples: - - value: 18 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mean seasonal temperature - is_a: core field - slot_uri: MIXS:0000643 - multivalued: false - range: QuantityValue - season_use: - name: season_use - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The seasons the space is occupied - title: seasonal use - examples: - - value: Winter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - seasonal use - is_a: core field - slot_uri: MIXS:0000830 - multivalued: false - range: season_use_enum - secondary_treatment: - name: secondary_treatment - annotations: - expected_value: - tag: expected_value - value: secondary treatment type - occurrence: - tag: occurrence - value: '1' - description: The process for substantially degrading the biological content of - the sewage - title: secondary treatment - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - secondary treatment - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000351 - multivalued: false - range: TextValue - sediment_type: - name: sediment_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Information about the sediment type based on major constituents - title: sediment type - examples: - - value: biogenous - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sediment type - is_a: core field - slot_uri: MIXS:0001078 - multivalued: false - range: sediment_type_enum - seq_meth: - name: seq_meth - annotations: - expected_value: - tag: expected_value - value: Text or OBI - description: Sequencing machine used. Where possible the term should be taken - from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103). - title: sequencing method - examples: - - value: 454 Genome Sequencer FLX [OBI:0000702] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sequencing method - is_a: sequencing field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000050 - multivalued: false - range: TextValue - seq_quality_check: - name: seq_quality_check - annotations: - expected_value: - tag: expected_value - value: none or manually edited - description: Indicate if the sequence has been called by automatic systems (none) - or undergone a manual editing procedure (e.g. by inspecting the raw data or - chromatograms). Applied only for sequences that are not submitted to SRA,ENA - or DRA - title: sequence quality check - examples: - - value: none - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sequence quality check - is_a: sequencing field - string_serialization: '[none|manually edited]' - slot_uri: MIXS:0000051 - multivalued: false - range: TextValue - sewage_type: - name: sewage_type - annotations: - expected_value: - tag: expected_value - value: sewage type name - occurrence: - tag: occurrence - value: '1' - description: Type of wastewater treatment plant as municipial or industrial - title: sewage type - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sewage type - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000215 - multivalued: false - range: TextValue - shad_dev_water_mold: - name: shad_dev_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on the shading device - title: shading device signs of water/mold - examples: - - value: no presence of mold visible - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - shading device signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000834 - multivalued: false - range: string - shading_device_cond: - name: shading_device_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The physical condition of the shading device at the time of sampling - title: shading device condition - examples: - - value: new - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - shading device condition - is_a: core field - slot_uri: MIXS:0000831 - multivalued: false - range: shading_device_cond_enum - shading_device_loc: - name: shading_device_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The location of the shading device in relation to the built structure - title: shading device location - examples: - - value: exterior - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - shading device location - is_a: core field - string_serialization: '[exterior|interior]' - slot_uri: MIXS:0000832 - multivalued: false - range: TextValue - shading_device_mat: - name: shading_device_mat - annotations: - expected_value: - tag: expected_value - value: material name - occurrence: - tag: occurrence - value: '1' - description: The material the shading device is composed of - title: shading device material - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - shading device material - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000245 - multivalued: false - range: TextValue - shading_device_type: - name: shading_device_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of shading device - title: shading device type - examples: - - value: slatted aluminum awning - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - shading device type - is_a: core field - slot_uri: MIXS:0000835 - multivalued: false - range: shading_device_type_enum - sieving: - name: sieving - annotations: - expected_value: - tag: expected_value - value: design name and/or size;amount - occurrence: - tag: occurrence - value: '1' - description: Collection design of pooled samples and/or sieve size and amount - of sample sieved - title: composite design/sieving - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - composite design/sieving - is_a: core field - string_serialization: '{{text}|{float} {unit}};{float} {unit}' - slot_uri: MIXS:0000322 - multivalued: false - range: TextValue - silicate: - name: silicate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of silicate - title: silicate - examples: - - value: 0.05 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - silicate - is_a: core field - slot_uri: MIXS:0000184 - multivalued: false - range: QuantityValue - size_frac: - name: size_frac - annotations: - expected_value: - tag: expected_value - value: filter size value range - description: Filtering pore size used in sample preparation - title: size fraction selected - examples: - - value: 0-0.22 micrometer - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - size fraction selected - is_a: nucleic acid sequence source field - string_serialization: '{float}-{float} {unit}' - slot_uri: MIXS:0000017 - multivalued: false - range: TextValue - size_frac_low: - name: size_frac_low - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: micrometer - occurrence: - tag: occurrence - value: '1' - description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. - Materials larger than the size threshold are excluded from the sample - title: size-fraction lower threshold - examples: - - value: 0.2 micrometer - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - size-fraction lower threshold - is_a: core field - slot_uri: MIXS:0000735 - multivalued: false - range: QuantityValue - size_frac_up: - name: size_frac_up - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: micrometer - occurrence: - tag: occurrence - value: '1' - description: Refers to the mesh/pore size used to retain the sample. Materials - smaller than the size threshold are excluded from the sample - title: size-fraction upper threshold - examples: - - value: 20 micrometer - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - size-fraction upper threshold - is_a: core field - slot_uri: MIXS:0000736 - multivalued: false - range: QuantityValue - slope_aspect: - name: slope_aspect - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree - occurrence: - tag: occurrence - value: '1' - description: The direction a slope faces. While looking down a slope use a compass - to record the direction you are facing (direction or degrees); e.g., nw or 315 - degrees. This measure provides an indication of sun and wind exposure that will - influence soil temperature and evapotranspiration. - title: slope aspect - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - slope aspect - is_a: core field - slot_uri: MIXS:0000647 - multivalued: false - range: QuantityValue - slope_gradient: - name: slope_gradient - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: Commonly called 'slope'. The angle between ground surface and a horizontal - line (in percent). This is the direction that overland water would flow. This - measure is usually taken with a hand level meter or clinometer - title: slope gradient - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - slope gradient - is_a: core field - slot_uri: MIXS:0000646 - multivalued: false - range: QuantityValue - sludge_retent_time: - name: sludge_retent_time - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: hours - occurrence: - tag: occurrence - value: '1' - description: The time activated sludge remains in reactor - title: sludge retention time - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sludge retention time - is_a: core field - slot_uri: MIXS:0000669 - multivalued: false - range: QuantityValue - sodium: - name: sodium - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Sodium concentration in the sample - title: sodium - examples: - - value: 10.5 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sodium - is_a: core field - slot_uri: MIXS:0000428 - multivalued: false - range: QuantityValue - soil_horizon: - name: soil_horizon - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Specific layer in the land area which measures parallel to the soil - surface and possesses physical characteristics which differ from the layers - above and beneath - title: soil horizon - examples: - - value: A horizon - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon - is_a: core field - slot_uri: MIXS:0001082 - multivalued: false - range: soil_horizon_enum - soil_text_measure: - name: soil_text_measure - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The relative proportion of different grain sizes of mineral particles - in a soil, as described using a standard system; express as % sand (50 um to - 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty - clay loam) optional. - title: soil texture measurement - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil texture measurement - is_a: core field - slot_uri: MIXS:0000335 - multivalued: false - range: QuantityValue - soil_texture_meth: - name: soil_texture_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining soil texture - title: soil texture method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil texture method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000336 - multivalued: false - range: string - soil_type: - name: soil_type - annotations: - expected_value: - tag: expected_value - value: ENVO_00001998 - occurrence: - tag: occurrence - value: '1' - description: Description of the soil type or classification. This field accepts - terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms - can be separated by pipes. - title: soil type - examples: - - value: plinthosol [ENVO:00002250] - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil type - is_a: core field - string_serialization: '{termLabel} {[termID]}' - slot_uri: MIXS:0000332 - multivalued: false - range: TextValue - soil_type_meth: - name: soil_type_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining soil series name or other - lower-level classification - title: soil type method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil type method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000334 - multivalued: false - range: TextValue - solar_irradiance: - name: solar_irradiance - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: kilowatts per square meter per day, ergs per square centimeter per - second - occurrence: - tag: occurrence - value: '1' - description: The amount of solar energy that arrives at a specific area of a surface - during a specific time interval - title: solar irradiance - examples: - - value: 1.36 kilowatts per square meter per day - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - solar irradiance - is_a: core field - slot_uri: MIXS:0000112 - multivalued: false - range: QuantityValue - soluble_inorg_mat: - name: soluble_inorg_mat - annotations: - expected_value: - tag: expected_value - value: soluble inorganic material name;measurement value - preferred_unit: - tag: preferred_unit - value: gram, microgram, mole per liter, gram per liter, parts per million - occurrence: - tag: occurrence - value: m - description: Concentration of substances such as ammonia, road-salt, sea-salt, - cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - title: soluble inorganic material - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soluble inorganic material - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000672 - multivalued: true - range: TextValue - soluble_org_mat: - name: soluble_org_mat - annotations: - expected_value: - tag: expected_value - value: soluble organic material name;measurement value - preferred_unit: - tag: preferred_unit - value: gram, microgram, mole per liter, gram per liter, parts per million - occurrence: - tag: occurrence - value: m - description: Concentration of substances such as urea, fruit sugars, soluble proteins, - drugs, pharmaceuticals, etc. - title: soluble organic material - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soluble organic material - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000673 - multivalued: true - range: TextValue - soluble_react_phosp: - name: soluble_react_phosp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of soluble reactive phosphorus - title: soluble reactive phosphorus - examples: - - value: 0.1 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soluble reactive phosphorus - is_a: core field - slot_uri: MIXS:0000738 - multivalued: false - range: QuantityValue - source_mat_id: - name: source_mat_id - annotations: - expected_value: - tag: expected_value - value: 'for cultures of microorganisms: identifiers for two culture collections; - for other material a unique arbitrary identifer' - description: A unique identifier assigned to a material sample (as defined by - http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular - digital record of a material sample) used for extracting nucleic acids, and - subsequent sequencing. The identifier can refer either to the original material - collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, - /bio_material, or /culture_collection may or may not share the same value as - the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id - may both contain 'UAM:Herps:14' , referring to both the specimen voucher and - sampled tissue with the same identifier. However, the /culture_collection qualifier - may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id - would refer to an identifier from some derived culture from which the nucleic - acids were extracted (e.g. xatc123 or ark:/2154/R2). - title: source material identifiers - examples: - - value: MPI012345 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - source material identifiers - is_a: nucleic acid sequence source field - string_serialization: '{text}' - slot_uri: MIXS:0000026 - multivalued: false - range: TextValue - space_typ_state: - name: space_typ_state - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Customary or normal state of the space - title: space typical state - examples: - - value: typically occupied - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - space typical state - is_a: core field - string_serialization: '[typically occupied|typically unoccupied]' - slot_uri: MIXS:0000770 - multivalued: false - range: TextValue - specific: - name: specific - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'The building specifications. If design is chosen, indicate phase: - conceptual, schematic, design development, construction documents' - title: specifications - examples: - - value: construction - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - specifications - is_a: core field - slot_uri: MIXS:0000836 - multivalued: false - range: specific_enum - specific_humidity: - name: specific_humidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram of air, kilogram of air - occurrence: - tag: occurrence - value: '1' - description: The mass of water vapour in a unit mass of moist air, usually expressed - as grams of vapour per kilogram of air, or, in air conditioning, as grains per - pound. - title: specific humidity - examples: - - value: 15 per kilogram of air - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - specific humidity - is_a: core field - slot_uri: MIXS:0000214 - multivalued: false - range: QuantityValue - sr_dep_env: - name: sr_dep_env - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - title: source rock depositional environment - examples: - - value: Marine - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - source rock depositional environment - is_a: core field - slot_uri: MIXS:0000996 - multivalued: false - range: sr_dep_env_enum - sr_geol_age: - name: sr_geol_age - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - title: source rock geological age - examples: - - value: Silurian - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - source rock geological age - is_a: core field - slot_uri: MIXS:0000997 - multivalued: false - range: sr_geol_age_enum - sr_kerog_type: - name: sr_kerog_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic - and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ - fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris - (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). - If "other" is specified, please propose entry in "additional info" field' - title: source rock kerogen type - examples: - - value: Type IV - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - source rock kerogen type - is_a: core field - slot_uri: MIXS:0000994 - multivalued: false - range: sr_kerog_type_enum - sr_lithology: - name: sr_lithology - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - title: source rock lithology - examples: - - value: Coal - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - source rock lithology - is_a: core field - slot_uri: MIXS:0000995 - multivalued: false - range: sr_lithology_enum - standing_water_regm: - name: standing_water_regm - annotations: - expected_value: - tag: expected_value - value: standing water type;treatment interval and duration - occurrence: - tag: occurrence - value: m - description: Treatment involving an exposure to standing water during a plant's - life span, types can be flood water or standing water, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple regimens - title: standing water regimen - examples: - - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - standing water regimen - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0001069 - multivalued: true - range: TextValue - store_cond: - name: store_cond - annotations: - expected_value: - tag: expected_value - value: storage condition type;duration - occurrence: - tag: occurrence - value: '1' - description: Explain how and for how long the soil sample was stored before DNA - extraction (fresh/frozen/other). - title: storage conditions - examples: - - value: -20 degree Celsius freezer;P2Y10D - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - storage conditions - is_a: core field - string_serialization: '{text};{duration}' - slot_uri: MIXS:0000327 - multivalued: false - range: TextValue - substructure_type: - name: substructure_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: The substructure or under building is that largely hidden section - of the building which is built off the foundations to the ground floor level - title: substructure type - examples: - - value: basement - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - substructure type - is_a: core field - slot_uri: MIXS:0000767 - multivalued: true - range: substructure_type_enum - sulfate: - name: sulfate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of sulfate in the sample - title: sulfate - examples: - - value: 5 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sulfate - is_a: core field - slot_uri: MIXS:0000423 - multivalued: false - range: QuantityValue - sulfate_fw: - name: sulfate_fw - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Original sulfate concentration in the hydrocarbon resource - title: sulfate in formation water - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sulfate in formation water - is_a: core field - slot_uri: MIXS:0000407 - multivalued: false - range: QuantityValue - sulfide: - name: sulfide - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of sulfide in the sample - title: sulfide - examples: - - value: 2 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sulfide - is_a: core field - slot_uri: MIXS:0000424 - multivalued: false - range: QuantityValue - surf_air_cont: - name: surf_air_cont - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: Contaminant identified on surface - title: surface-air contaminant - examples: - - value: radon - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface-air contaminant - is_a: core field - slot_uri: MIXS:0000759 - multivalued: true - range: surf_air_cont_enum - surf_humidity: - name: surf_humidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percentage - occurrence: - tag: occurrence - value: '1' - description: 'Surfaces: water activity as a function of air and material moisture' - title: surface humidity - examples: - - value: 10% - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface humidity - is_a: core field - slot_uri: MIXS:0000123 - multivalued: false - range: QuantityValue - surf_material: - name: surf_material - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Surface materials at the point of sampling - title: surface material - examples: - - value: wood - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface material - is_a: core field - slot_uri: MIXS:0000758 - multivalued: false - range: surf_material_enum - surf_moisture: - name: surf_moisture - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: parts per million, gram per cubic meter, gram per square meter - occurrence: - tag: occurrence - value: '1' - description: Water held on a surface - title: surface moisture - examples: - - value: 0.01 gram per square meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface moisture - is_a: core field - slot_uri: MIXS:0000128 - multivalued: false - range: QuantityValue - surf_moisture_ph: - name: surf_moisture_ph - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: ph measurement of surface - title: surface moisture pH - examples: - - value: '7' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface moisture pH - is_a: core field - slot_uri: MIXS:0000760 - multivalued: false - range: double - surf_temp: - name: surf_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Temperature of the surface at the time of sampling - title: surface temperature - examples: - - value: 15 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - surface temperature - is_a: core field - slot_uri: MIXS:0000125 - multivalued: false - range: QuantityValue - suspend_part_matter: - name: suspend_part_matter - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of suspended particulate matter - title: suspended particulate matter - examples: - - value: 0.5 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - suspended particulate matter - is_a: core field - slot_uri: MIXS:0000741 - multivalued: false - range: QuantityValue - suspend_solids: - name: suspend_solids - annotations: - expected_value: - tag: expected_value - value: suspended solid name;measurement value - preferred_unit: - tag: preferred_unit - value: gram, microgram, milligram per liter, mole per liter, gram per liter, - part per million - occurrence: - tag: occurrence - value: m - description: Concentration of substances including a wide variety of material, - such as silt, decaying plant and animal matter; can include multiple substances - title: suspended solids - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - suspended solids - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000150 - multivalued: true - range: TextValue - tan: - name: tan - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: 'Total Acid Number¬†(TAN) is a measurement of acidity that is determined - by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize - the acids in one gram of oil.¬†It is an important quality measurement of¬†crude - oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' - title: total acid number - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total acid number - is_a: core field - slot_uri: MIXS:0000120 - multivalued: false - range: QuantityValue - target_gene: - name: target_gene - annotations: - expected_value: - tag: expected_value - value: gene name - description: Targeted gene or locus name for marker gene studies - title: target gene - examples: - - value: 16S rRNA, 18S rRNA, nif, amoA, rpo - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - target gene - is_a: sequencing field - string_serialization: '{text}' - slot_uri: MIXS:0000044 - multivalued: false - range: TextValue - target_subfragment: - name: target_subfragment - annotations: - expected_value: - tag: expected_value - value: gene fragment name - description: Name of subfragment of a gene or locus. Important to e.g. identify - special regions on marker genes like V6 on 16S rRNA - title: target subfragment - examples: - - value: V6, V9, ITS - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - target subfragment - is_a: sequencing field - string_serialization: '{text}' - slot_uri: MIXS:0000045 - multivalued: false - range: TextValue - temp: - name: temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - description: Temperature of the sample at the time of sampling. - title: temperature - examples: - - value: 25 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - temperature - is_a: environment field - slot_uri: MIXS:0000113 - multivalued: false - range: QuantityValue - temp_out: - name: temp_out - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The recorded temperature value at sampling time outside - title: temperature outside house - examples: - - value: 5 degree Celsius - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - temperature outside house - is_a: core field - slot_uri: MIXS:0000197 - multivalued: false - range: QuantityValue - tertiary_treatment: - name: tertiary_treatment - annotations: - expected_value: - tag: expected_value - value: tertiary treatment type - occurrence: - tag: occurrence - value: '1' - description: The process providing a final treatment stage to raise the effluent - quality before it is discharged to the receiving environment - title: tertiary treatment - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - tertiary treatment - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000352 - multivalued: false - range: TextValue - tidal_stage: - name: tidal_stage - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Stage of tide - title: tidal stage - examples: - - value: high tide - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - tidal stage - is_a: core field - slot_uri: MIXS:0000750 - multivalued: false - range: tidal_stage_enum - tillage: - name: tillage - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m - description: Note method(s) used for tilling - title: history/tillage - examples: - - value: chisel - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - history/tillage - is_a: core field - slot_uri: MIXS:0001081 - multivalued: true - range: tillage_enum - tiss_cult_growth_med: - name: tiss_cult_growth_med - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' - description: Description of plant tissue culture growth media used - title: tissue culture growth media - examples: - - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - tissue culture growth media - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001070 - multivalued: false - range: TextValue - toluene: - name: toluene - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of toluene in the sample - title: toluene - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - toluene - is_a: core field - slot_uri: MIXS:0000154 - multivalued: false - range: QuantityValue - tot_carb: - name: tot_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Total carbon content - title: total carbon - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total carbon - is_a: core field - slot_uri: MIXS:0000525 - multivalued: false - range: QuantityValue - tot_depth_water_col: - name: tot_depth_water_col - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: Measurement of total depth of water column - title: total depth of water column - examples: - - value: 500 meter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total depth of water column - is_a: core field - slot_uri: MIXS:0000634 - multivalued: false - range: QuantityValue - tot_diss_nitro: - name: tot_diss_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured - by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' - title: total dissolved nitrogen - examples: - - value: 40 microgram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total dissolved nitrogen - is_a: core field - slot_uri: MIXS:0000744 - multivalued: false - range: QuantityValue - tot_inorg_nitro: - name: tot_inorg_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' - description: Total inorganic nitrogen content - title: total inorganic nitrogen - examples: - - value: 40 microgram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total inorganic nitrogen - is_a: core field - slot_uri: MIXS:0000745 - multivalued: false - range: QuantityValue - tot_iron: - name: tot_iron - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, milligram per kilogram - occurrence: - tag: occurrence - value: '1' - description: Concentration of total iron in the sample - title: total iron - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total iron - is_a: core field - slot_uri: MIXS:0000105 - multivalued: false - range: QuantityValue - tot_nitro: - name: tot_nitro - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: 'Total nitrogen concentration of water samples, calculated by: total - nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured - without filtering, reported as nitrogen' - title: total nitrogen concentration - examples: - - value: 50 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total nitrogen concentration - is_a: core field - slot_uri: MIXS:0000102 - multivalued: false - range: QuantityValue - tot_nitro_cont_meth: - name: tot_nitro_cont_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the total nitrogen - title: total nitrogen content method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total nitrogen content method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000338 - multivalued: false - range: string - tot_nitro_content: - name: tot_nitro_content - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Total nitrogen content of the sample - title: total nitrogen content - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total nitrogen content - is_a: core field - slot_uri: MIXS:0000530 - multivalued: false - range: QuantityValue - tot_org_c_meth: - name: tot_org_c_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining total organic carbon - title: total organic carbon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total organic carbon method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000337 - multivalued: false - range: TextValue - tot_org_carb: - name: tot_org_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram Carbon per kilogram sample material - occurrence: - tag: occurrence - value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition - otherwise: total organic carbon content' - title: total organic carbon - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total organic carbon - is_a: core field - slot_uri: MIXS:0000533 - multivalued: false - range: QuantityValue - tot_part_carb: - name: tot_part_carb - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Total particulate carbon content - title: total particulate carbon - examples: - - value: 35 micromole per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total particulate carbon - is_a: core field - slot_uri: MIXS:0000747 - multivalued: false - range: QuantityValue - tot_phosp: - name: tot_phosp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total - phosphorus = total dissolved phosphorus + particulate phosphorus' - title: total phosphorus - examples: - - value: 0.03 milligram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total phosphorus - is_a: core field - slot_uri: MIXS:0000117 - multivalued: false - range: QuantityValue - tot_phosphate: - name: tot_phosphate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' - description: Total amount or concentration of phosphate - title: total phosphate - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total phosphate - is_a: core field - slot_uri: MIXS:0000689 - multivalued: false - range: QuantityValue - tot_sulfur: - name: tot_sulfur - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of total sulfur in the sample - title: total sulfur - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - total sulfur - is_a: core field - slot_uri: MIXS:0000419 - multivalued: false - range: QuantityValue - train_line: - name: train_line - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The subway line name - title: train line - examples: - - value: red - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - train line - is_a: core field - slot_uri: MIXS:0000837 - multivalued: false - range: train_line_enum - train_stat_loc: - name: train_stat_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The train station collection location - title: train station collection location - examples: - - value: forest hills - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - train station collection location - is_a: core field - slot_uri: MIXS:0000838 - multivalued: false - range: train_stat_loc_enum - train_stop_loc: - name: train_stop_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The train stop collection location - title: train stop collection location - examples: - - value: end - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - train stop collection location - is_a: core field - slot_uri: MIXS:0000839 - multivalued: false - range: train_stop_loc_enum - turbidity: - name: turbidity - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: formazin turbidity unit, formazin nephelometric units - occurrence: - tag: occurrence - value: '1' - description: Measure of the amount of cloudiness or haziness in water caused by - individual particles - title: turbidity - examples: - - value: 0.3 nephelometric turbidity units - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - turbidity - is_a: core field - slot_uri: MIXS:0000191 - multivalued: false - range: QuantityValue - tvdss_of_hcr_press: - name: tvdss_of_hcr_press - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original pressure was measured (e.g. 1578 m). - title: depth (TVDSS) of hydrocarbon resource pressure - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - depth (TVDSS) of hydrocarbon resource pressure - is_a: core field - slot_uri: MIXS:0000397 - multivalued: false - range: QuantityValue - tvdss_of_hcr_temp: - name: tvdss_of_hcr_temp - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter - occurrence: - tag: occurrence - value: '1' - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original temperature was measured (e.g. 1345 m). - title: depth (TVDSS) of hydrocarbon resource temperature - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - depth (TVDSS) of hydrocarbon resource temperature - is_a: core field - slot_uri: MIXS:0000394 - multivalued: false - range: QuantityValue - typ_occup_density: - name: typ_occup_density - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: Customary or normal density of occupants - title: typical occupant density - examples: - - value: '25' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - typical occupant density - is_a: core field - slot_uri: MIXS:0000771 - multivalued: false - range: double - ventilation_rate: - name: ventilation_rate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: cubic meter per minute, liters per second - occurrence: - tag: occurrence - value: '1' - description: Ventilation rate of the system in the sampled premises - title: ventilation rate - examples: - - value: 750 cubic meter per minute - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ventilation rate - is_a: core field - slot_uri: MIXS:0000114 - multivalued: false - range: QuantityValue - ventilation_type: - name: ventilation_type - annotations: - expected_value: - tag: expected_value - value: ventilation type name - occurrence: - tag: occurrence - value: '1' - description: Ventilation system used in the sampled premises - title: ventilation type - examples: - - value: Operable windows - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - ventilation type - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000756 - multivalued: false - range: TextValue - vfa: - name: vfa - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of Volatile Fatty Acids in the sample - title: volatile fatty acids - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - volatile fatty acids - is_a: core field - slot_uri: MIXS:0000152 - multivalued: false - range: QuantityValue - vfa_fw: - name: vfa_fw - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Original volatile fatty acid concentration in the hydrocarbon resource - title: vfa in formation water - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - vfa in formation water - is_a: core field - slot_uri: MIXS:0000408 - multivalued: false - range: QuantityValue - vis_media: - name: vis_media - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The building visual media - title: visual media - examples: - - value: 3D scans - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - visual media - is_a: core field - slot_uri: MIXS:0000840 - multivalued: false - range: vis_media_enum - viscosity: - name: viscosity - annotations: - expected_value: - tag: expected_value - value: measurement value;measurement value - preferred_unit: - tag: preferred_unit - value: cP at degree Celsius - occurrence: - tag: occurrence - value: '1' - description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile - stress (e.g. 3.5 cp; 100 ¬∞C) - title: viscosity - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - viscosity - is_a: core field - string_serialization: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000126 - multivalued: false - range: TextValue - volatile_org_comp: - name: volatile_org_comp - annotations: - expected_value: - tag: expected_value - value: volatile organic compound name;measurement value - preferred_unit: - tag: preferred_unit - value: microgram per cubic meter, parts per million, nanogram per liter - occurrence: - tag: occurrence - value: m - description: Concentration of carbon-based chemicals that easily evaporate at - room temperature; can report multiple volatile organic compounds by entering - numeric values preceded by name of compound - title: volatile organic compounds - examples: - - value: formaldehyde;500 nanogram per liter - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - volatile organic compounds - is_a: core field - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000115 - multivalued: true - range: TextValue - wall_area: - name: wall_area - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The total area of the sampled room's walls - title: wall area - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall area - is_a: core field - slot_uri: MIXS:0000198 - multivalued: false - range: QuantityValue - wall_const_type: - name: wall_const_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The building class of the wall defined by the composition of the - building elements and fire-resistance rating. - title: wall construction type - examples: - - value: fire resistive - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall construction type - is_a: core field - slot_uri: MIXS:0000841 - multivalued: false - range: wall_const_type_enum - wall_finish_mat: - name: wall_finish_mat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The material utilized to finish the outer most layer of the wall - title: wall finish material - examples: - - value: wood - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall finish material - is_a: core field - slot_uri: MIXS:0000842 - multivalued: false - range: wall_finish_mat_enum - wall_height: - name: wall_height - annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit - value: centimeter - occurrence: - tag: occurrence - value: '1' - description: The average height of the walls in the sampled room - title: wall height - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall height - is_a: core field - slot_uri: MIXS:0000221 - multivalued: false - range: QuantityValue - wall_loc: - name: wall_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The relative location of the wall within the room - title: wall location - examples: - - value: north - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall location - is_a: core field - slot_uri: MIXS:0000843 - multivalued: false - range: wall_loc_enum - wall_surf_treatment: - name: wall_surf_treatment - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The surface treatment of interior wall - title: wall surface treatment - examples: - - value: paneling - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall surface treatment - is_a: core field - slot_uri: MIXS:0000845 - multivalued: false - range: wall_surf_treatment_enum - wall_texture: - name: wall_texture - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The feel, appearance, or consistency of a wall surface - title: wall texture - examples: - - value: popcorn - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall texture - is_a: core field - slot_uri: MIXS:0000846 - multivalued: false - range: wall_texture_enum - wall_thermal_mass: - name: wall_thermal_mass - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The ability of the wall to provide inertia against temperature fluctuations. - Generally this means concrete or concrete block that is either exposed or covered - only with paint - title: wall thermal mass - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall thermal mass - is_a: core field - slot_uri: MIXS:0000222 - multivalued: false - range: QuantityValue - wall_water_mold: - name: wall_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on a wall - title: wall signs of water/mold - examples: - - value: no presence of mold visible - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wall signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000844 - multivalued: false - range: TextValue - wastewater_type: - name: wastewater_type - annotations: - expected_value: - tag: expected_value - value: wastewater type name - occurrence: - tag: occurrence - value: '1' - description: The origin of wastewater such as human waste, rainfall, storm drains, - etc. - title: wastewater type - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wastewater type - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000353 - multivalued: false - range: TextValue - water_cont_soil_meth: - name: water_cont_soil_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the water content of soil - title: water content method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water content method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000323 - multivalued: false - range: string - water_content: - name: water_content - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram per gram or cubic centimeter per cubic centimeter - occurrence: - tag: occurrence - value: '1' - description: Water content measurement - title: water content - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water content - is_a: core field - slot_uri: MIXS:0000185 - multivalued: false - range: string - water_current: - name: water_current - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: cubic meter per second, knots - occurrence: - tag: occurrence - value: '1' - description: Measurement of magnitude and direction of flow within a fluid - title: water current - examples: - - value: 10 cubic meter per second - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water current - is_a: core field - slot_uri: MIXS:0000203 - multivalued: false - range: QuantityValue - water_cut: - name: water_cut - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: percent - occurrence: - tag: occurrence - value: '1' - description: Current amount of water (%) in a produced fluid stream; or the average - of the combined streams - title: water cut - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water cut - is_a: core field - slot_uri: MIXS:0000454 - multivalued: false - range: QuantityValue - water_feat_size: - name: water_feat_size - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: square meter - occurrence: - tag: occurrence - value: '1' - description: The size of the water feature - title: water feature size - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water feature size - is_a: core field - slot_uri: MIXS:0000223 - multivalued: false - range: QuantityValue - water_feat_type: - name: water_feat_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of water feature present within the building being sampled - title: water feature type - examples: - - value: stream - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water feature type - is_a: core field - slot_uri: MIXS:0000847 - multivalued: false - range: water_feat_type_enum - water_prod_rate: - name: water_prod_rate - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: cubic meter per day - occurrence: - tag: occurrence - value: '1' - description: Water production rates per well (e.g. 987 m3 / day) - title: water production rate - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water production rate - is_a: core field - slot_uri: MIXS:0000453 - multivalued: false - range: QuantityValue - water_temp_regm: - name: water_temp_regm - annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: degree Celsius - occurrence: - tag: occurrence - value: m - description: Information about treatment involving an exposure to water with varying - degree of temperature, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple regimens - title: water temperature regimen - examples: - - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - water temperature regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000590 - multivalued: true - range: TextValue - watering_regm: - name: watering_regm - annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit - value: milliliter, liter - occurrence: - tag: occurrence - value: m - description: Information about treatment involving an exposure to watering frequencies, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple regimens - title: watering regimen - examples: - - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - watering regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000591 - multivalued: true - range: TextValue - weekday: - name: weekday - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The day of the week when sampling occurred - title: weekday - examples: - - value: Sunday - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - weekday - is_a: core field - slot_uri: MIXS:0000848 - multivalued: false - range: weekday_enum - win: - name: win - annotations: - expected_value: - tag: expected_value - value: text - occurrence: - tag: occurrence - value: '1' - description: 'A unique identifier of a well or wellbore. This is part of the Global - Framework for Well Identification initiative which is compiled by the Professional - Petroleum Data Management Association (PPDM) in an effort to improve well identification - systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' - title: well identification number - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - well identification number - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000297 - multivalued: false - range: TextValue - wind_direction: - name: wind_direction - annotations: - expected_value: - tag: expected_value - value: wind direction name - occurrence: - tag: occurrence - value: '1' - description: Wind direction is the direction from which a wind originates - title: wind direction - examples: - - value: Northwest - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wind direction - is_a: core field - string_serialization: '{text}' - slot_uri: MIXS:0000757 - multivalued: false - range: TextValue - wind_speed: - name: wind_speed - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter per second, kilometer per hour - occurrence: - tag: occurrence - value: '1' - description: Speed of wind measured at the time of sampling - title: wind speed - examples: - - value: 21 kilometer per hour - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - wind speed - is_a: core field - slot_uri: MIXS:0000118 - multivalued: false - range: QuantityValue - window_cond: - name: window_cond - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The physical condition of the window at the time of sampling - title: window condition - examples: - - value: rupture - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window condition - is_a: core field - slot_uri: MIXS:0000849 - multivalued: false - range: window_cond_enum - window_cover: - name: window_cover - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of window covering - title: window covering - examples: - - value: curtains - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window covering - is_a: core field - slot_uri: MIXS:0000850 - multivalued: false - range: window_cover_enum - window_horiz_pos: - name: window_horiz_pos - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The horizontal position of the window on the wall - title: window horizontal position - examples: - - value: middle - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window horizontal position - is_a: core field - slot_uri: MIXS:0000851 - multivalued: false - range: window_horiz_pos_enum - window_loc: - name: window_loc - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The relative location of the window within the room - title: window location - examples: - - value: west - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window location - is_a: core field - slot_uri: MIXS:0000852 - multivalued: false - range: window_loc_enum - window_mat: - name: window_mat - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of material used to finish a window - title: window material - examples: - - value: wood - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window material - is_a: core field - slot_uri: MIXS:0000853 - multivalued: false - range: window_mat_enum - window_open_freq: - name: window_open_freq - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: The number of times windows are opened per week - title: window open frequency - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window open frequency - is_a: core field - slot_uri: MIXS:0000246 - multivalued: false - range: TextValue - window_size: - name: window_size - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: inch, meter - occurrence: - tag: occurrence - value: '1' - description: The window's length and width - title: window area/size - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window area/size - is_a: core field - string_serialization: '{float} {unit} x {float} {unit}' - slot_uri: MIXS:0000224 - multivalued: false - range: TextValue - window_status: - name: window_status - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Defines whether the windows were open or closed during environmental - testing - title: window status - examples: - - value: open - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window status - is_a: core field - string_serialization: '[closed|open]' - slot_uri: MIXS:0000855 - multivalued: false - range: TextValue - window_type: - name: window_type - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The type of windows - title: window type - examples: - - value: fixed window - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window type - is_a: core field - slot_uri: MIXS:0000856 - multivalued: false - range: window_type_enum - window_vert_pos: - name: window_vert_pos - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The vertical position of the window on the wall - title: window vertical position - examples: - - value: middle - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window vertical position - is_a: core field - slot_uri: MIXS:0000857 - multivalued: false - range: window_vert_pos_enum - window_water_mold: - name: window_water_mold - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on the window. - title: window signs of water/mold - examples: - - value: no presence of mold visible - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - window signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' - slot_uri: MIXS:0000854 - multivalued: false - range: TextValue - xylene: - name: xylene - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' - description: Concentration of xylene in the sample - title: xylene - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - xylene - is_a: core field - slot_uri: MIXS:0000156 - multivalued: false - range: QuantityValue - core field: - name: core field - description: basic fields - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - environment field: - name: environment field - description: field describing environmental aspect of a sample - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - sequencing field: - name: sequencing field - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - emsl_store_temp: - name: emsl_store_temp - description: The temperature at which the sample should be stored upon delivery - to EMSL - title: EMSL sample storage temperature, deg. C - todos: - - add 'see_alsos' with link to NEXUS info - comments: - - Enter a temperature in celsius. Numeric portion only. - examples: - - value: '-80' - from_schema: https://w3id.org/nmdc/nmdc - rank: 4 - string_serialization: '{float}' - slot_group: EMSL - recommended: true - project_id: - name: project_id - description: Proposal IDs or names associated with dataset - title: project ID - from_schema: https://w3id.org/nmdc/nmdc - rank: 1 - string_serialization: '{text}' - slot_group: EMSL - recommended: true - replicate_number: - name: replicate_number - description: If sending biological replicates, indicate the rep number here. - title: replicate number - comments: - - This will guide staff in ensuring your samples are blocked & randomized correctly - from_schema: https://w3id.org/nmdc/nmdc - rank: 6 - string_serialization: '{integer}' - slot_group: EMSL - recommended: true - sample_shipped: - name: sample_shipped - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of - sample sent to EMSL. - title: sample shipped amount - comments: - - This field is only required when completing metadata for samples being submitted - to EMSL for analyses. - examples: - - value: 15 g - - value: 100 uL - - value: 5 mL - from_schema: https://w3id.org/nmdc/nmdc - rank: 3 - string_serialization: '{float} {unit}' - slot_group: EMSL - recommended: true - sample_type: - name: sample_type - description: Type of sample being submitted - title: sample type - comments: - - This can vary from 'environmental package' if the sample is an extraction. - examples: - - value: water extracted soil - from_schema: https://w3id.org/nmdc/nmdc - rank: 2 - slot_group: EMSL - range: SampleTypeEnum - recommended: true - technical_reps: - name: technical_reps - description: If sending technical replicates of the same sample, indicate the - replicate count. - title: number technical replicate - comments: - - This field is only required when completing metadata for samples being submitted - to EMSL for analyses. - examples: - - value: '2' - from_schema: https://w3id.org/nmdc/nmdc - rank: 5 - string_serialization: '{integer}' - slot_group: EMSL - recommended: true - dna_collect_site: - name: dna_collect_site - description: Provide information on the site your DNA sample was collected from - title: DNA collection site - examples: - - value: untreated pond water - from_schema: https://w3id.org/nmdc/nmdc - rank: 15 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_cont_type: - name: dna_cont_type - description: Tube or plate (96-well) - title: DNA container type - examples: - - value: plate - from_schema: https://w3id.org/nmdc/nmdc - rank: 10 - slot_group: JGI-Metagenomics - range: JgiContTypeEnum - recommended: true - dna_cont_well: - name: dna_cont_well - title: DNA plate position - comments: - - Required when 'plate' is selected for container type. - - Leave blank if the sample will be shipped in a tube. - - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not - pass validation. - - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). - examples: - - value: B2 - from_schema: https://w3id.org/nmdc/nmdc - rank: 11 - string_serialization: '{96 well plate pos}' - slot_group: JGI-Metagenomics - recommended: true - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ - dna_container_id: - name: dna_container_id - title: DNA container label - comments: - - Must be unique across all tubes and plates, and <20 characters. All samples - in a plate should have the same plate label. - examples: - - value: Pond_MT_041618 - from_schema: https://w3id.org/nmdc/nmdc - rank: 9 - string_serialization: '{text < 20 characters}' - slot_group: JGI-Metagenomics - recommended: true - dna_dnase: - name: dna_dnase - title: DNase treatment DNA - comments: - - Note DNase treatment is required for all RNA samples. - examples: - - value: 'no' - from_schema: https://w3id.org/nmdc/nmdc - rank: 13 - slot_group: JGI-Metagenomics - range: YesNoEnum - recommended: true - dna_isolate_meth: - name: dna_isolate_meth - description: Describe the method/protocol/kit used to extract DNA/RNA. - title: DNA isolation method - examples: - - value: phenol/chloroform extraction - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Sample Isolation Method - rank: 16 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_organisms: - name: dna_organisms - description: List any organisms known or suspected to grow in co-culture, as well - as estimated % of the organism in that culture. - title: DNA expected organisms - examples: - - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - from_schema: https://w3id.org/nmdc/nmdc - rank: 14 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_project_contact: - name: dna_project_contact - title: DNA seq project contact - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: John Jones - from_schema: https://w3id.org/nmdc/nmdc - rank: 18 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_samp_id: - name: dna_samp_id - title: DNA sample ID - todos: - - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't - have two identifiers. How to force uniqueness? Moot because that column will - be prefilled? - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '187654' - from_schema: https://w3id.org/nmdc/nmdc - rank: 3 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_sample_format: - name: dna_sample_format - description: Solution in which the DNA sample has been suspended - title: DNA sample format - examples: - - value: Water - from_schema: https://w3id.org/nmdc/nmdc - rank: 12 - slot_group: JGI-Metagenomics - range: DNASampleFormatEnum - recommended: true - dna_sample_name: - name: dna_sample_name - description: Give the DNA sample a name that is meaningful to you. Sample names - must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. - title: DNA sample name - examples: - - value: JGI_pond_041618 - from_schema: https://w3id.org/nmdc/nmdc - rank: 4 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_seq_project: - name: dna_seq_project - title: DNA seq project ID - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '1191234' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Seq Project ID - rank: 1 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_seq_project_pi: - name: dna_seq_project_pi - title: DNA seq project PI - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: Jane Johnson - from_schema: https://w3id.org/nmdc/nmdc - rank: 17 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_seq_project_name: - name: dna_seq_project_name - title: DNA seq project name - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: JGI Pond metagenomics - from_schema: https://w3id.org/nmdc/nmdc - rank: 2 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dna_volume: - name: dna_volume - title: DNA volume in ul - comments: - - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This - form accepts values < 25, but JGI may refuse to process them unless permission - has been granted by a project manager - examples: - - value: '25' - from_schema: https://w3id.org/nmdc/nmdc - rank: 6 - string_serialization: '{float}' - slot_group: JGI-Metagenomics - range: float - recommended: true - minimum_value: 0 - maximum_value: 1000 - proposal_dna: - name: proposal_dna - title: DNA proposal ID - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '504000' - from_schema: https://w3id.org/nmdc/nmdc - rank: 19 - string_serialization: '{text}' - slot_group: JGI-Metagenomics - recommended: true - dnase_rna: - name: dnase_rna - title: DNase treated - comments: - - Note DNase treatment is required for all RNA samples. - examples: - - value: 'no' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Was Sample DNAse treated? - rank: 13 - slot_group: JGI-Metatranscriptomics - range: YesNoEnum - recommended: true - proposal_rna: - name: proposal_rna - title: RNA proposal ID - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '504000' - from_schema: https://w3id.org/nmdc/nmdc - rank: 19 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_absorb1: - name: rna_absorb1 - description: 260/280 measurement of RNA sample purity - title: RNA absorbance 260/280 - comments: - - Recommended value is between 1 and 3. - examples: - - value: '2.02' - from_schema: https://w3id.org/nmdc/nmdc - rank: 7 - is_a: biomaterial_purity - string_serialization: '{float}' - slot_group: JGI-Metatranscriptomics - range: float - recommended: true - rna_absorb2: - name: rna_absorb2 - description: 260/230 measurement of RNA sample purity - title: RNA absorbance 260/230 - comments: - - Recommended value is between 1 and 3. - examples: - - value: '2.02' - from_schema: https://w3id.org/nmdc/nmdc - rank: 8 - is_a: biomaterial_purity - string_serialization: '{float}' - slot_group: JGI-Metatranscriptomics - range: float - recommended: true - rna_collect_site: - name: rna_collect_site - description: Provide information on the site your RNA sample was collected from - title: RNA collection site - examples: - - value: untreated pond water - from_schema: https://w3id.org/nmdc/nmdc - rank: 15 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_concentration: - name: rna_concentration - title: RNA concentration in ng/ul - comments: - - Units must be in ng/uL. Enter the numerical part only. Must be calculated using - a fluorometric method. Acceptable values are 0-2000. - examples: - - value: '100' - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - nmdc:nucleic_acid_concentration - rank: 5 - string_serialization: '{float}' - slot_group: JGI-Metatranscriptomics - range: float - recommended: true - minimum_value: 0 - maximum_value: 1000 - rna_cont_type: - name: rna_cont_type - description: Tube or plate (96-well) - title: RNA container type - examples: - - value: plate - from_schema: https://w3id.org/nmdc/nmdc - rank: 10 - slot_group: JGI-Metatranscriptomics - range: JgiContTypeEnum - recommended: true - rna_cont_well: - name: rna_cont_well - title: RNA plate position - comments: - - Required when 'plate' is selected for container type. - - Leave blank if the sample will be shipped in a tube. - - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not - pass validation. - - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). - examples: - - value: B2 - from_schema: https://w3id.org/nmdc/nmdc - rank: 11 - string_serialization: '{96 well plate pos}' - slot_group: JGI-Metatranscriptomics - recommended: true - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ - rna_container_id: - name: rna_container_id - title: RNA container label - comments: - - Must be unique across all tubes and plates, and <20 characters. All samples - in a plate should have the same plate label. - examples: - - value: Pond_MT_041618 - from_schema: https://w3id.org/nmdc/nmdc - rank: 9 - string_serialization: '{text < 20 characters}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_isolate_meth: - name: rna_isolate_meth - description: Describe the method/protocol/kit used to extract DNA/RNA. - title: RNA isolation method - examples: - - value: phenol/chloroform extraction - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Sample Isolation Method - rank: 16 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_organisms: - name: rna_organisms - description: List any organisms known or suspected to grow in co-culture, as well - as estimated % of the organism in that culture. - title: RNA expected organisms - examples: - - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - from_schema: https://w3id.org/nmdc/nmdc - rank: 14 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_project_contact: - name: rna_project_contact - title: RNA seq project contact - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: John Jones - from_schema: https://w3id.org/nmdc/nmdc - rank: 18 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_samp_id: - name: rna_samp_id - title: RNA sample ID - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '187654' - from_schema: https://w3id.org/nmdc/nmdc - rank: 3 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_sample_format: - name: rna_sample_format - description: Solution in which the RNA sample has been suspended - title: RNA sample format - examples: - - value: Water - from_schema: https://w3id.org/nmdc/nmdc - rank: 12 - slot_group: JGI-Metatranscriptomics - range: RNASampleFormatEnum - recommended: true - rna_sample_name: - name: rna_sample_name - description: Give the RNA sample a name that is meaningful to you. Sample names - must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. - title: RNA sample name - examples: - - value: JGI_pond_041618 - from_schema: https://w3id.org/nmdc/nmdc - rank: 4 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - minimum_value: 0 - maximum_value: 2000 - rna_seq_project: - name: rna_seq_project - title: RNA seq project ID - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: '1191234' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Seq Project ID - rank: 1 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_seq_project_pi: - name: rna_seq_project_pi - title: RNA seq project PI - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: Jane Johnson - from_schema: https://w3id.org/nmdc/nmdc - rank: 17 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_seq_project_name: - name: rna_seq_project_name - title: RNA seq project name - comments: - - Do not edit these values. A template will be provided by NMDC in which these - values have been pre-filled. - examples: - - value: JGI Pond metatranscriptomics - from_schema: https://w3id.org/nmdc/nmdc - rank: 2 - string_serialization: '{text}' - slot_group: JGI-Metatranscriptomics - recommended: true - rna_volume: - name: rna_volume - title: RNA volume in ul - comments: - - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This - form accepts values < 25, but JGI may refuse to process them unless permission - has been granted by a project manager - examples: - - value: '25' - from_schema: https://w3id.org/nmdc/nmdc - rank: 6 - string_serialization: '{float}' - slot_group: JGI-Metatranscriptomics - range: float - recommended: true - minimum_value: 0 - maximum_value: 1000 - collection_date_inc: - name: collection_date_inc - description: Date the incubation was harvested/collected/ended. Only relevant - for incubation samples. - title: incubation collection date - notes: - - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision - date only - comments: - - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 - are all acceptable. - examples: - - value: 2021-04-15, 2021-04 and 2021 are all acceptable. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000011 - rank: 2 - string_serialization: '{date, arbitrary precision}' - slot_group: MIxS Inspired - recommended: true - collection_time: - name: collection_time - description: The time of sampling, either as an instance (single point) or interval. - title: collection time, GMT - notes: - - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional - time only - comments: - - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' - examples: - - value: 13:33 or 13:33:55 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000011 - rank: 1 - string_serialization: '{time, seconds optional}' - slot_group: MIxS Inspired - recommended: true - collection_time_inc: - name: collection_time_inc - description: Time the incubation was harvested/collected/ended. Only relevant - for incubation samples. - title: incubation collection time, GMT - notes: - - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional - time only - comments: - - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' - examples: - - value: 13:33 or 13:33:55 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000011 - rank: 3 - string_serialization: '{time, seconds optional}' - slot_group: MIxS Inspired - recommended: true - experimental_factor_other: - name: experimental_factor_other - description: Other details about your sample that you feel can't be accurately - represented in the available columns. - title: experimental factor- other - comments: - - This slot accepts open-ended text about your sample. - - We recommend using key:value pairs. - - Provided pairs will be considered for inclusion as future slots/terms in this - data collection template. - examples: - - value: 'experimental treatment: value' - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000008 - - MIXS:0000300 - rank: 7 - string_serialization: '{text}' - slot_group: MIxS Inspired - recommended: true - filter_method: - name: filter_method - description: Type of filter used or how the sample was filtered - title: filter method - comments: - - describe the filter or provide a catalog number and manufacturer - examples: - - value: C18 - - value: Basix PES, 13-100-106 FisherSci - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000765 - rank: 6 - string_serialization: '{text}' - slot_group: MIxS Inspired - recommended: true - isotope_exposure: - name: isotope_exposure - description: List isotope exposure or addition applied to your sample. - title: isotope exposure/addition - todos: - - Can we make the H218O correctly super and subscripted? - comments: - - This is required when your experimental design includes the use of isotopically - labeled compounds - examples: - - value: 13C glucose - - value: H218O - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000751 - rank: 16 - string_serialization: '{termLabel} {[termID]}; {timestamp}' - slot_group: MIxS Inspired - recommended: true - micro_biomass_c_meth: - name: micro_biomass_c_meth - description: Reference or method used in determining microbial biomass carbon - title: microbial biomass carbon method - todos: - - How should we separate values? | or ;? lets be consistent - comments: - - required if "microbial_biomass_c" is provided - examples: - - value: https://doi.org/10.1016/0038-0717(87)90052-6 - - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000339 - rank: 11 - string_serialization: '{PMID}|{DOI}|{URL}' - slot_group: MIxS Inspired - recommended: true - micro_biomass_n_meth: - name: micro_biomass_n_meth - description: Reference or method used in determining microbial biomass nitrogen - title: microbial biomass nitrogen method - comments: - - required if "microbial_biomass_n" is provided - examples: - - value: https://doi.org/10.1016/0038-0717(87)90052-6 - - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000339 - rank: 13 - string_serialization: '{PMID}|{DOI}|{URL}' - slot_group: MIxS Inspired - microbial_biomass_c: - name: microbial_biomass_c - description: The part of the organic matter in the soil that constitutes living - microorganisms smaller than 5-10 micrometer. - title: microbial biomass carbon - comments: - - If you provide this, correction factors used for conversion to the final units - and method are required - examples: - - value: 0.05 ug C/g dry soil - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000650 - rank: 10 - string_serialization: '{float} {unit}' - slot_group: MIxS Inspired - microbial_biomass_n: - name: microbial_biomass_n - description: The part of the organic matter in the soil that constitutes living - microorganisms smaller than 5-10 micrometer. - title: microbial biomass nitrogen - comments: - - If you provide this, correction factors used for conversion to the final units - and method are required - examples: - - value: 0.05 ug N/g dry soil - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000650 - rank: 12 - string_serialization: '{float} {unit}' - slot_group: MIxS Inspired - non_microb_biomass: - name: non_microb_biomass - description: Amount of biomass; should include the name for the part of biomass - measured, e.g.insect, plant, total. Can include multiple measurements separated - by ; - title: non-microbial biomass - examples: - - value: insect 0.23 ug; plant 1g - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000174 - - MIXS:0000650 - rank: 8 - string_serialization: '{text};{float} {unit}' - slot_group: MIxS Inspired - non_microb_biomass_method: - name: non_microb_biomass_method - description: Reference or method used in determining biomass - title: non-microbial biomass method - comments: - - required if "non-microbial biomass" is provided - examples: - - value: https://doi.org/10.1038/s41467-021-26181-3 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000650 - rank: 9 - string_serialization: '{PMID}|{DOI}|{URL}' - slot_group: MIxS Inspired - org_nitro_method: - name: org_nitro_method - description: Method used for obtaining organic nitrogen - title: organic nitrogen method - comments: - - required if "org_nitro" is provided - examples: - - value: https://doi.org/10.1016/0038-0717(85)90144-0 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000338 - - MIXS:0000205 - rank: 14 - string_serialization: '{PMID}|{DOI}|{URL}' - slot_group: MIxS Inspired - other_treatment: - name: other_treatment - description: Other treatments applied to your samples that are not applicable - to the provided fields - title: other treatments - notes: - - Values entered here will be used to determine potential new slots. - comments: - - This is an open text field to provide any treatments that cannot be captured - in the provided slots. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000300 - rank: 15 - string_serialization: '{text}' - slot_group: MIxS Inspired - recommended: true - start_date_inc: - name: start_date_inc - description: Date the incubation was started. Only relevant for incubation samples. - title: incubation start date - notes: - - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision - date only - comments: - - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 - are all acceptable. - examples: - - value: 2021-04-15, 2021-04 and 2021 are all acceptable. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000011 - rank: 4 - string_serialization: '{date, arbitrary precision}' - slot_group: MIxS Inspired - recommended: true - start_time_inc: - name: start_time_inc - description: Time the incubation was started. Only relevant for incubation samples. - title: incubation start time, GMT - notes: - - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional - time only - comments: - - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' - examples: - - value: 13:33 or 13:33:55 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIXS:0000011 - rank: 5 - string_serialization: '{time, seconds optional}' - slot_group: MIxS Inspired - recommended: true - analysis_type: - name: analysis_type - description: Select all the data types associated or available for this biosample - title: analysis/data type - examples: - - value: metagenomics; metabolomics; proteomics - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:investigation_type - rank: 3 - multivalued: true - slot_group: Sample ID - range: AnalysisTypeEnum - recommended: true - sample_link: - name: sample_link - description: A unique identifier to assign parent-child, subsample, or sibling - samples. This is relevant when a sample or other material was used to generate - the new sample. - title: sample linkage - comments: - - 'This field allows multiple entries separated by ; (Examples: Soil collected - from the field will link with the soil used in an incubation. The soil a plant - was grown in links to the plant sample. An original culture sample was transferred - to a new vial and generated a new sample)' - examples: - - value: IGSN:DSJ0284 - from_schema: https://w3id.org/nmdc/nmdc - rank: 5 - string_serialization: '{text}:{text}' - multivalued: true - slot_group: Sample ID - range: string - recommended: true - processing_institution: - name: processing_institution - description: The organization that processed the sample. - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: processing_institution_enum - designated_class: - name: designated_class - notes: - - MAM prefers to use this functionality in a `type` class and to eliminate '...type...' - from the names of any NMDC-owned elements - - this would be required on all instances in a polymorphic Database slot, like - planned_process_set - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/microbiomedata/nmdc-schema/issues/1048 - - https://github.com/microbiomedata/nmdc-schema/issues/1233 - designates_type: true - range: uriorcurie - external_database_identifiers: - name: external_database_identifiers - description: Link to corresponding identifier in external database - notes: - - had tried ranges of external identifier and string - comments: - - The value of this field is always a registered CURIE - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - skos:closeMatch - is_a: alternative_identifiers - abstract: true - multivalued: true - range: external_identifier - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ - dna_absorb1: - name: dna_absorb1 - description: 260/280 measurement of DNA sample purity - title: DNA absorbance 260/280 - comments: - - Recommended value is between 1 and 3. - examples: - - value: '2.02' - from_schema: https://w3id.org/nmdc/nmdc - rank: 7 - is_a: biomaterial_purity - slot_group: JGI-Metagenomics - range: float - recommended: true - dna_absorb2: - name: dna_absorb2 - description: 260/230 measurement of DNA sample purity - title: DNA absorbance 260/230 - comments: - - Recommended value is between 1 and 3. - examples: - - value: '2.02' - from_schema: https://w3id.org/nmdc/nmdc - rank: 8 - is_a: biomaterial_purity - slot_group: JGI-Metagenomics - range: float - recommended: true - dna_concentration: - name: dna_concentration - title: DNA concentration in ng/ul - comments: - - Units must be in ng/uL. Enter the numerical part only. Must be calculated using - a fluorometric method. Acceptable values are 0-2000. - examples: - - value: '100' - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - nmdc:nucleic_acid_concentration - rank: 5 - slot_group: JGI-Metagenomics - range: float - recommended: true - minimum_value: 0 - maximum_value: 2000 - extraction_target: - name: extraction_target - from_schema: https://w3id.org/nmdc/nmdc - rank: 1000 - range: ExtractionTargetEnum - id: - name: id - description: A unique identifier for a thing. Must be either a CURIE shorthand - for a URI or a complete URI - notes: - - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?' - - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters - will be accepted - - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked - via per-class id slot usage assertions - - minting authority shoulders should probably be enumerated and checked in the - pattern - examples: - - value: nmdc:mgmag-00-x012.1_7_c1 - description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248 - from_schema: https://w3id.org/nmdc/nmdc - identifier: true - range: uriorcurie - required: true - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ - name: - name: name - description: A human readable label for an entity - from_schema: https://w3id.org/nmdc/nmdc - range: string - description: - name: description - description: a human-readable description of a thing - from_schema: https://w3id.org/nmdc/nmdc - slot_uri: dcterms:description - range: string - type: - name: type - description: An optional string that specifies the type object. This is used - to allow for searches for different kinds of objects. - deprecated: Due to confusion about what values are used for this slot, it is best - not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. - MAM removed designates_type and rdf:type slot uri 2022-11-30 - examples: - - value: nmdc:Biosample - - value: nmdc:Study - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/microbiomedata/nmdc-schema/issues/1233 - range: string - title: - name: title - description: A name given to the entity that differs from the name/label programmatically - assigned to it. For example, when extracting study information for GOLD, the - GOLD system has assigned a name/label. However, for display purposes, we may - also wish the capture the title of the proposal that was used to fund the study. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - dcterms:title - range: string - alternative_titles: - name: alternative_titles - description: A list of alternative titles for the entity. The distinction between - title and alternative titles is application-specific. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - dcterms:alternative - multivalued: true - range: string - alternative_names: - name: alternative_names - description: A list of alternative names used to refer to the entity. The distinction - between name and alternative names is application-specific. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - dcterms:alternative - - skos:altLabel - multivalued: true - range: string - alternative_descriptions: - name: alternative_descriptions - description: A list of alternative descriptions for the entity. The distinction - between description and alternative descriptions is application-specific. - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: string - alternative_identifiers: - name: alternative_identifiers - description: A list of alternative identifiers for the entity. - from_schema: https://w3id.org/nmdc/nmdc - multivalued: true - range: uriorcurie - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ - start_date: - name: start_date - description: The date on which any process or activity was started - todos: - - add date string validation pattern - comments: - - We are using string representations of dates until all components of our ecosystem - can handle ISO 8610 dates - - The date should be formatted as YYYY-MM-DD - from_schema: https://w3id.org/nmdc/nmdc - range: string - end_date: - name: end_date - description: The date on which any process or activity was ended - todos: - - add date string validation pattern - comments: - - We are using string representations of dates until all components of our ecosystem - can handle ISO 8610 dates - - The date should be formatted as YYYY-MM-DD - from_schema: https://w3id.org/nmdc/nmdc - range: string - protocol_link: - name: protocol_link - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: Protocol - biomaterial_purity: - name: biomaterial_purity - from_schema: https://w3id.org/nmdc/nmdc - domain: ProcessedSample - range: QuantityValue - qc_failure_what: - name: qc_failure_what - description: Provides a summary about what caused a lab or workflow process to - fail - comments: - - For example Low read count from a sequencer, malformed fastq files, etc) - from_schema: https://w3id.org/nmdc/nmdc - domain: FailureCategorization - range: FailureWhatEnum - qc_failure_where: - name: qc_failure_where - description: Describes the nmdc schema class that corresonds to where the failure - occurred. Most commonly this would be the same as Class that generated the results. - comments: - - If the assembly size was too small to proceed to annotation failure_where would - be MetagenomeAssembly. - from_schema: https://w3id.org/nmdc/nmdc - domain: FailureCategorization - range: FailureWhereEnum - qc_comment: - name: qc_comment - description: Slot to store additional comments about laboratory or workflow output. - For workflow output it may describe the particular workflow stage that failed. - (ie Failed at call-stage due to a malformed fastq file). - from_schema: https://w3id.org/nmdc/nmdc - range: string - instrument_name: - name: instrument_name - description: The name of the instrument that was used for processing the sample. - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - img_identifiers: - name: img_identifiers - description: A list of identifiers that relate the biosample to records in the - IMG database. - title: IMG Identifiers - todos: - - add is_a or mixin modeling, like other external_database_identifiers - - what class would IMG records belong to?! Are they Studies, Biosamples, or something - else? - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - pattern: ^img\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\/\.]*$ - igsn_identifiers: - name: igsn_identifiers - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - gold_identifiers: - name: gold_identifiers - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/ - mixin: true - emsl_identifiers: - name: emsl_identifiers - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - mgnify_identifiers: - name: mgnify_identifiers - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ebi.ac.uk/metagenomics/ - mixin: true - insdc_identifiers: - name: insdc_identifiers - description: Any identifier covered by the International Nucleotide Sequence Database - Collaboration - comments: - - note that we deliberately abstract over which of the partner databases accepted - the initial submission - - 'the first letter of the accession indicates which partner accepted the initial - submission: E for ENA, D for DDBJ, or S or N for NCBI.' - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.insdc.org/ - - https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html - aliases: - - EBI identifiers - - NCBI identifiers - - DDBJ identifiers - mixin: true - neon_identifiers: - name: neon_identifiers - description: identifiers for entities according to NEON - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - jgi_portal_identifiers: - name: jgi_portal_identifiers - description: identifiers for entities according to JGI Portal - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - gnps_identifiers: - name: gnps_identifiers - from_schema: https://w3id.org/nmdc/nmdc - mixin: true - study_identifiers: - name: study_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - abstract: true - jgi_portal_study_identifiers: - name: jgi_portal_study_identifiers - id_prefixes: - - jgi.proposal - description: Identifiers that link a NMDC study to a website hosting raw and analyzed - data for a JGI proposal. The suffix of the curie can used to query the GOLD - API and is interoperable with an award DOI from OSTI and a GOLD study identifier. - title: JGI Portal Study identifiers - comments: - - Could this could be considered a related identifier? - - Curie suffix is the Site Award Number from an OSTI award page - - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD - study identifier gold:Gs0154044 - - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html - examples: - - value: jgi.proposal:507130 - from_schema: https://w3id.org/nmdc/nmdc - is_a: study_identifiers - mixins: - - jgi_portal_identifiers - domain: Study - pattern: ^jgi.proposal:\d+$ - neon_study_identifiers: - name: neon_study_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: study_identifiers - mixins: - - neon_identifiers - domain: Study - insdc_sra_ena_study_identifiers: - name: insdc_sra_ena_study_identifiers - description: identifiers for corresponding project in INSDC SRA / ENA - examples: - - value: https://bioregistry.io/insdc.sra:SRP121659 - description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 - metatranscriptome - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/bioregistry/bioregistry/issues/109 - - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies - - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies - aliases: - - EBI ENA study identifiers - - NCBI SRA identifiers - - DDBJ SRA identifiers - is_a: study_identifiers - mixins: - - insdc_identifiers - pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$ - insdc_bioproject_identifiers: - name: insdc_bioproject_identifiers - description: identifiers for corresponding project in INSDC Bioproject - comments: - - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?) - one to one - examples: - - value: https://bioregistry.io/bioproject:PRJNA366857 - description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 - metatranscriptome - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://www.ncbi.nlm.nih.gov/bioproject/ - - https://www.ddbj.nig.ac.jp/bioproject/index-e.html - aliases: - - NCBI bioproject identifiers - - DDBJ bioproject identifiers - is_a: study_identifiers - mixins: - - insdc_identifiers - pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$ - gold_study_identifiers: - name: gold_study_identifiers - description: identifiers for corresponding project(s) in GOLD - title: GOLD Study Identifiers - comments: - - uses the prefix GS (but possibly in a different case) - examples: - - value: https://bioregistry.io/gold:Gs0110115 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://gold.jgi.doe.gov/studies - is_a: study_identifiers - mixins: - - gold_identifiers - domain: Study - pattern: ^gold:Gs[0-9]+$ - mgnify_project_identifiers: - name: mgnify_project_identifiers - description: identifiers for corresponding project in MGnify - examples: - - value: https://bioregistry.io/mgnify.proj:MGYS00005757 - from_schema: https://w3id.org/nmdc/nmdc - is_a: study_identifiers - mixins: - - mgnify_identifiers - domain: Study - pattern: ^mgnify.proj:[A-Z]+[0-9]+$ - gnps_task_identifiers: - name: gnps_task_identifiers - description: identifiers that link a NMDC study to a web-based report about metabolomics - analysis progress and results - title: GNPS task identifiers - comments: - - this could be considered a related identifier, as the metabolomics progress - and results aren't a study per se - - this identifier was registered with bioregistry but not identifiers.org - examples: - - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/ - is_a: study_identifiers - mixins: - - gnps_identifiers - domain: Study - pattern: ^gnps\.task:[a-f0-9]+$ - emsl_project_identifiers: - name: emsl_project_identifiers - description: Identifiers that link a NMDC study to the EMSL user facility website - hosting the project description of an EMSL user project - title: EMSL Project Identifiers - todos: - - elaborate on description - notes: - - these identifiers are all currently 5 digits long but that could change in the - future - examples: - - value: emsl.project:60141 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437 - is_a: study_identifiers - mixins: - - emsl_identifiers - domain: Study - pattern: ^emsl\.project:[0-9]{5}$ - biosample_identifiers: - name: biosample_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - abstract: true - neon_biosample_identifiers: - name: neon_biosample_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: biosample_identifiers - mixins: - - neon_identifiers - gold_biosample_identifiers: - name: gold_biosample_identifiers - description: identifiers for corresponding sample in GOLD - examples: - - value: https://bioregistry.io/gold:Gb0312930 - from_schema: https://w3id.org/nmdc/nmdc - is_a: biosample_identifiers - mixins: - - gold_identifiers - range: uriorcurie - pattern: ^gold:Gb[0-9]+$ - insdc_biosample_identifiers: - name: insdc_biosample_identifiers - description: identifiers for corresponding sample in INSDC - examples: - - value: https://bioregistry.io/biosample:SAMEA5989477 - - value: https://bioregistry.io/biosample:SAMD00212331 - description: I13_N_5-10 sample from Soil fungal diversity along elevational - gradients - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/bioregistry/bioregistry/issues/108 - - https://www.ebi.ac.uk/biosamples/ - - https://www.ncbi.nlm.nih.gov/biosample - - https://www.ddbj.nig.ac.jp/biosample/index-e.html - aliases: - - EBI biosample identifiers - - NCBI biosample identifiers - - DDBJ biosample identifiers - is_a: biosample_identifiers - mixins: - - insdc_identifiers - pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$ - insdc_secondary_sample_identifiers: - name: insdc_secondary_sample_identifiers - description: secondary identifiers for corresponding sample in INSDC - comments: - - ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340 - -> SAMD00212331 - - MGnify uses these as their primary sample IDs - examples: - - value: https://bioregistry.io/insdc.sra:DRS166340 - description: I13_N_5-10 sample from Soil fungal diversity along elevational - gradients - from_schema: https://w3id.org/nmdc/nmdc - is_a: biosample_identifiers - mixins: - - insdc_identifiers - pattern: ^biosample:(E|D|S)RS[0-9]{6,}$ - emsl_biosample_identifiers: - name: emsl_biosample_identifiers - description: A list of identifiers for the biosample from the EMSL database. This - is used to link the biosample, as modeled by NMDC, to the biosample in the planned - EMSL NEXUS database. - title: EMSL Biosample Identifiers - todos: - - removed "planned" once NEXUS is online - - determine real expansion for emsl prefix - from_schema: https://w3id.org/nmdc/nmdc - is_a: biosample_identifiers - mixins: - - emsl_identifiers - igsn_biosample_identifiers: - name: igsn_biosample_identifiers - description: A list of identifiers for the biosample from the IGSN database. - title: IGSN Biosample Identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: biosample_identifiers - mixins: - - igsn_identifiers - omics_processing_identifiers: - name: omics_processing_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - abstract: true - gold_sequencing_project_identifiers: - name: gold_sequencing_project_identifiers - description: identifiers for corresponding sequencing project in GOLD - examples: - - value: https://bioregistry.io/gold:Gp0108335 - from_schema: https://w3id.org/nmdc/nmdc - is_a: omics_processing_identifiers - mixins: - - gold_identifiers - domain: OmicsProcessing - pattern: ^gold:Gp[0-9]+$ - insdc_experiment_identifiers: - name: insdc_experiment_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - mixins: - - insdc_identifiers - domain: OmicsProcessing - pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$ - analysis_identifiers: - name: analysis_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: external_database_identifiers - abstract: true - gold_analysis_project_identifiers: - name: gold_analysis_project_identifiers - description: identifiers for corresponding analysis project in GOLD - examples: - - value: https://bioregistry.io/gold:Ga0526289 - from_schema: https://w3id.org/nmdc/nmdc - is_a: analysis_identifiers - mixins: - - gold_identifiers - pattern: ^gold:Ga[0-9]+$ - insdc_analysis_identifiers: - name: insdc_analysis_identifiers - comments: - - in INSDC this is a run but it corresponds to a GOLD analysis - examples: - - value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479 - description: Illumina MiSeq paired end sequencing of SAMD00212331 - - value: https://www.ebi.ac.uk/ena/browser/view/ERR436051 - from_schema: https://w3id.org/nmdc/nmdc - is_a: analysis_identifiers - mixins: - - insdc_identifiers - pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$ - mgnify_analysis_identifiers: - name: mgnify_analysis_identifiers - notes: - - 'removed pattern: "^mgnify:MGYA[0-9]+$" ## TODO https://github.com/bioregistry/bioregistry/issues/109' - examples: - - value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270 - description: combined analyses (taxonomic, functional) of sample ERS438107 - from_schema: https://w3id.org/nmdc/nmdc - is_a: analysis_identifiers - mixins: - - mgnify_identifiers - assembly_identifiers: - name: assembly_identifiers - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - insdc_assembly_identifiers: - name: insdc_assembly_identifiers - from_schema: https://w3id.org/nmdc/nmdc - is_a: assembly_identifiers - mixins: - - insdc_identifiers - pattern: ^insdc.sra:[A-Z]+[0-9]+(\.[0-9]+)?$ - started_at_time: - name: started_at_time - notes: - - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ - It may not be complete, but it is good enough for now.' - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:startedAtTime - domain: Activity - range: string - pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ - ended_at_time: - name: ended_at_time - notes: - - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ - It may not be complete, but it is good enough for now.' - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:endedAtTime - domain: Activity - pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ - was_informed_by: - name: was_informed_by - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:wasInformedBy - range: OmicsProcessing - was_generated_by: - name: was_generated_by - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:wasGeneratedBy - range: Activity - pattern: ^^(nmdc):(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$|^^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}$ - interpolated: true - any_of: - - range: Activity - - range: OmicsProcessing - used: - name: used - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:used - domain: Activity - metagenome_assembly_parameter: - name: metagenome_assembly_parameter - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - has_peptide_quantifications: - name: has_peptide_quantifications - from_schema: https://w3id.org/nmdc/nmdc - domain: MetaproteomicsAnalysisActivity - multivalued: true - range: PeptideQuantification - asm_score: - name: asm_score - description: A score for comparing metagenomic assembly quality from same sample. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaffolds: - name: scaffolds - description: Total sequence count of all scaffolds. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_logsum: - name: scaf_logsum - description: The sum of the (length*log(length)) of all scaffolds, times some - constant. Increase the contiguity, the score will increase - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_powsum: - name: scaf_powsum - description: Powersum of all scaffolds is the same as logsum except that it uses - the sum of (length*(length^P)) for some power P (default P=0.25). - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_max: - name: scaf_max - description: Maximum scaffold length. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_bp: - name: scaf_bp - description: Total size in bp of all scaffolds. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_n50: - name: scaf_n50 - description: Given a set of scaffolds, each with its own length, the N50 count - is defined as the smallest number of scaffolds whose length sum makes up half - of genome size. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_n90: - name: scaf_n90 - description: Given a set of scaffolds, each with its own length, the N90 count - is defined as the smallest number of scaffolds whose length sum makes up 90% - of genome size. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_l50: - name: scaf_l50 - description: Given a set of scaffolds, the L50 is defined as the sequence length - of the shortest scaffold at 50% of the total genome length. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_l90: - name: scaf_l90 - description: The L90 statistic is less than or equal to the L50 statistic; it - is the length for which the collection of all scaffolds of that length or longer - contains at least 90% of the sum of the lengths of all scaffolds. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_n_gt50k: - name: scaf_n_gt50k - description: Total sequence count of scaffolds greater than 50 KB. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_l_gt50k: - name: scaf_l_gt50k - description: Total size in bp of all scaffolds greater than 50 KB. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - scaf_pct_gt50k: - name: scaf_pct_gt50k - description: Total sequence size percentage of scaffolds greater than 50 KB. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - contigs: - name: contigs - description: The sum of the (length*log(length)) of all contigs, times some constant. Increase - the contiguity, the score will increase - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - contig_bp: - name: contig_bp - description: Total size in bp of all contigs. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_n50: - name: ctg_n50 - description: Given a set of contigs, each with its own length, the N50 count is - defined as the smallest number_of_contigs whose length sum makes up half of - genome size. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_l50: - name: ctg_l50 - description: Given a set of contigs, the L50 is defined as the sequence length - of the shortest contig at 50% of the total genome length. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_n90: - name: ctg_n90 - description: Given a set of contigs, each with its own length, the N90 count is - defined as the smallest number of contigs whose length sum makes up 90% of genome - size. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_l90: - name: ctg_l90 - description: The L90 statistic is less than or equal to the L50 statistic; it - is the length for which the collection of all contigs of that length or longer - contains at least 90% of the sum of the lengths of all contigs. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_logsum: - name: ctg_logsum - description: Maximum contig length. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_powsum: - name: ctg_powsum - description: Powersum of all contigs is the same as logsum except that it uses - the sum of (length*(length^P)) for some power P (default P=0.25). - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - ctg_max: - name: ctg_max - description: Maximum contig length. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - gap_pct: - name: gap_pct - description: The gap size percentage of all scaffolds. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - gc_std: - name: gc_std - description: Standard deviation of GC content of all contigs. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - gc_avg: - name: gc_avg - description: Average of GC content of all contigs. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - num_input_reads: - name: num_input_reads - description: The sequence count number of input reads for assembly. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - num_aligned_reads: - name: num_aligned_reads - description: The sequence count number of input reads aligned to assembled contigs. - from_schema: https://w3id.org/nmdc/nmdc - is_a: metagenome_assembly_parameter - range: float - read_qc_analysis_statistic: - name: read_qc_analysis_statistic - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - mags_list: - name: mags_list - from_schema: https://w3id.org/nmdc/nmdc - domain: MagsAnalysisActivity - multivalued: true - range: MagBin - too_short_contig_num: - name: too_short_contig_num - from_schema: https://w3id.org/nmdc/nmdc - range: integer - binned_contig_num: - name: binned_contig_num - from_schema: https://w3id.org/nmdc/nmdc - range: integer - input_contig_num: - name: input_contig_num - from_schema: https://w3id.org/nmdc/nmdc - range: integer - unbinned_contig_num: - name: unbinned_contig_num - from_schema: https://w3id.org/nmdc/nmdc - range: integer - low_depth_contig_num: - name: low_depth_contig_num - from_schema: https://w3id.org/nmdc/nmdc - range: integer - input_read_count: - name: input_read_count - description: The sequence count number of input reads for QC analysis. - from_schema: https://w3id.org/nmdc/nmdc - is_a: read_qc_analysis_statistic - range: float - input_base_count: - name: input_base_count - description: The nucleotide base count number of input reads for QC analysis. - from_schema: https://w3id.org/nmdc/nmdc - is_a: read_qc_analysis_statistic - range: float - output_read_count: - name: output_read_count - description: After QC analysis sequence count number. - from_schema: https://w3id.org/nmdc/nmdc - is_a: read_qc_analysis_statistic - range: float - output_base_count: - name: output_base_count - description: After QC analysis nucleotide base count number. - from_schema: https://w3id.org/nmdc/nmdc - is_a: read_qc_analysis_statistic - range: float - output_read_bases: - name: output_read_bases - description: TODO - from_schema: https://w3id.org/nmdc/nmdc - range: float - input_read_bases: - name: input_read_bases - description: 'TODO ' - from_schema: https://w3id.org/nmdc/nmdc - range: float - has_calibration: - name: has_calibration - description: A reference to a file that holds calibration information. - from_schema: https://w3id.org/nmdc/nmdc - range: string - has_metabolite_quantifications: - name: has_metabolite_quantifications - from_schema: https://w3id.org/nmdc/nmdc - domain: MetabolomicsAnalysisActivity - multivalued: true - range: MetaboliteQuantification - version: - name: version - from_schema: https://w3id.org/nmdc/nmdc - domain: Activity - range: string -classes: - FailureCategorization: - name: FailureCategorization - from_schema: https://w3id.org/nmdc/nmdc - slots: - - qc_failure_what - - qc_failure_where - FunctionalAnnotationAggMember: - name: FunctionalAnnotationAggMember - from_schema: https://w3id.org/nmdc/nmdc - slots: - - metagenome_annotation_id - - gene_function_id - - count - slot_usage: - metagenome_annotation_id: - name: metagenome_annotation_id - pattern: ^(nmdc):(wfmgan)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - Database: - name: Database - description: An abstract holder for any set of metadata and data. It does not - need to correspond to an actual managed database top level holder class. When - translated to JSON-Schema this is the 'root' object. It should contain pointers - to other objects of interest. For MongoDB, the lists of objects that Database - slots point to correspond to **collections**. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - NMDC metadata object - slots: - - biosample_set - - collecting_biosamples_from_site_set - - data_object_set - - extraction_set - - field_research_site_set - - functional_annotation_agg - - functional_annotation_set - - genome_feature_set - - library_preparation_set - - mags_activity_set - - metabolomics_analysis_activity_set - - metagenome_annotation_activity_set - - metagenome_assembly_set - - metagenome_sequencing_activity_set - - metaproteomics_analysis_activity_set - - metatranscriptome_activity_set - - nom_analysis_activity_set - - omics_processing_set - - planned_process_set - - pooling_set - - processed_sample_set - - read_based_taxonomy_analysis_activity_set - - read_qc_analysis_activity_set - - study_set - tree_root: true - Pooling: - name: Pooling - description: physical combination of several instances of like material. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - OBI:0600016 - is_a: BiosampleProcessing - slot_usage: - has_input: - name: has_input - required: true - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - minimum_cardinality: 2 - has_output: - name: has_output - required: true - pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$' - interpolated: true - minimum_cardinality: 1 - maximum_cardinality: 1 - id: - name: id - required: true - pattern: ^(nmdc):poolp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$' - interpolated: true - class_uri: nmdc:Pooling - Extraction: - name: Extraction - description: A material separation in which a desired component of an input material - is separated from the remainder. - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - OBI:0302884 - is_a: PlannedProcess - slots: - - extractant - - extraction_method - - extraction_target - - input_mass - - volume - slot_usage: - has_input: - name: has_input - required: true - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - required: true - pattern: ^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - id: - name: id - required: true - pattern: ^(nmdc):extrp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$' - interpolated: true - volume: - name: volume - description: The volume of the solvent/solute being used, not the input. - class_uri: nmdc:Extraction - SolutionComponent: - name: SolutionComponent - description: One constituent of a solution - from_schema: https://w3id.org/nmdc/nmdc - slots: - - compound - - concentration - Solution: - name: Solution - description: A mixture that is homogeneous, made up of two or more scattered molecular - aggregates, one playing the role of solute and the other playing the role of - solvent. - notes: - - TODO review the description, possibly more descriptive modeling to allow solvent - to be used - - TODO consider making a "Fluid" class - comments: - - We acknowledge that users of the nmdc-schema may instantiate Solution with only - a single component which goes against the letter of the description. - - The solution class may be used to instantiate a single component in the has_solution_components - slot - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - mixture - - solvent - slots: - - has_solution_components - - volume - Protocol: - name: Protocol - from_schema: https://w3id.org/nmdc/nmdc - slots: - - url - - name - LibraryPreparation: - name: LibraryPreparation - comments: - - OBI:0000711 specifies a DNA input (but not ONLY a DNA input) - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - LibraryConstruction - close_mappings: - - OBI:0000711 - is_a: BiosampleProcessing - slots: - - library_preparation_kit - - library_type - - pcr_cycles - slot_usage: - has_input: - name: has_input - required: true - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - has_output: - name: has_output - required: true - pattern: ^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - id: - name: id - required: true - pattern: ^(nmdc):libprp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$' - interpolated: true - class_uri: nmdc:LibraryPreparation - FieldResearchSite: - name: FieldResearchSite - description: A site, outside of a laboratory, from which biosamples may be collected. - title: Field Research Site - comments: - - Provides grouping of biosamples at level that's more specific than belonging - to the same study - - be very clear that this could be part of a larger site - - In Bioscales, one might say that rhizosphere soil and bulk soil from around - the same plant were obtained at the same site. In this case, the site would - correspond to one tree. - - might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833 - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - research plot - is_a: Site - slots: - - cur_vegetation - - elev - - geo_loc_name - - habitat - - lat_lon - - local_class - - part_of - - soil_type - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$' - interpolated: true - part_of: - name: part_of - range: FieldResearchSite - pattern: ^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$' - interpolated: true - CollectingBiosamplesFromSite: - name: CollectingBiosamplesFromSite - title: Collecting Biosamples From Site - comments: - - this illustrates implementing a Biosample relation with a process class - from_schema: https://w3id.org/nmdc/nmdc - close_mappings: - - OBI:0000744 - is_a: PlannedProcess - slot_usage: - has_input: - name: has_input - range: Site - required: true - pattern: ^(nmdc):(frsite|site)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$' - interpolated: true - has_output: - name: has_output - range: Biosample - required: true - pattern: ^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$' - interpolated: true - id: - name: id - required: true - pattern: ^(nmdc):clsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$' - interpolated: true - DataObject: - name: DataObject - description: An object that primarily consists of symbols that represent information. Files, - records, and omics data are examples of data objects. - in_subset: - - data object subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: NamedThing - slots: - - file_size_bytes - - md5_checksum - - data_object_type - - compression_type - - was_generated_by - - url - - type - slot_usage: - name: - name: name - required: true - description: - name: description - required: true - id: - name: id - required: true - pattern: ^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$' - interpolated: true - was_generated_by: - name: was_generated_by - pattern: ^^(nmdc):(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$|^^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}$ - interpolated: true - Biosample: - name: Biosample - description: Biological source material which can be characterized by an experiment. - alt_descriptions: - embl.ena: - source: embl.ena - description: A sample contains information about the sequenced source material. - Samples are associated with checklists, which define the fields used to - annotate the samples. Samples are always associated with a taxon. - notes: - - could add GOLD and EBI's biosample definitions to the alt_descriptions? - in_subset: - - sample subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - sample - - material sample - - specimen - - biospecimen - exact_mappings: - - OBI:0000747 - - NCIT:C43412 - - http://purl.obolibrary.org/obo/FBcv_0003024 - is_a: MaterialEntity - slots: - - host_disease_stat - - neon_biosample_identifiers - - host_taxid - - embargoed - - collected_from - - type - - img_identifiers - - samp_name - - biosample_categories - - type - - part_of - - id - - alternative_identifiers - - gold_biosample_identifiers - - insdc_biosample_identifiers - - emsl_biosample_identifiers - - igsn_biosample_identifiers - - abs_air_humidity - - add_recov_method - - additional_info - - address - - adj_room - - aero_struc - - agrochem_addition - - air_PM_concen - - air_temp - - air_temp_regm - - al_sat - - al_sat_meth - - alkalinity - - alkalinity_method - - alkyl_diethers - - alt - - aminopept_act - - ammonium - - ammonium_nitrogen - - amount_light - - ances_data - - annual_precpt - - annual_temp - - antibiotic_regm - - api - - arch_struc - - aromatics_pc - - asphaltenes_pc - - atmospheric_data - - avg_dew_point - - avg_occup - - avg_temp - - bac_prod - - bac_resp - - bacteria_carb_prod - - barometric_press - - basin - - bathroom_count - - bedroom_count - - benzene - - biochem_oxygen_dem - - biocide - - biocide_admin_method - - biol_stat - - biomass - - biotic_regm - - biotic_relationship - - bishomohopanol - - blood_press_diast - - blood_press_syst - - bromide - - build_docs - - build_occup_type - - building_setting - - built_struc_age - - built_struc_set - - built_struc_type - - calcium - - carb_dioxide - - carb_monoxide - - carb_nitro_ratio - - ceil_area - - ceil_cond - - ceil_finish_mat - - ceil_struc - - ceil_texture - - ceil_thermal_mass - - ceil_type - - ceil_water_mold - - chem_administration - - chem_mutagen - - chem_oxygen_dem - - chem_treat_method - - chem_treatment - - chimera_check - - chloride - - chlorophyll - - climate_environment - - collection_date - - conduc - - cool_syst_id - - core field - - crop_rotation - - cult_root_med - - cur_land_use - - cur_vegetation - - cur_vegetation_meth - - date_last_rain - - density - - depos_env - - depth - - dew_point - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_inorg_nitro - - diss_inorg_phosp - - diss_iron - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - diss_oxygen_fluid - - dna_cont_well - - door_comp_type - - door_cond - - door_direct - - door_loc - - door_mat - - door_move - - door_size - - door_type - - door_type_metal - - door_type_wood - - door_water_mold - - down_par - - drainage_class - - drawings - - ecosystem - - ecosystem_category - - ecosystem_subtype - - ecosystem_type - - efficiency_percent - - elev - - elevator - - emulsions - - env_broad_scale - - env_local_scale - - env_medium - - env_package - - environment field - - escalator - - ethylbenzene - - exp_duct - - exp_pipe - - experimental_factor - - ext_door - - ext_wall_orient - - ext_window_orient - - extreme_event - - fao_class - - fertilizer_regm - - field - - filter_type - - fire - - fireplace_type - - flooding - - floor_age - - floor_area - - floor_cond - - floor_count - - floor_finish_mat - - floor_struc - - floor_thermal_mass - - floor_water_mold - - fluor - - freq_clean - - freq_cook - - fungicide_regm - - furniture - - gaseous_environment - - gaseous_substances - - gender_restroom - - genetic_mod - - geo_loc_name - - glucosidase_act - - gravidity - - gravity - - growth_facil - - growth_habit - - growth_hormone_regm - - hall_count - - handidness - - hc_produced - - hcr - - hcr_fw_salinity - - hcr_geol_age - - hcr_pressure - - hcr_temp - - heat_cool_type - - heat_deliv_loc - - heat_sys_deliv_meth - - heat_system_id - - heavy_metals - - heavy_metals_meth - - height_carper_fiber - - herbicide_regm - - horizon_meth - - host_age - - host_body_habitat - - host_body_product - - host_body_site - - host_body_temp - - host_color - - host_common_name - - host_diet - - host_dry_mass - - host_family_relation - - host_genotype - - host_growth_cond - - host_height - - host_last_meal - - host_length - - host_life_stage - - host_phenotype - - host_sex - - host_shape - - host_subject_id - - host_subspecf_genlin - - host_substrate - - host_symbiont - - host_taxid - - host_tot_mass - - host_wet_mass - - humidity - - humidity_regm - - indoor_space - - indoor_surf - - indust_eff_percent - - inorg_particles - - inside_lux - - int_wall_cond - - investigation field - - iw_bt_date_well - - iwf - - last_clean - - lat_lon - - lbc_thirty - - lbceq - - light_intensity - - light_regm - - light_type - - link_addit_analys - - link_class_info - - link_climate_info - - lithology - - local_class - - local_class_meth - - magnesium - - manganese - - max_occup - - mean_frict_vel - - mean_peak_frict_vel - - mech_struc - - mechanical_damage - - methane - - micro_biomass_meth - - microbial_biomass - - mineral_nutr_regm - - misc_param - - n_alkanes - - nitrate - - nitrate_nitrogen - - nitrite - - nitrite_nitrogen - - nitro - - non_min_nutr_regm - - nucl_acid_amp - - nucl_acid_ext - - nucleic acid sequence source field - - number_pets - - number_plants - - number_resident - - occup_density_samp - - occup_document - - occup_samp - - org_carb - - org_count_qpcr_info - - org_matter - - org_nitro - - org_particles - - organism_count - - owc_tvdss - - oxy_stat_samp - - oxygen - - part_org_carb - - part_org_nitro - - particle_class - - pcr_cond - - pcr_primers - - permeability - - perturbation - - pesticide_regm - - petroleum_hydrocarb - - ph - - ph_meth - - ph_regm - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - photon_flux - - plant_growth_med - - plant_product - - plant_sex - - plant_struc - - pollutants - - pool_dna_extracts - - porosity - - potassium - - pour_point - - pre_treatment - - pres_animal_insect - - pressure - - prev_land_use_meth - - previous_land_use - - primary_prod - - primary_treatment - - prod_rate - - prod_start_date - - profile_position - - quad_pos - - radiation_regm - - rainfall_regm - - reactor_type - - redox_potential - - rel_air_humidity - - rel_humidity_out - - rel_samp_loc - - reservoir - - resins_pc - - room_air_exch_rate - - room_architec_elem - - room_condt - - room_connected - - room_count - - room_dim - - room_door_dist - - room_door_share - - room_hallway - - room_loc - - room_moist_dam_hist - - room_net_area - - room_occup - - room_samp_pos - - room_type - - room_vol - - room_wall_share - - room_window_count - - root_cond - - root_med_carbon - - root_med_macronutr - - root_med_micronutr - - root_med_ph - - root_med_regl - - root_med_solid - - root_med_suppl - - salinity - - salinity_meth - - salt_regm - - samp_capt_status - - samp_collec_device - - samp_collec_method - - samp_collect_point - - samp_dis_stage - - samp_floor - - samp_loc_corr_rate - - samp_mat_process - - samp_md - - samp_name - - samp_preserv - - samp_room_id - - samp_size - - samp_sort_meth - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_subtype - - samp_taxon_id - - samp_time_out - - samp_transport_cond - - samp_tvdss - - samp_type - - samp_vol_we_dna_ext - - samp_weather - - samp_well_name - - saturates_pc - - season - - season_environment - - season_precpt - - season_temp - - season_use - - secondary_treatment - - sediment_type - - seq_meth - - seq_quality_check - - sequencing field - - sewage_type - - shad_dev_water_mold - - shading_device_cond - - shading_device_loc - - shading_device_mat - - shading_device_type - - sieving - - silicate - - size_frac - - size_frac_low - - size_frac_up - - slope_aspect - - slope_gradient - - sludge_retent_time - - sodium - - soil_horizon - - soil_text_measure - - soil_texture_meth - - soil_type - - soil_type_meth - - solar_irradiance - - soluble_inorg_mat - - soluble_org_mat - - soluble_react_phosp - - source_mat_id - - space_typ_state - - specific - - specific_ecosystem - - specific_humidity - - sr_dep_env - - sr_geol_age - - sr_kerog_type - - sr_lithology - - standing_water_regm - - store_cond - - substructure_type - - sulfate - - sulfate_fw - - sulfide - - surf_air_cont - - surf_humidity - - surf_material - - surf_moisture - - surf_moisture_ph - - surf_temp - - suspend_part_matter - - suspend_solids - - tan - - target_gene - - target_subfragment - - temp - - temp_out - - tertiary_treatment - - tidal_stage - - tillage - - tiss_cult_growth_med - - toluene - - tot_carb - - tot_depth_water_col - - tot_diss_nitro - - tot_inorg_nitro - - tot_iron - - tot_nitro - - tot_nitro_cont_meth - - tot_nitro_content - - tot_org_c_meth - - tot_org_carb - - tot_part_carb - - tot_phosp - - tot_phosphate - - tot_sulfur - - train_line - - train_stat_loc - - train_stop_loc - - turbidity - - tvdss_of_hcr_press - - tvdss_of_hcr_temp - - typ_occup_density - - ventilation_rate - - ventilation_type - - vfa - - vfa_fw - - vis_media - - viscosity - - volatile_org_comp - - wall_area - - wall_const_type - - wall_finish_mat - - wall_height - - wall_loc - - wall_surf_treatment - - wall_texture - - wall_thermal_mass - - wall_water_mold - - wastewater_type - - water_cont_soil_meth - - water_content - - water_current - - water_cut - - water_feat_size - - water_feat_type - - water_prod_rate - - water_temp_regm - - watering_regm - - weekday - - win - - wind_direction - - wind_speed - - window_cond - - window_cover - - window_horiz_pos - - window_loc - - window_mat - - window_open_freq - - window_size - - window_status - - window_type - - window_vert_pos - - window_water_mold - - xylene - - zinc - - ecosystem - - ecosystem_category - - ecosystem_type - - ecosystem_subtype - - specific_ecosystem - - add_date - - community - - habitat - - host_name - - location - - mod_date - - ncbi_taxonomy_name - - proport_woa_temperature - - salinity_category - - sample_collection_site - - soluble_iron_micromol - - subsurface_depth - - air_temp_regm - - biotic_regm - - biotic_relationship - - climate_environment - - experimental_factor - - gaseous_environment - - growth_facil - - humidity_regm - - light_regm - - phosphate - - samp_collec_method - - samp_size - - source_mat_id - - watering_regm - - dna_absorb1 - - dna_absorb2 - - dna_collect_site - - dna_concentration - - dna_cont_type - - dna_cont_well - - dna_container_id - - dna_dnase - - dna_isolate_meth - - dna_organisms - - dna_project_contact - - dna_samp_id - - dna_sample_format - - dna_sample_name - - dna_seq_project - - dna_seq_project_pi - - dna_seq_project_name - - dna_volume - - proposal_dna - - dnase_rna - - proposal_rna - - rna_absorb1 - - rna_absorb2 - - rna_collect_site - - rna_concentration - - rna_cont_type - - rna_cont_well - - rna_container_id - - rna_isolate_meth - - rna_organisms - - rna_project_contact - - rna_samp_id - - rna_sample_format - - rna_sample_name - - rna_seq_project - - rna_seq_project_pi - - rna_seq_project_name - - rna_volume - - collection_date_inc - - collection_time - - collection_time_inc - - experimental_factor_other - - filter_method - - isotope_exposure - - micro_biomass_c_meth - - micro_biomass_n_meth - - microbial_biomass_c - - microbial_biomass_n - - non_microb_biomass - - non_microb_biomass_method - - org_nitro_method - - other_treatment - - start_date_inc - - start_time_inc - - project_id - - replicate_number - - sample_shipped - - sample_type - - technical_reps - - analysis_type - - sample_link - - bulk_elect_conductivity - - infiltrations - - zinc - - manganese - - ammonium_nitrogen - - nitrate_nitrogen - - nitrite_nitrogen - - lbc_thirty - - lbceq - slot_usage: - collected_from: - name: collected_from - pattern: ^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$' - interpolated: true - elev: - name: elev - title: elevation, meters - comments: - - All elevations must be reported in meters. Provide the numerical portion - only. - - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, - if needed, to help estimate the elevation based on latitude and longitude - coordinates. - examples: - - value: '100' - id: - name: id - description: An NMDC assigned unique identifier for a biosample submitted - to NMDC. - required: true - pattern: ^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$' - interpolated: true - gold_biosample_identifiers: - name: gold_biosample_identifiers - annotations: - tooltip: - tag: tooltip - value: Provide the GOLD biosample IDs associated with this biosample. - description: Unique identifier for a biosample submitted to GOLD that matches - the NMDC submitted biosample - comments: - - This is the ID provided by GOLD that starts with 'GB' - alternative_identifiers: - name: alternative_identifiers - description: Unique identifier for a biosample submitted to additional resources. - Matches the entity that has been submitted to NMDC - lat_lon: - name: lat_lon - notes: - - This is currently a required field but it's not clear if this should be - required for human hosts - env_broad_scale: - name: env_broad_scale - required: true - env_local_scale: - name: env_local_scale - required: true - env_medium: - name: env_medium - required: true - part_of: - name: part_of - range: Study - required: true - pattern: ^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$' - interpolated: true - fire: - name: fire - annotations: - expected_value: - tag: expected_value - value: date string - todos: - - is "to" acceptable? Is there a better way to request that be written? - comments: - - Provide the date the fire occurred. If extended burning occurred provide - the date range. - examples: - - value: '1871-10-10' - - value: 1871-10-01 to 1871-10-31 - pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$ - flooding: - name: flooding - annotations: - expected_value: - tag: expected_value - value: date string - todos: - - is "to" acceptable? Is there a better way to request that be written? - - What about if the "day" isn't known? Is this ok? - comments: - - Provide the date the flood occurred. If extended flooding occurred provide - the date range. - examples: - - value: '1927-04-15' - - value: 1927-04 to 1927-05 - extreme_event: - name: extreme_event - annotations: - expected_value: - tag: expected_value - value: date, string - examples: - - value: 1980-05-18, volcanic eruption - slope_aspect: - name: slope_aspect - description: The direction a slope faces. While looking down a slope use a - compass to record the direction you are facing (direction or degrees). This - measure provides an indication of sun and wind exposure that will influence - soil temperature and evapotranspiration. - comments: - - Aspect is the orientation of slope, measured clockwise in degrees from 0 - to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, - and 270 is west-facing. - examples: - - value: '35' - slope_gradient: - name: slope_gradient - todos: - - Slope is a percent. How does the validation work? Check to correct examples - examples: - - value: 10% - - value: 10 % - - value: '0.10' - al_sat: - name: al_sat - description: The relative abundance of aluminum in the sample - title: aluminum saturation/ extreme unusual properties - todos: - - Example & validation. Can we configure things so that 27% & 27 % & 0.27 - will validate? - - I think it's weird the way GSC writes the title. I recommend this change. - Thoughts? I would argue this isn't an extreme unusual property. It's just - a biogeochemical measurement. - notes: - - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like - all cations, aluminum held by the cation exchange complex is in equilibrium - with aluminum in the soil solution. - examples: - - value: 27% - al_sat_meth: - name: al_sat_meth - description: Reference or method used in determining Aluminum saturation - title: aluminum saturation method/ extreme unusual properties - todos: - - I think it's weird the way GSC writes the title. I recommend this change. - Thoughts? - comments: - - Required when aluminum saturation is provided. - examples: - - value: https://doi.org/10.1371/journal.pone.0176357 - annual_precpt: - name: annual_precpt - examples: - - value: 8.94 inch - cur_vegetation: - name: cur_vegetation - description: Vegetation classification from one or more standard classification - systems, or agricultural crop - todos: - - Recommend changing this from text value to some king of ontology? - comments: - - Values provided here can be specific species of vegetation or vegetation - regions - - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region - examples: - - value: deciduous forest - - value: forest - - value: Bauhinia variegata - cur_vegetation_meth: - name: cur_vegetation_meth - todos: - - I'm not sure this is a DOI, PMID, or URI. Should pool the community and - find out how they accomplish this if provided. - comments: - - Required when current vegetation is provided. - examples: - - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x - heavy_metals: - name: heavy_metals - description: Heavy metals present in the sample and their concentrations. - title: heavy metals/ extreme unusual properties - todos: - - Example & validation. Can we configure things so that 27% & 27 % & 0.27 - will validate? - - I think it's weird the way GSC writes the title. I recommend this change. - Thoughts? I would argue this isn't an extreme unusual property. It's just - a biogeochemical measurement. - comments: - - For multiple heavy metals and concentrations, separate by ; - examples: - - value: mercury 0.09 micrograms per gram - - value: mercury 0.09 ug/g; chromium 0.03 ug/g - heavy_metals_meth: - name: heavy_metals_meth - title: heavy metals method/ extreme unusual properties - comments: - - Required when heavy metals are provided - - If different methods are used for multiple metals, indicate the metal and - method. Separate metals by ; - examples: - - value: https://doi.org/10.3390/ijms9040434 - - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8 - multivalued: true - season_precpt: - name: season_precpt - title: average seasonal precipitation - todos: - - check validation & examples. always mm? so value only? Or value + unit - notes: - - mean and average are the same thing, but it seems like bad practice to not - be consistent. Changed mean to average - comments: - - Seasons are defined as spring (March, April, May), summer (June, July, August), - autumn (September, October, November) and winter (December, January, February). - examples: - - value: 0.4 inch - - value: 10.16 mm - water_cont_soil_meth: - name: water_cont_soil_meth - todos: - - Why is it soil water content method in the name but not the title? Is this - slot used in other samples? - - Soil water content can be measure MANY ways and often, multiple ways are - used in one experiment (gravimetric water content and water holding capacity - and water filled pore space, to name a few). - - Should this be multi valued? How to we manage and validate this? - comments: - - Required if providing water content - examples: - - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503 - - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm - water_content: - name: water_content - annotations: - expected_value: - tag: expected_value - value: string - preferred_unit: - tag: preferred_unit - value: gram per gram or cubic centimeter per cubic centimeter - todos: - - value in preferred unit is too limiting. need to change this - - check and correct validation so examples are accepted - - how to manage multiple water content methods? - examples: - - value: 0.75 g water/g dry soil - - value: 75% water holding capacity - - value: 1.1 g fresh weight/ dry weight - - value: 10% water filled pore space - multivalued: true - ph_meth: - name: ph_meth - comments: - - This can include a link to the instrument used or a citation for the method. - examples: - - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB - - value: https://doi.org/10.2136/sssabookser5.3.c16 - tot_carb: - name: tot_carb - todos: - - is this inorganic and organic? both? could use some clarification. - - ug/L doesn't seem like the right units. Should check this slots usage in - databases and re-evaluate. I couldn't find any references that provided - this data in this format - examples: - - value: 1 ug/L - tot_nitro_cont_meth: - name: tot_nitro_cont_meth - examples: - - value: https://doi.org/10.2134/agronmonogr9.2.c32 - - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo - tot_nitro_content: - name: tot_nitro_content - examples: - - value: 5 mg N/ L - tot_org_c_meth: - name: tot_org_c_meth - examples: - - value: https://doi.org/10.1080/07352680902776556 - tot_org_carb: - name: tot_org_carb - todos: - - check description. How are they different? - examples: - - value: 5 mg N/ L - salinity_meth: - name: salinity_meth - examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 - sieving: - name: sieving - todos: - - check validation and examples - comments: - - Describe how samples were composited or sieved. - - Use 'sample link' to indicate which samples were combined. - examples: - - value: combined 2 cores | 4mm sieved - - value: 4 mm sieved and homogenized - - value: 50 g | 5 cores | 2 mm sieved - climate_environment: - name: climate_environment - todos: - - description says "can include multiple climates" but multivalued is set - to false - - add examples, i need to see some examples to add correctly formatted example. - gaseous_environment: - name: gaseous_environment - todos: - - would like to see usage examples for this slot. Requiring micromole/L seems - too limiting and doesn't match expected_value value - - did I do this right? keep the example that's provided and add another? so - as to not override - examples: - - value: CO2; 500ppm above ambient; constant - - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - watering_regm: - name: watering_regm - examples: - - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - - value: 75% water holding capacity; constant - source_mat_id: - name: source_mat_id - description: A globally unique identifier assigned to the biological sample. - title: source material identifier - todos: - - Currently, the comments say to use UUIDs. However, if we implement assigning - NMDC identifiers with the minter we dont need to require a GUID. It can - be an optional field to fill out only if they already have a resolvable - ID. - comments: - - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), - NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These - IDs enable linking to derived analytes and subsamples. If you have not assigned - FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). - examples: - - value: IGSN:AU1243 - - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002 - unique_keys: - samp_name_unique_key: - unique_key_name: samp_name_unique_key - unique_key_slots: - - samp_name - rules: - - preconditions: - slot_conditions: - dna_cont_well: - name: dna_cont_well - pattern: .+ - postconditions: - slot_conditions: - dna_cont_type: - name: dna_cont_type - equals_string: plate - description: DNA samples shipped to JGI for metagenomic analysis in tubes can't - have any value for their plate position. - title: dna_well_requires_plate - - preconditions: - slot_conditions: - dna_cont_type: - name: dna_cont_type - equals_string: plate - postconditions: - slot_conditions: - dna_cont_well: - name: dna_cont_well - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ - description: DNA samples in plates must have a plate position that matches the - regex. Note the requirement for an empty string in the tube case. Waiting - for value_present validation to be added to runtime - title: dna_plate_requires_well - - preconditions: - slot_conditions: - rna_cont_well: - name: rna_cont_well - pattern: .+ - postconditions: - slot_conditions: - rna_cont_type: - name: rna_cont_type - equals_string: plate - description: RNA samples shipped to JGI for metagenomic analysis in tubes can't - have any value for their plate position. - title: rna_well_requires_plate - - preconditions: - slot_conditions: - rna_cont_type: - name: rna_cont_type - equals_string: plate - postconditions: - slot_conditions: - rna_cont_well: - name: rna_cont_well - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ - description: RNA samples in plates must have a plate position that matches the - regex. Note the requirement for an empty string in the tube case. Waiting - for value_present validation to be added to runtime - title: rna_plate_requires_well - Doi: - name: Doi - description: A centrally registered identifier symbol used to uniquely identify - objects given by the International DOI Foundation. The DOI system is particularly - used for electronic documents. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - DOIs - - digital object identifiers - exact_mappings: - - OBI:0002110 - slots: - - doi_value - - doi_provider - - doi_category - rules: - - preconditions: - slot_conditions: - doi_category: - name: doi_category - any_of: - - equals_string: dataset_doi - - equals_string: award_doi - postconditions: - slot_conditions: - doi_provider: - name: doi_provider - required: true - description: If doi_category is a publication_doi, then doi_provider is not - required. Otherwise, doi_provider is required. - title: dataset_award_dois_required - Study: - name: Study - description: A study summarizes the overall goal of a research initiative and - outlines the key objective of its underlying projects. - alt_descriptions: - embl.ena: - source: embl.ena - description: A study (project) groups together data submitted to the archive - and controls its release date. A study accession is typically used when - citing data submitted to ENA - todos: - - determine how to get data values for submitted_to_insdc, investigation_type, - experimental_factor - - project_name is redundant with name, so excluding it - notes: - - sample GOLD link https://bioregistry.io/gold:Gs0110115 - - sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ? - - sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757 - - GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, - but no longer for the Study.id - comments: - - The Study class can include both consortia and research studies. - in_subset: - - sample subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - proposal - - research proposal - - research study - - investigation - - project - - umbrella project - - research initiative - exact_mappings: - - OBI:0000066 - - SIO:000747 - - NCIT:C41198 - - ISA:Investigation - broad_mappings: - - prov:Activity - is_a: NamedThing - slots: - - emsl_project_identifiers - - neon_study_identifiers - - jgi_portal_study_identifiers - - id - - alternative_identifiers - - gnps_task_identifiers - - alternative_descriptions - - alternative_names - - alternative_titles - - description - - associated_dois - - ecosystem - - ecosystem_category - - ecosystem_subtype - - ecosystem_type - - funding_sources - - gold_study_identifiers - - has_credit_associations - - study_category - - insdc_bioproject_identifiers - - mgnify_project_identifiers - - notes - - objective - - part_of - - principal_investigator - - related_identifiers - - relevant_protocols - - specific_ecosystem - - study_image - - title - - type - - websites - - homepage_website - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$' - interpolated: true - name: - name: name - annotations: - tooltip: - tag: tooltip - value: Provide a name for the study your samples will belong with. - websites: - name: websites - annotations: - tooltip: - tag: tooltip - value: Link to the Principal Investigator's research lab webpage or the - study webpage associated with this collection of samples. Multiple links - can be provided. - homepage_website: - name: homepage_website - annotations: - tooltip: - tag: tooltip - value: Link to the consortium's homepage if the study_category is a consortium. - description: - name: description - annotations: - tooltip: - tag: tooltip - value: Provide a brief description of your study. - description: A brief, link-free summary of a Study - comments: - - Include links in other Study slots, such as websites or dois. - notes: - name: notes - annotations: - tooltip: - tag: tooltip - value: Add any additional notes or comments about this study. - alternative_identifiers: - name: alternative_identifiers - description: Unique identifier for a study submitted to additional resources. - Matches that which has been submitted to NMDC - alternative_names: - name: alternative_names - annotations: - tooltip: - tag: tooltip - value: Project, study, or sample set names the are also associated with - this submission or other names / identifiers for this study. - related_identifiers: - name: related_identifiers - description: Unique identifier for a study submitted to additional resources. - Similar, but not necessarily identical to that which has been submitted - to NMDC - insdc_bioproject_identifiers: - name: insdc_bioproject_identifiers - annotations: - tooltip: - tag: tooltip - value: Provide the NCBI BioProject Accession Number associated with the - listed NCBI BioProject Title. - description: Unique identifier for a bioproject submitted to INSDC that relates - to the NMDC submitted study. - part_of: - name: part_of - description: Links a study or consortium to a parent (or umbrella) study or - consortium. - comments: - - Value is the id of the umbrella study or consortium. - range: Study - pattern: ^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$' - interpolated: true - BiosampleProcessing: - name: BiosampleProcessing - description: A process that takes one or more biosamples as inputs and generates - one or more biosamples as outputs. An example of an output includes samples - cultivated from another sample. - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - material processing - broad_mappings: - - OBI:0000094 - is_a: PlannedProcess - slots: - - has_input - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):bsmprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}$' - interpolated: true - has_input: - name: has_input - range: Biosample - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - range: ProcessedSample - pattern: ^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - SubSamplingProcess: - name: SubSamplingProcess - description: 'Separating a sample aliquot from the starting material for downstream - activity. - - ' - todos: - - add intermediate class between PlannedProcess and this (MaterialProcessing potentially) - - Montana to visit slot descriptions - - add 'has_output' usage for processed sample - James - notes: - - A subsample may be (a) a portion of the sample obtained by selection or division; - (b) an individual unit of the lot taken as part of the sample; (c) the final - unit of multistage sampling. The term 'subsample' is used either in the sense - of a 'sample of a sample' or as a synonym for 'unit'. In practice, the meaning - is usually apparent from the context or is defined. - from_schema: https://w3id.org/nmdc/nmdc - related_mappings: - - OBI:0000744 - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - - ORCID:0000-0001-9076-6066 - - ORCID:0009-0008-4013-7737 - is_a: PlannedProcess - slots: - - container_size - - contained_in - - temperature - - volume - - mass - slot_usage: - volume: - name: volume - description: The output volume of the SubSampling Process. - mass: - name: mass - description: The output mass of the SubSampling Process. - has_input: - name: has_input - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - description: The subsample. - range: ProcessedSample - pattern: ^(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - MixingProcess: - name: MixingProcess - description: 'The combining of components, particles or layers into a more homogeneous - state. - - ' - comments: - - The mixing may be achieved manually or mechanically by shifting the material - with stirrers or pumps or by revolving or shaking the container. - - The process must not permit segregation of particles of different size or properties. - - Homogeneity may be considered to have been achieved in a practical sense when - the sampling error of the processed portion is negligible compared to the total - error of the measurement system. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - is_a: PlannedProcess - slots: - - duration - slot_usage: - has_input: - name: has_input - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - description: The mixed sample. - range: ProcessedSample - pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$' - interpolated: true - FiltrationProcess: - name: FiltrationProcess - description: The process of segregation of phases; e.g. the separation of suspended - solids from a liquid or gas, usually by forcing a carrier gas or liquid through - a porous medium. - from_schema: https://w3id.org/nmdc/nmdc - related_mappings: - - CHMO:0001640 - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-8683-0050 - - ORCID:0000-0001-9076-6066 - - ORCID:0009-0008-4013-7737 - is_a: PlannedProcess - slots: - - conditionings - - container_size - - filter_material - - filter_pore_size - - filtration_category - - is_pressurized - - separation_method - - volume - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):filtpr-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$' - interpolated: true - volume: - name: volume - description: The volume of sample filtered. - has_input: - name: has_input - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - range: ProcessedSample - pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$' - interpolated: true - ChromatographicSeparationProcess: - name: ChromatographicSeparationProcess - description: The process of using a selective partitioning of the analyte or interferent - between two immiscible phases. - from_schema: https://w3id.org/nmdc/nmdc - contributors: - - ORCID:0009-0001-1555-1601 - - ORCID:0000-0002-1368-8217 - is_a: PlannedProcess - slots: - - ordered_mobile_phases - - stationary_phase - - temperature - slot_usage: - has_input: - name: has_input - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - has_output: - name: has_output - range: ProcessedSample - pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$' - interpolated: true - OmicsProcessing: - name: OmicsProcessing - description: The methods and processes used to generate omics data from a biosample - or organism. - alt_descriptions: - embl.ena: - source: embl.ena - description: An experiment contains information about a sequencing experiment - including library and instrument details. - in_subset: - - sample subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - omics assay - - sequencing project - - experiment - broad_mappings: - - OBI:0000070 - - ISA:Assay - is_a: PlannedProcess - slots: - - add_date - - chimera_check - - gold_sequencing_project_identifiers - - has_input - - has_output - - insdc_bioproject_identifiers - - insdc_experiment_identifiers - - instrument_name - - mod_date - - ncbi_project_name - - nucl_acid_amp - - nucl_acid_ext - - omics_type - - part_of - - pcr_cond - - pcr_primers - - principal_investigator - - processing_institution - - samp_vol_we_dna_ext - - seq_meth - - seq_quality_check - - target_gene - - target_subfragment - - type - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}$' - interpolated: true - has_input: - name: has_input - required: true - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - any_of: - - range: Biosample - - range: ProcessedSample - part_of: - name: part_of - range: Study - pattern: ^(nmdc):(sty)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$' - interpolated: true - has_output: - name: has_output - range: DataObject - pattern: ^(nmdc):(dobj)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$' - interpolated: true - CreditAssociation: - name: CreditAssociation - description: This class supports binding associated researchers to studies. There - will be at least a slot for a CRediT Contributor Role and for a person value. - Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at - https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://casrai.org/credit/ - aliases: - - study role - - credit table - - associated researchers - slots: - - applies_to_person - - applied_roles - - type - class_uri: prov:Association - NamedThing: - name: NamedThing - description: a databased entity or concept/class - from_schema: https://w3id.org/nmdc/nmdc - abstract: true - slots: - - id - - name - - description - - alternative_identifiers - MaterialEntity: - name: MaterialEntity - title: Material Entity - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - Material - - Physical entity - is_a: NamedThing - abstract: true - ProcessedSample: - name: ProcessedSample - title: Processed Sample - from_schema: https://w3id.org/nmdc/nmdc - is_a: MaterialEntity - slots: - - biomaterial_purity - - dna_absorb1 - - dna_concentration - - external_database_identifiers - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$' - interpolated: true - AnalyticalSample: - name: AnalyticalSample - title: Analytical Sample - from_schema: https://w3id.org/nmdc/nmdc - is_a: MaterialEntity - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):ansm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}$' - interpolated: true - Site: - name: Site - title: Site - comments: - - BCO sample collection site ? - from_schema: https://w3id.org/nmdc/nmdc - is_a: MaterialEntity - abstract: true - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):site-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}$' - interpolated: true - PlannedProcess: - name: PlannedProcess - title: Planned Process - from_schema: https://w3id.org/nmdc/nmdc - is_a: NamedThing - abstract: true - slots: - - designated_class - - end_date - - has_input - - has_output - - processing_institution - - protocol_link - - start_date - - instrument_name - - qc_status - - qc_comment - - has_failure_categorization - slot_usage: - designated_class: - name: designated_class - comments: - - required on all instances in a polymorphic Database slot like planned_process_set - class_uri: OBI:0000011 - OntologyClass: - name: OntologyClass - notes: - - The identifiers for terms from external ontologies can't have their ids constrained - to the nmdc namespace - from_schema: https://w3id.org/nmdc/nmdc - is_a: NamedThing - slot_usage: - id: - name: id - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ - EnvironmentalMaterialTerm: - name: EnvironmentalMaterialTerm - from_schema: https://w3id.org/nmdc/nmdc - is_a: OntologyClass - AttributeValue: - name: AttributeValue - description: The value for any value of a attribute for a sample. This object - can hold both the un-normalized atomic value and the structured value - from_schema: https://w3id.org/nmdc/nmdc - slots: - - has_raw_value - slot_usage: - type: - name: type - description: An optional string that specified the type of object. - QuantityValue: - name: QuantityValue - description: A simple quantity, e.g. 2cm - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - schema:QuantityValue - is_a: AttributeValue - slots: - - has_maximum_numeric_value - - has_minimum_numeric_value - - has_numeric_value - - has_raw_value - - has_unit - slot_usage: - has_raw_value: - name: has_raw_value - description: Unnormalized atomic string representation, should in syntax {number} - {unit} - has_unit: - name: has_unit - description: The unit of the quantity - has_numeric_value: - name: has_numeric_value - description: The number part of the quantity - range: double - ImageValue: - name: ImageValue - description: An attribute value representing an image. - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - url - - description - - display_order - PersonValue: - name: PersonValue - description: An attribute value representing a person - todos: - - add additional fields e.g for institution - - deprecate "has_raw_value" in favor of "name" - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - email - - name - - orcid - - profile_image_url - - websites - slot_usage: - orcid: - name: orcid - annotations: - tooltip: - tag: tooltip - value: Open Researcher and Contributor ID for this person. See https://orcid.org - email: - name: email - annotations: - tooltip: - tag: tooltip - value: Email address for this person. - has_raw_value: - name: has_raw_value - description: The full name of the Investigator in format FIRST LAST. - notes: - - May eventually be deprecated in favor of "name". - name: - name: name - annotations: - tooltip: - tag: tooltip - value: First name, middle initial, and last name of this person. - description: The full name of the Investigator. It should follow the format - FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL - is optional. - MagBin: - name: MagBin - from_schema: https://w3id.org/nmdc/nmdc - slots: - - bin_name - - bin_quality - - completeness - - contamination - - gene_count - - gtdbtk_class - - gtdbtk_domain - - gtdbtk_family - - gtdbtk_genus - - gtdbtk_order - - gtdbtk_phylum - - gtdbtk_species - - members_id - - num_16s - - num_23s - - num_5s - - num_t_rna - - number_of_contig - - total_bases - - type - MetaboliteQuantification: - name: MetaboliteQuantification - description: This is used to link a metabolomics analysis workflow to a specific - metabolite - from_schema: https://w3id.org/nmdc/nmdc - slots: - - alternative_identifiers - - highest_similarity_score - - metabolite_quantified - PeptideQuantification: - name: PeptideQuantification - description: This is used to link a metaproteomics analysis workflow to a specific - peptide sequence and related information - from_schema: https://w3id.org/nmdc/nmdc - slots: - - all_proteins - - best_protein - - min_q_value - - peptide_sequence - - peptide_spectral_count - - peptide_sum_masic_abundance - ProteinQuantification: - name: ProteinQuantification - description: This is used to link a metaproteomics analysis workflow to a specific - protein - from_schema: https://w3id.org/nmdc/nmdc - slots: - - all_proteins - - best_protein - - peptide_sequence_count - - protein_spectral_count - - protein_sum_masic_abundance - slot_usage: - best_protein: - name: best_protein - description: the specific protein identifier most correctly grouped to its - associated peptide sequences - all_proteins: - name: all_proteins - description: the grouped list of protein identifiers associated with the peptide - sequences that were grouped to a best protein - ChemicalEntity: - name: ChemicalEntity - id_prefixes: - - cas - - CHEBI - - CHEMBL.COMPOUND - - DRUGBANK - - HMDB - - KEGG.COMPOUND - - MESH - - PUBCHEM.COMPOUND - description: An atom or molecule that can be represented with a chemical formula. - Include lipids, glycans, natural products, drugs. There may be different terms - for distinct acid-base forms, protonation states - comments: - - As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode - to this class. - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html - aliases: - - metabolite - - chemical substance - - chemical compound - - chemical - exact_mappings: - - biolink:ChemicalSubstance - is_a: OntologyClass - slots: - - chemical_formula - - inchi - - inchi_key - - smiles - GeneProduct: - name: GeneProduct - id_prefixes: - - PR - - UniProtKB - - gtpo - description: A molecule encoded by a gene that has an evolved function - notes: - - we may include a more general gene product class in future to allow for ncRNA - annotation - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - biolink:GeneProduct - is_a: NamedThing - TextValue: - name: TextValue - description: A basic string value - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - language - UrlValue: - name: UrlValue - description: A value that is a string that conforms to URL syntax - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - TimestampValue: - name: TimestampValue - description: A value that is a timestamp. The range should be ISO-8601 - notes: - - 'removed the following slots: year, month, day' - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - IntegerValue: - name: IntegerValue - description: A value that is an integer - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - has_numeric_value - BooleanValue: - name: BooleanValue - description: A value that is a boolean - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - has_boolean_value - ControlledTermValue: - name: ControlledTermValue - description: A controlled term or class from an ontology - todos: - - add fields for ontology, branch - from_schema: https://w3id.org/nmdc/nmdc - is_a: AttributeValue - slots: - - term - ControlledIdentifiedTermValue: - name: ControlledIdentifiedTermValue - description: A controlled term or class from an ontology, requiring the presence - of term with an id - notes: - - To be used for slots like env_broad_scale - from_schema: https://w3id.org/nmdc/nmdc - is_a: ControlledTermValue - slot_usage: - term: - name: term - required: true - GeolocationValue: - name: GeolocationValue - description: A normalized value for a location on the earth's surface - notes: - - 'what did ''to_str: {latitude} {longitude}'' mean?' - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - schema:GeoCoordinates - is_a: AttributeValue - slots: - - latitude - - longitude - slot_usage: - has_raw_value: - name: has_raw_value - description: The raw value for a geolocation should follow {latitude} {longitude} - latitude: - name: latitude - required: true - longitude: - name: longitude - required: true - GenomeFeature: - name: GenomeFeature - description: A feature localized to an interval along a genome - comments: - - corresponds to an entry in GFF3 - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md - slots: - - encodes - - end - - feature_type - - phase - - seqid - - start - - strand - slot_usage: - seqid: - name: seqid - required: true - start: - name: start - required: true - end: - name: end - required: true - FunctionalAnnotationTerm: - name: FunctionalAnnotationTerm - description: Abstract grouping class for any term/descriptor that can be applied - to a functional unit of a genome (protein, ncRNA, complex). - todos: - - decide if this should be used for product naming - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - function - - FunctionalAnnotation - is_a: OntologyClass - abstract: true - Pathway: - name: Pathway - id_prefixes: - - KEGG_PATHWAY - - COG - description: A pathway is a sequence of steps/reactions carried out by an organism - or community of organisms - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - biological process - - metabolic pathway - - signaling pathway - exact_mappings: - - biolink:Pathway - is_a: FunctionalAnnotationTerm - slots: - - has_part - slot_usage: - has_part: - name: has_part - description: A pathway can be broken down to a series of reaction step - required: true - Reaction: - name: Reaction - id_prefixes: - - KEGG.REACTION - - RHEA - - MetaCyc - - EC - - GO - - MetaNetX - - SEED - - RetroRules - description: An individual biochemical transformation carried out by a functional - unit of an organism, in which a collection of substrates are transformed into - a collection of products. Can also represent transporters - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - biolink:MolecularActivity - is_a: FunctionalAnnotationTerm - slots: - - direction - - is_balanced - - is_diastereoselective - - is_fully_characterized - - is_stereo - - is_transport - - left_participants - - right_participants - - smarts_string - ReactionParticipant: - name: ReactionParticipant - description: Instances of this link a reaction to a chemical entity participant - from_schema: https://w3id.org/nmdc/nmdc - slots: - - chemical - - stoichiometry - OrthologyGroup: - name: OrthologyGroup - id_prefixes: - - CATH - - EGGNOG - - KEGG.ORTHOLOGY - - PANTHER.FAMILY - - PFAM - - SUPFAM - - TIGRFAM - description: A set of genes or gene products in which all members are orthologous - notes: - - KEGG.ORTHOLOGY prefix is used for KO numbers - from_schema: https://w3id.org/nmdc/nmdc - exact_mappings: - - biolink:GeneFamily - is_a: FunctionalAnnotationTerm - FunctionalAnnotation: - name: FunctionalAnnotation - description: An assignment of a function term (e.g. reaction or pathway) that - is executed by a gene product, or which the gene product plays an active role - in. Functional annotations can be assigned manually by curators, or automatically - in workflows. In the context of NMDC, all function annotation is performed automatically, - typically using HMM or Blast type methods - notes: - - move id slot usage patterns to has_function slot usage? - from_schema: https://w3id.org/nmdc/nmdc - see_also: - - https://img.jgi.doe.gov/docs/functional-annotation.pdf - - https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl - narrow_mappings: - - biolink:GeneToGoTermAssociation - slots: - - has_function - - subject - - was_generated_by - slot_usage: - has_function: - name: has_function - notes: - - this slot had been called id - - Still missing patterns for COG and RetroRules. - - These patterns aren't tied to the listed prefixes. A discussion about that - possibility had been started, including the question of whether these lists - are intended to be open examples or closed - type: - name: type - description: TODO - range: OntologyClass - was_generated_by: - name: was_generated_by - description: provenance for the annotation. - notes: - - To be consistent with the rest of the NMDC schema we use the PROV annotation - model, rather than GPAD - range: MetagenomeAnnotationActivity - pattern: ^(nmdc):(wfmgan)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - Activity: - name: Activity - description: Something that occurs over a period of time and acts upon or with - entities; it may include consuming, processing, transforming, modifying, relocating, - using, or generating entities. - notes: - - removed was_associated_with because we are trying to avoid instantiating id-less - Agents - comments: - - to be replaced with PlannedProcess in the monterey-schema - from_schema: https://w3id.org/nmdc/nmdc - mappings: - - prov:Activity - abstract: true - slots: - - id - - name - - started_at_time - - ended_at_time - - was_informed_by - - used - slot_usage: - was_informed_by: - name: was_informed_by - pattern: ^(nmdc):(omprc)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(omprc)-{id_shoulder}-{id_blade}$' - interpolated: true - WorkflowExecutionActivity: - name: WorkflowExecutionActivity - description: Represents an instance of an execution of a particular workflow - alt_descriptions: - embl.ena: - source: embl.ena - description: An analysis contains secondary analysis results derived from - sequence reads (e.g. a genome assembly) - comments: - - Each instance of this (and all other) activities is a distinct run with start - and stop times, potentially with different inputs and outputs - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - analysis - is_a: Activity - abstract: true - slots: - - execution_resource - - git_url - - has_input - - has_output - - part_of - - type - - version - - qc_status - - qc_comment - - has_failure_categorization - - alternative_identifiers - slot_usage: - started_at_time: - name: started_at_time - required: true - ended_at_time: - name: ended_at_time - required: true - git_url: - name: git_url - required: true - has_input: - name: has_input - required: true - pattern: ^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$' - interpolated: true - has_output: - name: has_output - pattern: ^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$' - interpolated: true - execution_resource: - name: execution_resource - required: true - type: - name: type - required: true - id: - name: id - required: true - pattern: ^(nmdc):wf-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - rules: - - preconditions: - slot_conditions: - qc_status: - name: qc_status - equals_string: pass - postconditions: - slot_conditions: - has_output: - name: has_output - required: true - description: If qc_status has a value of pass, then the has_output slot is required. - title: qc_status_pass_has_output_required - - preconditions: - slot_conditions: - qc_status: - name: qc_status - value_presence: ABSENT - postconditions: - slot_conditions: - has_output: - name: has_output - required: true - description: If qc_status is not specified, then the has_output slot is required. - title: qc_status_pass_null_has_output_required - MetagenomeAssembly: - name: MetagenomeAssembly - description: A workflow execution activity that converts sequencing reads into - an assembled metagenome. - comments: - - instances of this class may use a de novo assembly strategy in most or all cases - relevant to NMDC - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - - asm_score - - scaffolds - - scaf_logsum - - scaf_powsum - - scaf_max - - scaf_bp - - scaf_n50 - - scaf_n90 - - scaf_l50 - - scaf_l90 - - scaf_n_gt50k - - scaf_l_gt50k - - scaf_pct_gt50k - - contigs - - contig_bp - - ctg_n50 - - ctg_l50 - - ctg_n90 - - ctg_l90 - - ctg_logsum - - ctg_powsum - - ctg_max - - gap_pct - - gc_std - - gc_avg - - num_input_reads - - num_aligned_reads - - insdc_assembly_identifiers - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmgas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetatranscriptomeAssembly: - name: MetatranscriptomeAssembly - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - asm_score - - scaffolds - - scaf_logsum - - scaf_powsum - - scaf_max - - scaf_bp - - scaf_n50 - - scaf_n90 - - scaf_l50 - - scaf_l90 - - scaf_n_gt50k - - scaf_l_gt50k - - scaf_pct_gt50k - - contigs - - contig_bp - - ctg_n50 - - ctg_l50 - - ctg_n90 - - ctg_l90 - - ctg_logsum - - ctg_powsum - - ctg_max - - gap_pct - - gc_std - - gc_avg - - num_input_reads - - num_aligned_reads - - insdc_assembly_identifiers - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmtas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetagenomeAnnotationActivity: - name: MetagenomeAnnotationActivity - description: A workflow execution activity that provides functional and structural - annotation of assembled metagenome contigs - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - - gold_analysis_project_identifiers - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmgan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetatranscriptomeAnnotationActivity: - name: MetatranscriptomeAnnotationActivity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - - gold_analysis_project_identifiers - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmtan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetatranscriptomeActivity: - name: MetatranscriptomeActivity - description: A metatranscriptome activity that e.g. pools assembly and annotation - activity. - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MagsAnalysisActivity: - name: MagsAnalysisActivity - description: A workflow execution activity that uses computational binning tools - to group assembled contigs into genomes - title: Metagenome-Assembled Genome analysis activity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - - input_contig_num - - binned_contig_num - - too_short_contig_num - - low_depth_contig_num - - unbinned_contig_num - - mags_list - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmag-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetagenomeSequencingActivity: - name: MetagenomeSequencingActivity - description: Initial sequencing activity that precedes any analysis. This activity - has output(s) that are the raw sequencing data. - title: Metagenome sequencing activity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmsa-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - has_input: - name: has_input - pattern: ^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$' - interpolated: true - ReadQcAnalysisActivity: - name: ReadQcAnalysisActivity - description: A workflow execution activity that performs quality control on raw - Illumina reads including quality trimming, artifact removal, linker trimming, - adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant - removal - title: Read quality control analysis activity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - - input_read_count - - input_base_count - - output_read_count - - output_base_count - - input_read_bases - - output_read_bases - - version - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfrqc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - ReadBasedTaxonomyAnalysisActivity: - name: ReadBasedTaxonomyAnalysisActivity - description: A workflow execution activity that performs taxonomy classification - using sequencing reads - title: Read based analysis activity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - type - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfrbt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetabolomicsAnalysisActivity: - name: MetabolomicsAnalysisActivity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - has_calibration - - has_metabolite_quantifications - slot_usage: - id: - name: id - required: true - pattern: ^(nmdc):wfmb-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - MetaproteomicsAnalysisActivity: - name: MetaproteomicsAnalysisActivity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - has_peptide_quantifications - slot_usage: - used: - name: used - description: The instrument used to collect the data used in the analysis - id: - name: id - required: true - pattern: ^(nmdc):wfmp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true - NomAnalysisActivity: - name: NomAnalysisActivity - in_subset: - - workflow subset - from_schema: https://w3id.org/nmdc/nmdc - is_a: WorkflowExecutionActivity - slots: - - has_calibration - slot_usage: - used: - name: used - description: The instrument used to collect the data used in the analysis - id: - name: id - required: true - pattern: ^(nmdc):wfnom-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[0-9]{1,})$ - structured_pattern: - syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$' - interpolated: true -source_file: src/schema/nmdc.yaml -settings: - id_nmdc_prefix: - setting_key: id_nmdc_prefix - setting_value: ^(nmdc) - id_shoulder: - setting_key: id_shoulder - setting_value: ([0-9][a-z]{0,6}[0-9]) - id_blade: - setting_key: id_blade - setting_value: ([A-Za-z0-9]{1,}) - id_version: - setting_key: id_version - setting_value: (\.[0-9]{1,}) - id_locus: - setting_key: id_locus - setting_value: (_[A-Za-z0-9_\.-]+)?$ diff --git a/poetry.lock b/poetry.lock index e35b446475..de8dd1c31a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -209,13 +209,13 @@ files = [ [[package]] name = "cachetools" -version = "5.3.3" +version = "5.4.0" description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" files = [ - {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"}, - {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"}, + {file = "cachetools-5.4.0-py3-none-any.whl", hash = "sha256:3ae3b49a3d5e28a77a0be2b37dbcb89005058959cb2323858c2657c4a8cab474"}, + {file = "cachetools-5.4.0.tar.gz", hash = "sha256:b8adc2e7c07f105ced7bc56dbb6dfbe7c4a00acce20e2227b3f355be89bc6827"}, ] [[package]] @@ -444,13 +444,13 @@ files = [ [[package]] name = "curies" -version = "0.7.9" +version = "0.7.10" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." optional = false python-versions = ">=3.8" files = [ - {file = "curies-0.7.9-py3-none-any.whl", hash = "sha256:e4c5beb91642376953c94db0ee2fb5d2b011c3b16749516436114ba61442f260"}, - {file = "curies-0.7.9.tar.gz", hash = "sha256:3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8"}, + {file = "curies-0.7.10-py3-none-any.whl", hash = "sha256:ad80f420dd76b6f3e921a245370ff6ab7473c48c29c17254970c03cd2e58af5f"}, + {file = "curies-0.7.10.tar.gz", hash = "sha256:98a7ceb94710fab3a02727a7f85ba0719dd22be5fc8b5f2ad1d7d4cfc47d64ce"}, ] [package.dependencies] @@ -569,13 +569,13 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto [[package]] name = "exceptiongroup" -version = "1.2.1" +version = "1.2.2" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" files = [ - {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"}, - {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"}, + {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"}, + {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"}, ] [package.extras] @@ -785,13 +785,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] [[package]] name = "google-api-python-client" -version = "2.136.0" +version = "2.137.0" description = "Google API Client Library for Python" optional = false python-versions = ">=3.7" files = [ - {file = "google-api-python-client-2.136.0.tar.gz", hash = "sha256:161c722c8864e7ed39393e2b7eea76ef4e1c933a6a59f9d7c70409b6635f225d"}, - {file = "google_api_python_client-2.136.0-py2.py3-none-any.whl", hash = "sha256:5a554c8b5edf0a609b905d89d7ced82e8f6ac31da1e4d8d5684ef63dbc0e49f5"}, + {file = "google_api_python_client-2.137.0-py2.py3-none-any.whl", hash = "sha256:a8b5c5724885e5be9f5368739aa0ccf416627da4ebd914b410a090c18f84d692"}, + {file = "google_api_python_client-2.137.0.tar.gz", hash = "sha256:e739cb74aac8258b1886cb853b0722d47c81fe07ad649d7f2206f06530513c04"}, ] [package.dependencies] @@ -803,13 +803,13 @@ uritemplate = ">=3.0.1,<5" [[package]] name = "google-auth" -version = "2.31.0" +version = "2.32.0" description = "Google Authentication Library" optional = false python-versions = ">=3.7" files = [ - {file = "google-auth-2.31.0.tar.gz", hash = "sha256:87805c36970047247c8afe614d4e3af8eceafc1ebba0c679fe75ddd1d575e871"}, - {file = "google_auth-2.31.0-py2.py3-none-any.whl", hash = "sha256:042c4702efa9f7d3c48d3a69341c209381b125faa6dbf3ebe56bc7e40ae05c23"}, + {file = "google_auth-2.32.0-py2.py3-none-any.whl", hash = "sha256:53326ea2ebec768070a94bee4e1b9194c9646ea0c2bd72422785bd0f9abfad7b"}, + {file = "google_auth-2.32.0.tar.gz", hash = "sha256:49315be72c55a6a37d62819e3573f6b416aca00721f7e3e31a008d928bf64022"}, ] [package.dependencies] @@ -841,13 +841,13 @@ httplib2 = ">=0.19.0" [[package]] name = "google-auth-oauthlib" -version = "1.2.0" +version = "1.2.1" description = "Google Authentication Library" optional = false python-versions = ">=3.6" files = [ - {file = "google-auth-oauthlib-1.2.0.tar.gz", hash = "sha256:292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8"}, - {file = "google_auth_oauthlib-1.2.0-py2.py3-none-any.whl", hash = "sha256:297c1ce4cb13a99b5834c74a1fe03252e1e499716718b190f56bcb9c4abc4faf"}, + {file = "google_auth_oauthlib-1.2.1-py2.py3-none-any.whl", hash = "sha256:2d58a27262d55aa1b87678c3ba7142a080098cbc2024f903c62355deb235d91f"}, + {file = "google_auth_oauthlib-1.2.1.tar.gz", hash = "sha256:afd0cad092a2eaa53cd8e8298557d6de1034c6cb4a740500b5357b648af97263"}, ] [package.dependencies] @@ -1331,13 +1331,13 @@ files = [ [[package]] name = "jsonschema" -version = "4.22.0" +version = "4.23.0" description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" files = [ - {file = "jsonschema-4.22.0-py3-none-any.whl", hash = "sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802"}, - {file = "jsonschema-4.22.0.tar.gz", hash = "sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7"}, + {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"}, + {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"}, ] [package.dependencies] @@ -1356,7 +1356,7 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\" [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] -format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"] [[package]] name = "jsonschema-specifications" @@ -1830,13 +1830,13 @@ pyyaml = ">=5.1" [[package]] name = "mkdocs-material" -version = "9.5.28" +version = "9.5.29" description = "Documentation that simply works" optional = false python-versions = ">=3.8" files = [ - {file = "mkdocs_material-9.5.28-py3-none-any.whl", hash = "sha256:ff48b11b2a9f705dd210409ec3b418ab443dd36d96915bcba45a41f10ea27bfd"}, - {file = "mkdocs_material-9.5.28.tar.gz", hash = "sha256:9cba305283ad1600e3d0a67abe72d7a058b54793b47be39930911a588fe0336b"}, + {file = "mkdocs_material-9.5.29-py3-none-any.whl", hash = "sha256:afc1f508e2662ded95f0a35a329e8a5acd73ee88ca07ba73836eb6fcdae5d8b4"}, + {file = "mkdocs_material-9.5.29.tar.gz", hash = "sha256:3e977598ec15a4ddad5c4dfc9e08edab6023edb51e88f0729bd27be77e3d322a"}, ] [package.dependencies] @@ -3511,13 +3511,13 @@ SQLAlchemy-Utils = ">=0.38.2,<0.39.0" [[package]] name = "setuptools" -version = "70.2.0" +version = "70.3.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "setuptools-70.2.0-py3-none-any.whl", hash = "sha256:b8b8060bb426838fbe942479c90296ce976249451118ef566a5a0b7d8b78fb05"}, - {file = "setuptools-70.2.0.tar.gz", hash = "sha256:bd63e505105011b25c3c11f753f7e3b8465ea739efddaccef8f0efac2137bac1"}, + {file = "setuptools-70.3.0-py3-none-any.whl", hash = "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc"}, + {file = "setuptools-70.3.0.tar.gz", hash = "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5"}, ] [package.extras] @@ -3974,13 +3974,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "validators" -version = "0.31.0" +version = "0.33.0" description = "Python Data Validation for Humans™" optional = false python-versions = ">=3.8" files = [ - {file = "validators-0.31.0-py3-none-any.whl", hash = "sha256:e15a600d81555a4cd409b17bf55946c5edec7748e776afc85ed0a19bdee54e56"}, - {file = "validators-0.31.0.tar.gz", hash = "sha256:de7574fc56a231c788162f3e7da15bc2053c5ff9e0281d9ff1afb3a7b69498df"}, + {file = "validators-0.33.0-py3-none-any.whl", hash = "sha256:134b586a98894f8139865953899fc2daeb3d0c35569552c5518f089ae43ed075"}, + {file = "validators-0.33.0.tar.gz", hash = "sha256:535867e9617f0100e676a1257ba1e206b9bfd847ddc171e4d44811f07ff0bfbf"}, ] [package.extras] diff --git a/project.Makefile b/project.Makefile index 7cd5d7cd5c..abb4a67fda 100644 --- a/project.Makefile +++ b/project.Makefile @@ -9,8 +9,11 @@ FD_ROOT=local/fuseki-data/databases SCHEMA_NAME = $(shell bash ./utils/get-value.sh name) SOURCE_SCHEMA_PATH = $(shell bash ./utils/get-value.sh source_schema_path) -.PHONY: dump-validate-report-convert-mongodb examples-clean linkml-validate-mongodb mixs-yaml-clean mixs-deepdiff \ -rdf-clean shuttle-clean +.PHONY: examples-clean \ +mixs-yaml-clean \ +rdf-clean \ +shuttle-clean \ +squeaky-clean examples-clean: rm -rf examples/output @@ -22,17 +25,19 @@ mixs-yaml-clean: rdf-clean: rm -rf \ OmicsProcessing.rq \ + local/mongo_as_* + +shuttle-clean: + rm -rf \ + local/mixs_regen/mixs_subset.yaml \ + local/mixs_regen/mixs_subset_modified.yaml.bak \ local/mongo_as_nmdc_database.ttl \ local/mongo_as_nmdc_database_cuire_repaired.ttl \ local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl \ local/mongo_as_nmdc_database_rdf_safe.yaml \ local/mongo_as_nmdc_database_validation.log \ local/mongo_as_unvalidated_nmdc_database.yaml - -shuttle-clean: - #rm -rf local/mixs_regen/mixs_subset_modified.yaml # triggers complete regeneration rm -rf local/mixs_regen/*.yaml - rm -rf $@.bak mkdir -p local/mixs_regen touch local/mixs_regen/.gitkeep @@ -41,7 +46,7 @@ src/schema/mixs.yaml: shuttle-clean local/mixs_regen/mixs_subset_modified_inj_en mv $(word 2,$^) $@ rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak -local/mixs_regen/mixs_subset.yaml: assets/import_mixs_slots_regardless.tsv +local/mixs_regen/mixs_subset.yaml: assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv $(RUN) do_shuttle \ --recipient_model assets/other_mixs_yaml_files/mixs_template.yaml \ --config_tsv $< \ @@ -109,6 +114,14 @@ examples/output/Biosample-exhaustive_report.yaml: src/data/valid/Biosample-exhas --output-yaml-file $@ \ --schema-path src/schema/nmdc.yaml +examples/output/Pooling-minimal-report.yaml: src/data/valid/Pooling-minimal.yaml + mkdir -p $(@D) # create parent directory + poetry run exhaustion-check \ + --class-name Pooling \ + --instance-yaml-file $< \ + --output-yaml-file $@ \ + --schema-path src/schema/nmdc.yaml + examples/output/Biosample-exhasutive-pretty-sorted.yaml: src/data/valid/Biosample-exhasutive.yaml $(RUN) pretty-sort-yaml \ -i $< \ @@ -141,44 +154,45 @@ make-rdf: rdf-clean \ # todo: metagenome_sequencing_set and metagenome_sequencing_activity_set are degenerate # and can't be validated, migrated or converted to RDF +# --selected-collections activity_set \ +# --selected-collections collecting_biosamples_from_site_set \ +# --selected-collections data_object_set \ +# --selected-collections extraction_set \ +# --selected-collections field_research_site_set \ +# --selected-collections functional_annotation_set \ +# --selected-collections genome_feature_set \ +# --selected-collections library_preparation_set \ +# --selected-collections mags_activity_set \ +# --selected-collections mags_set \ +# --selected-collections material_sample_set \ +# --selected-collections metabolomics_analysis_activity_set \ +# --selected-collections metabolomics_analysis_set \ +# --selected-collections metagenome_annotation_activity_set \ +# --selected-collections metagenome_annotation_set \ +# --selected-collections metagenome_assembly_set \ +# --selected-collections metagenome_sequencing_activity_set \ +# --selected-collections metagenome_sequencing_set \ +# --selected-collections metap_gene_function_aggregation \ +# --selected-collections metatranscriptome_activity_set \ +# --selected-collections metatranscriptome_analysis_set \ +# --selected-collections nom_analysis_activity_set \ +# --selected-collections omics_processing_set \ +# --selected-collections planned_process_set \ +# --selected-collections pooling_set \ +# --selected-collections processed_sample_set \ +# --selected-collections read_based_taxonomy_analysis_activity_set \ +# --selected-collections read_qc_analysis_activity_set \ +# --selected-collections study_set \ +# --selected-collections workflow_chain_set \ +# --selected-collections workflow_execution_set \ + local/mongo_as_unvalidated_nmdc_database.yaml: date time $(RUN) pure-export \ --max-docs-per-coll 200000 \ --output-yaml $@ \ --schema-source src/schema/nmdc.yaml \ - --selected-collections activity_set \ --selected-collections biosample_set \ - --selected-collections collecting_biosamples_from_site_set \ - --selected-collections data_object_set \ - --selected-collections extraction_set \ - --selected-collections field_research_site_set \ - --selected-collections functional_annotation_set \ - --selected-collections genome_feature_set \ - --selected-collections library_preparation_set \ - --selected-collections mags_activity_set \ - --selected-collections mags_set \ - --selected-collections material_sample_set \ - --selected-collections metabolomics_analysis_activity_set \ - --selected-collections metabolomics_analysis_set \ - --selected-collections metagenome_annotation_activity_set \ - --selected-collections metagenome_annotation_set \ - --selected-collections metagenome_assembly_set \ - --selected-collections metagenome_sequencing_activity_set \ - --selected-collections metagenome_sequencing_set \ - --selected-collections metap_gene_function_aggregation \ - --selected-collections metatranscriptome_activity_set \ - --selected-collections metatranscriptome_analysis_set \ - --selected-collections nom_analysis_activity_set \ - --selected-collections omics_processing_set \ - --selected-collections planned_process_set \ - --selected-collections pooling_set \ - --selected-collections processed_sample_set \ - --selected-collections read_based_taxonomy_analysis_activity_set \ - --selected-collections read_qc_analysis_activity_set \ - --selected-collections study_set \ - --selected-collections workflow_chain_set \ - --selected-collections workflow_execution_set \ dump-from-api \ --client-base-url "https://api.microbiomedata.org" \ --endpoint-prefix nmdcschema \ diff --git a/pyproject.toml b/pyproject.toml index 456d914db5..50149aebcd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -99,17 +99,16 @@ docs = ["mkdocs-material"] anyuri-strings-to-iris = 'nmdc_schema.anyuri_strings_to_iris:expand_curies' build-datafile-from-api-requests = "nmdc_schema.build_datafile_from_api_requests:main" class-sparql = "nmdc_schema.class_sparql:main" +create-migrator = 'nmdc_schema.migrators.cli.create_migrator:create_migrator' fetch-nmdc-schema = "nmdc_schema.nmdc_data:get_nmdc_jsonschema" generate-import-slots-regardless = "nmdc_schema.generate_import_slots_regardless:main" get-mixs-slots-matching-slot-list = "nmdc_schema.get_mixs_slots_matching_slot_list:main" -get-mixs-slots-used-in-schema = "nmdc_schema.get_mixs_slots_used_in_schema:main" # see nmdc_schema/generate_import_slots_regardless.py -get-slots-from-class = "nmdc_schema.get_slots_from_class:main" # see tests/test_getters.py +get-mixs-slots-used-in-schema = "nmdc_schema.get_mixs_slots_used_in_schema:main" # see nmdc_schema/generate_import_slots_regardless.py git rm = "nmdc_schema.get_slots_from_class:main" # see tests/test_getters.py +get-study-id-from-filename = "src.scripts.get_study_id_from_filename:main" get-study-related-records = "src.scripts.nmdc_database_tools:cli" migration-recursion = 'nmdc_schema.migration_recursion:main' -create-migrator = 'nmdc_schema.migrators.cli.create_migrator:create_migrator' nmdc-data = "nmdc_schema.nmdc_data:cli" -nmdc-version = "nmdc_schema.nmdc_version:cli" -slot-range-type-reporter = "src.scripts.slot_range_type_reporter:cli" -get-study-id-from-filename = "src.scripts.get_study_id_from_filename:main" nmdc-ncbi-mapping = "src.scripts.ncbi_nmdc_exact_term_matching:cli" +nmdc-version = "nmdc_schema.nmdc_version:cli" pure-export = "nmdc_schema.dump_single_modality:cli" +slot-range-type-reporter = "src.scripts.slot_range_type_reporter:cli" diff --git a/src/data/valid/Biosample-exhasutive.yaml b/src/data/problem/Biosample-exhasutive.yaml similarity index 99% rename from src/data/valid/Biosample-exhasutive.yaml rename to src/data/problem/Biosample-exhasutive.yaml index 81dc6c1bb5..93a8062b64 100644 --- a/src/data/valid/Biosample-exhasutive.yaml +++ b/src/data/problem/Biosample-exhasutive.yaml @@ -274,8 +274,6 @@ redox_potential: has_raw_value: 300 millivolt salinity: has_raw_value: 25 practical salinity unit -salinity_meth: - has_raw_value: PMID:22895776 samp_mat_process: has_raw_value: filtering of seawater samp_store_dur: @@ -375,9 +373,6 @@ light_regm: phosphate: has_raw_value: 0.7 micromole per liter -#samp_collec_method: -# has_raw_value: swabbing -samp_collec_method: swabbing samp_size: has_raw_value: 5 liters source_mat_id: @@ -563,8 +558,6 @@ host_diet: - has_raw_value: xxx host_dry_mass: has_raw_value: xxx -host_family_relation: - - xxx host_genotype: has_raw_value: xxx host_growth_cond: @@ -841,7 +834,6 @@ root_med_suppl: salt_regm: - has_raw_value: xxx samp_capt_status: other -samp_collec_device: xxx samp_collect_point: well samp_dis_stage: dissemination @@ -914,8 +906,6 @@ sludge_retent_time: has_raw_value: xxx soil_horizon: O horizon -soil_text_measure: - has_raw_value: xxx soil_texture_meth: xxx solar_irradiance: diff --git a/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml b/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml deleted file mode 100644 index 1f599d8377..0000000000 --- a/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml +++ /dev/null @@ -1,563 +0,0 @@ -id: nmdc:bsm-99-dtTMNb -name: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -description: unconstrained text -alternative_identifiers: - - generic:xxx -part_of: - - nmdc:sty-00-987654 - - nmdc:sty-00-qwerty -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -embargoed: true -collected_from: nmdc:frsite-99-1234 -type: nmdc:Biosample. change this to require a class name or an enumeration -img_identifiers: - - img.taxon:abc123 -samp_name: see also name -biosample_categories: - - LTER - - FICUS -gold_biosample_identifiers: - - gold:Gb123456789 - - gold:Gb90909090 -insdc_biosample_identifiers: - - biosample:SAMN123456789 - - biosample:SAMN000 -emsl_biosample_identifiers: - - generic:xxx -igsn_biosample_identifiers: - - any:curie_1 - - any:curie_2 -agrochem_addition: - - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 -alkalinity: - has_raw_value: 50 milligram per liter -alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity -alkyl_diethers: - has_raw_value: 0.005 mole per liter -alt: - has_raw_value: 100 meter -al_sat: - has_raw_value: 0.1 mg/kg -al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 -aminopept_act: - has_raw_value: 0.269 mole per liter per hour -ammonium: - has_raw_value: 1.5 milligram per liter -annual_precpt: - has_raw_value: 0.5 milligram per liter -annual_temp: - has_raw_value: 12.5 degree Celsius -bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour -bishomohopanol: - has_raw_value: 14 microgram per liter -bromide: - has_raw_value: 0.05 parts per million -calcium: - has_raw_value: 0.2 micromole per liter -carb_nitro_ratio: - has_raw_value: "0.417361111" -chem_administration: - - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z -chloride: - has_raw_value: 5000 milligram per liter -chlorophyll: - has_raw_value: 5 milligram per cubic meter -cur_land_use: farmstead -cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" -cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 -crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M -density: - has_raw_value: 1000 kilogram per cubic meter -depth: - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter - has_numeric_value: 2.0 - has_minimum_numeric_value: 1.5 - has_maximum_numeric_value: 2.5 -diss_carb_dioxide: - has_raw_value: 5 milligram per liter -diss_hydrogen: - has_raw_value: 0.3 micromole per liter -diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram -diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter -diss_org_carb: - has_raw_value: 197 micromole per liter -diss_org_nitro: - has_raw_value: 0.05 micromole per liter -diss_oxygen: - has_raw_value: 175 micromole per kilogram -drainage_class: well - -# float() argument must be a string or a number, not 'JsonObj' -elev: 100 - -env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! - -# quoted or unqquoted OK -extreme_event: "2023-01-15" -fao_class: Fluvisols - -fire: 2000-11 to 2000-12 - -flooding: "2000-01-15" - -# quotes required to protect colon in value -geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' - -glucosidase_act: - has_raw_value: 5 mol per liter per hour -heavy_metals: - - has_raw_value: mercury;0.09 micrograms per gram - - has_raw_value: arsenic;0.09 micrograms per gram -heavy_metals_meth: - - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x -lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 -link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ -link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf -link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ -local_class: - has_raw_value: jicama soil -local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 -magnesium: - has_raw_value: 52.8 micromole per kilogram -mean_frict_vel: - has_raw_value: 0.5 meter per second -mean_peak_frict_vel: - has_raw_value: 1 meter per second -misc_param: - - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram -n_alkanes: - - has_raw_value: n-hexadecane;100 milligram per liter -nitrate: - has_raw_value: 65 micromole per liter -nitrite: - has_raw_value: 0.5 micromole per liter -org_matter: - has_raw_value: 1.75 milligram per cubic meter -org_nitro: - has_raw_value: 4 micromole per liter -organism_count: - - has_raw_value: ATP -oxy_stat_samp: aerobic -part_org_carb: - has_raw_value: 1.92 micromole per liter -perturbation: - - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M -petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter -ph: 11.22 -ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf -phaeopigments: - - has_raw_value: 2.5 milligram per cubic meter -phosplipid_fatt_acid: - - has_raw_value: 2.98 milligram per liter -pool_dna_extracts: - has_raw_value: yes, 5 -potassium: - has_raw_value: 463 milligram per liter -pressure: - has_raw_value: 50 atmosphere -profile_position: summit -redox_potential: - has_raw_value: 300 millivolt -salinity: - has_raw_value: 25 practical salinity unit -salinity_meth: - has_raw_value: PMID:22895776 -samp_mat_process: - has_raw_value: filtering of seawater -samp_store_dur: - has_raw_value: P1Y6M -samp_store_loc: - has_raw_value: Freezer no:5 -samp_taxon_id: - has_raw_value: soil metagenome [NCBItaxon:410658] - term: - id: NCBItaxon:410658 - name: soil metagenome -samp_store_temp: - has_raw_value: -80 degree Celsius -samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter -season_temp: - has_raw_value: 18 degree Celsius -season_precpt: - has_raw_value: 75 millimeters -sieving: - has_raw_value: MIxS does not provide an example -size_frac_low: - has_raw_value: 0.2 micrometer -size_frac_up: - has_raw_value: 20 micrometer -slope_gradient: - has_raw_value: MIxS does not provide an example -slope_aspect: - has_raw_value: MIxS does not provide an example -sodium: - has_raw_value: 10.5 milligram per liter -soil_type: - has_raw_value: plinthosol [ENVO:00002250] -soil_type_meth: - has_raw_value: Frederick series -store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D -sulfate: - has_raw_value: 5 micromole per liter -sulfide: - has_raw_value: 2 micromole per liter -temp: - has_raw_value: 25 degree Celsius -tillage: - - chisel -tidal_stage: high tide -tot_carb: - has_raw_value: MIxS does not provide an example -tot_depth_water_col: - has_raw_value: 500 meter -tot_diss_nitro: - has_raw_value: 40 microgram per liter -tot_org_carb: - has_raw_value: 2% -tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf -tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil -tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 -tot_phosp: - has_raw_value: 0.03 milligram per liter -water_content: - - MIxS doesn't provide an example 1 - - MIxS doesn't provide an example 2 -water_cont_soil_meth: MIxS doesn't provide an example -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_type: unconstrained text -ecosystem_subtype: unconstrained text -specific_ecosystem: unconstrained text -add_date: '2021-03-31' -community: no_example_from_mixs -habitat: unconstrained text -host_name: snail is an example value, but unconstrained text is accepted at this point -location: unconstrained text. should we even keep this slot? check if it ahs been - used in MongoDB. -mod_date: "2023-01-25" -ncbi_taxonomy_name: soil metagenome -proport_woa_temperature: no example from MIxS -salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide - this slot any more -sample_collection_site: unconstrained text -soluble_iron_micromol: MIxS doesn't provide an example -subsurface_depth: - has_raw_value: MIxS does not provide an example -air_temp_regm: - - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture -biotic_relationship: parasite -climate_environment: - - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad -gaseous_environment: - - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] -humidity_regm: - - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer -phosphate: - has_raw_value: 0.7 micromole per liter - -samp_collec_method: swabbing -samp_size: - has_raw_value: 5 liters -source_mat_id: - has_raw_value: MPI012345 -watering_regm: - - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -dna_absorb1: 2.02 -dna_absorb2: 2.02 -dna_collect_site: untreated pond water -dna_concentration: 100 -#dna_cont_type: plate -#dna_cont_well: C2 -dna_container_id: Pond_MT_041618 - -# dna_dnase expects a yes or no enumerated string. unquoated yes gets converted into Boolean True, whcih isn't acceptable in this case -dna_dnase: 'yes' - -dna_isolate_meth: phenol/chloroform extraction -dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -dna_project_contact: John Jones -dna_samp_id: "187654" -dna_sample_format: 10 mM Tris-HCl -dna_sample_name: JGI_pond_041618 -dna_seq_project: "1191234" -dna_seq_project_pi: Jane Johnson -dna_seq_project_name: JGI Pond metagenomics -dna_volume: 25 -proposal_dna: "504000" -dnase_rna: 'yes' -proposal_rna: "504000" -rna_absorb1: 2.02 -rna_absorb2: 2.02 -rna_collect_site: untreated pond water -rna_concentration: 100 -rna_cont_type: plate -rna_cont_well: C2 -rna_container_id: Pond_MT_041618 -rna_isolate_meth: phenol/chloroform extraction -rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -rna_project_contact: John Jones -rna_samp_id: "187654" -rna_sample_format: 10 mM Tris-HCl -rna_sample_name: JGI_pond_041618 -rna_seq_project: "1191234" -rna_seq_project_pi: Jane Johnson -rna_seq_project_name: JGI Pond metagenomics -rna_volume: 25 -collection_date_inc: "2023-01-29" -collection_time: 05:42+0000 -collection_time_inc: 13:42+0000 -experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' -filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point -isotope_exposure: 13C glucose -micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -microbial_biomass_c: 0.05 ug C/g dry soil -microbial_biomass_n: 0.05 ug N/g dry soil -non_microb_biomass: insect 0.23 ug; plant 1g -non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 -org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 -other_treatment: unconstrained text -start_date_inc: "2023-01-27" -start_time_inc: "13:42+0000" -project_id: no example from MIxS -replicate_number: "1" -sample_shipped: 15 g -sample_type: soil - water extract -technical_reps: "2" -analysis_type: - - metabolomics - - metagenomics -sample_link: - - IGSN:DSJ0284 - - any:curie -zinc: - has_raw_value: 2.5 mg/kg -manganese: - has_raw_value: 24.7 mg/kg -ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter -nitrate_nitrogen: - has_raw_value: 0.29 mg/kg -nitrite_nitrogen: - has_raw_value: 1.2 mg/kg -lbc_thirty: - has_raw_value: 543 mg/kg -lbceq: - has_raw_value: 1575 mg/kg -host_taxid: - has_raw_value: "NCBITaxon:9606" - term: - id: NCBITaxon:9606 - -# abs_air_humidity: -# has_raw_value: xyz -# antibiotic_regm: -# - xyz -# aromatics_pc: xyz -# asphaltenes_pc: xyz -# atmospheric_data: -# - xyz -# avg_occup: 50 -# bathroom_count: 50 -# bedroom_count: 50 -# biocide_admin_method: xyz -# biomass: -# - xyz -# chem_mutagen: -# - xyz -# chem_treat_method: xyz - -collection_date: - has_raw_value: "2018-05-11" - -# cool_syst_id: 50 -# date_last_rain: -# has_raw_value: '2018-05-11' -# diether_lipids: -# - xyz -# elevator: 50 -# emsl_store_temp: xyz -# emulsions: -# - xyz -# escalator: 50 -# exp_pipe: -# has_raw_value: xyz -# ext_door: 50 -# fertilizer_regm: -# - xyz -# floor_count: 50 -# freq_clean: -# has_raw_value: xyz -# freq_cook: -# has_raw_value: xyz -# fungicide_regm: -# - xyz -# gaseous_substances: -# - xyz -# gravity: -# - xyz -# growth_hormone_regm: -# - xyz -# hall_count: 50 -# hcr_pressure: high -# hcr_temp: high -# heat_sys_deliv_meth: xyz -# heat_system_id: 50 -# herbicide_regm: -# - xyz -# host_body_product: -# has_raw_value: xyz -# host_body_site: -# has_raw_value: xyz -# host_family_relation: -# - xyz -# host_phenotype: -# has_raw_value: xyz -# host_subspecf_genlin: -# - xyz -# host_symbiont: -# - xyz -# inorg_particles: -# - xyz -# iw_bt_date_well: -# has_raw_value: xyz -# last_clean: -# has_raw_value: xyz -# max_occup: -# has_raw_value: xyz -# mineral_nutr_regm: -# - xyz -# non_min_nutr_regm: -# - xyz -# number_pets: -# has_raw_value: xyz -# number_plants: -# has_raw_value: xyz -# number_resident: -# has_raw_value: xyz -# occup_density_samp: -# has_raw_value: xyz -# occup_samp: -# has_raw_value: xyz -# org_count_qpcr_info: xyz -# org_particles: -# - xyz -# particle_class: -# - xyz -# permeability: xyz -# pesticide_regm: -# - xyz -# plant_growth_med: -# has_raw_value: xyz -# plant_struc: -# has_raw_value: xyz -# pollutants: -# - xyz -# porosity: xyz -# pres_animal_insect: dog;9 -# prev_land_use_meth: xyz -# prod_start_date: -# has_raw_value: xyz -# radiation_regm: -# - xyz -# rainfall_regm: -# - xyz -# rel_to_oxygen: microaerophilic -# resins_pc: xyz -# room_architec_elem: xyz -# room_count: 50 -# room_dim: xyz -# room_door_dist: xyz -# room_net_area: xyz -# room_occup: -# has_raw_value: xyz -# room_vol: xyz -# root_med_carbon: xyz -# root_med_macronutr: xyz -# root_med_micronutr: xyz -# root_med_ph: -# has_raw_value: xyz -# root_med_regl: xyz -# root_med_suppl: xyz -# salt_regm: -# - xyz -# samp_collec_device: xyz -# samp_loc_corr_rate: xyz -# samp_md: -# has_raw_value: xyz -# samp_preserv: xyz -# samp_room_id: 50 -# samp_time_out: 50 -# samp_transport_cond: xyz -# samp_tvdss: xyz -# saturates_pc: xyz -# shad_dev_water_mold: xyz -# size_frac: xyz -# soil_texture_meth: xyz -# soluble_inorg_mat: -# - xyz -# soluble_org_mat: -# - xyz -# suspend_solids: -# - xyz -# viscosity: xyz -# volatile_org_comp: -# - xyz -# water_temp_regm: -# - xyz -# window_open_freq: 50 -# window_size: xyz - diff --git a/src/data/valid/Database-biosample-exhasutive.yaml b/src/data/valid/Database-biosample-exhasutive.yaml deleted file mode 100644 index 0b333b1e96..0000000000 --- a/src/data/valid/Database-biosample-exhasutive.yaml +++ /dev/null @@ -1,1083 +0,0 @@ -biosample_set: - - abs_air_humidity: - has_raw_value: xxx - add_date: '2021-03-31' - add_recov_method: - has_raw_value: xxx - additional_info: - has_raw_value: xxx - address: - has_raw_value: xxx - adj_room: - has_raw_value: xxx - aero_struc: - has_raw_value: xxx - agrochem_addition: - - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 - air_PM_concen: - - has_raw_value: xxx - air_temp: - has_raw_value: xxx - air_temp_regm: - - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - al_sat: - has_raw_value: 0.1 mg/kg - al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 - alkalinity: - has_raw_value: 50 milligram per liter - alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity - alkyl_diethers: - has_raw_value: 0.005 mole per liter - alt: - has_raw_value: 100 meter - alternative_identifiers: - - generic:xxx - aminopept_act: - has_raw_value: 0.269 mole per liter per hour - ammonium: - has_raw_value: 1.5 milligram per liter - ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter - amount_light: - has_raw_value: xxx - analysis_type: - - metabolomics - - metagenomics - ances_data: - has_raw_value: xxx - annual_precpt: - has_raw_value: 0.5 milligram per liter - annual_temp: - has_raw_value: 12.5 degree Celsius - antibiotic_regm: - - has_raw_value: xxx - api: - has_raw_value: xxx - arch_struc: building - aromatics_pc: - has_raw_value: xxx - asphaltenes_pc: - has_raw_value: xxx - atmospheric_data: - - has_raw_value: xxx - avg_dew_point: - has_raw_value: xxx - avg_occup: - has_raw_value: xxx - avg_temp: - has_raw_value: xxx - bac_prod: - has_raw_value: xxx - bac_resp: - has_raw_value: xxx - bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour - barometric_press: - has_raw_value: xxx - basin: - has_raw_value: xxx - bathroom_count: - has_raw_value: xxx - bedroom_count: - has_raw_value: xxx - benzene: - has_raw_value: xxx - biochem_oxygen_dem: - has_raw_value: xxx - biocide: - has_raw_value: xxx - biocide_admin_method: - has_raw_value: xxx - biol_stat: wild - biomass: - - has_raw_value: xxx - biosample_categories: - - LTER - - FICUS - biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture - biotic_relationship: parasite - bishomohopanol: - has_raw_value: 14 microgram per liter - blood_press_diast: - has_raw_value: xxx - blood_press_syst: - has_raw_value: xxx - bromide: - has_raw_value: 0.05 parts per million - build_docs: building information model - build_occup_type: - - office - building_setting: urban - built_struc_age: - has_raw_value: xxx - built_struc_set: - has_raw_value: xxx - built_struc_type: - has_raw_value: xxx - calcium: - has_raw_value: 0.2 micromole per liter - carb_dioxide: - has_raw_value: xxx - carb_monoxide: - has_raw_value: xxx - carb_nitro_ratio: - has_raw_value: '0.417361111' - ceil_area: - has_raw_value: xxx - ceil_cond: new - ceil_finish_mat: drywall - ceil_struc: - has_raw_value: xxx - ceil_texture: crows feet - ceil_thermal_mass: - has_raw_value: xxx - ceil_type: cathedral - ceil_water_mold: - has_raw_value: xxx - chem_administration: - - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z - chem_mutagen: - - has_raw_value: xxx - chem_oxygen_dem: - has_raw_value: xxx - chem_treat_method: xxx - chem_treatment: - has_raw_value: xxx - chimera_check: - has_raw_value: xxx - chloride: - has_raw_value: 5000 milligram per liter - chlorophyll: - has_raw_value: 5 milligram per cubic meter - climate_environment: - - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - collected_from: nmdc:frsite-99-1234 - collection_date: - has_raw_value: xxx - collection_date_inc: '2023-01-29' - collection_time: 05:42+0000 - collection_time_inc: 13:42+0000 - community: no_example_from_mixs - conduc: - has_raw_value: xxx - cool_syst_id: - has_raw_value: xxx - crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M - cult_root_med: - has_raw_value: xxx - cur_land_use: farmstead - cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" - cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 - date_last_rain: - has_raw_value: xxx - density: - has_raw_value: 1000 kilogram per cubic meter - depos_env: other - depth: - has_maximum_numeric_value: 2.5 - has_minimum_numeric_value: 1.5 - has_numeric_value: 2.0 - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter - description: unconstrained text - dew_point: - has_raw_value: xxx - diether_lipids: - - has_raw_value: xxx - diss_carb_dioxide: - has_raw_value: 5 milligram per liter - diss_hydrogen: - has_raw_value: 0.3 micromole per liter - diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram - diss_inorg_nitro: - has_raw_value: xxx - diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter - diss_iron: - has_raw_value: xxx - diss_org_carb: - has_raw_value: 197 micromole per liter - diss_org_nitro: - has_raw_value: 0.05 micromole per liter - diss_oxygen: - has_raw_value: 175 micromole per kilogram - diss_oxygen_fluid: - has_raw_value: xxx - - drainage_class: well - elev: 100 - - extreme_event: '2023-01-15' - fao_class: Fluvisols - fire: 2000-11 to 2000-12 - flooding: '2000-01-15' - - link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ - link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf - link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ - local_class: - has_raw_value: jicama soil - local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 - magnesium: - has_raw_value: 52.8 micromole per kilogram - mean_frict_vel: - has_raw_value: 0.5 meter per second - mean_peak_frict_vel: - has_raw_value: 1 meter per second - misc_param: - - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram - n_alkanes: - - has_raw_value: n-hexadecane;100 milligram per liter - nitrate: - has_raw_value: 65 micromole per liter - nitrite: - has_raw_value: 0.5 micromole per liter - org_matter: - has_raw_value: 1.75 milligram per cubic meter - org_nitro: - has_raw_value: 4 micromole per liter - organism_count: - - has_raw_value: ATP - oxy_stat_samp: aerobic - part_org_carb: - has_raw_value: 1.92 micromole per liter - perturbation: - - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M - petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter - ph: 99.99 - ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf - phaeopigments: - - has_raw_value: 2.5 milligram per cubic meter - phosplipid_fatt_acid: - - has_raw_value: 2.98 milligram per liter - pool_dna_extracts: - has_raw_value: yes, 5 - potassium: - has_raw_value: 463 milligram per liter - pressure: - has_raw_value: 50 atmosphere - profile_position: summit - redox_potential: - has_raw_value: 300 millivolt - salinity: - has_raw_value: 25 practical salinity unit - salinity_meth: - has_raw_value: PMID:22895776 - samp_mat_process: - has_raw_value: filtering of seawater - samp_store_dur: - has_raw_value: P1Y6M - samp_store_loc: - has_raw_value: Freezer no:5 - samp_taxon_id: - has_raw_value: soil metagenome [NCBItaxon:410658] - term: - id: NCBItaxon:410658 - name: soil metagenome - samp_store_temp: - has_raw_value: -80 degree Celsius - samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter - season_temp: - has_raw_value: 18 degree Celsius - season_precpt: - has_raw_value: 75 millimeters - sieving: - has_raw_value: MIxS does not provide an example - size_frac_low: - has_raw_value: 0.2 micrometer - size_frac_up: - has_raw_value: 20 micrometer - slope_gradient: - has_raw_value: MIxS does not provide an example - slope_aspect: - has_raw_value: MIxS does not provide an example - sodium: - has_raw_value: 10.5 milligram per liter - soil_type: - has_raw_value: plinthosol [ENVO:00002250] - soil_type_meth: - has_raw_value: Frederick series - store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D - sulfate: - has_raw_value: 5 micromole per liter - sulfide: - has_raw_value: 2 micromole per liter - temp: - has_raw_value: 25 degree Celsius - tillage: - - chisel - tidal_stage: high tide - tot_carb: - has_raw_value: MIxS does not provide an example - tot_depth_water_col: - has_raw_value: 500 meter - tot_diss_nitro: - has_raw_value: 40 microgram per liter - tot_org_carb: - has_raw_value: 2% - tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf - tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil - #tot_nitro_cont_meth: - # has_raw_value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 - tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 - tot_phosp: - has_raw_value: 0.03 milligram per liter - - ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads - ecosystem_category: unconstrained text - ecosystem_type: unconstrained text - ecosystem_subtype: unconstrained text - specific_ecosystem: unconstrained text - - habitat: unconstrained text - host_name: snail is an example value, but unconstrained text is accepted at this point - location: unconstrained text. should we even keep this slot? check if it has been - used in MongoDB. - mod_date: '2023-01-25' - ncbi_taxonomy_name: soil metagenome - proport_woa_temperature: no example from MIxS - salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide - this slot any more - sample_collection_site: unconstrained text - soluble_iron_micromol: MIxS doesn't provide an example - subsurface_depth: - has_raw_value: MIxS does not provide an example - - experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad - gaseous_environment: - - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] - humidity_regm: - - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer - phosphate: - has_raw_value: 0.7 micromole per liter - #samp_collec_method: - # has_raw_value: swabbing - samp_collec_method: swabbing - samp_size: - has_raw_value: 5 liters - source_mat_id: - has_raw_value: MPI012345 - - dna_absorb1: 2.02 - dna_absorb2: 2.02 - dna_collect_site: untreated pond water - dna_concentration: 100 - #dna_cont_type: plate - #dna_cont_well: C2 - dna_container_id: Pond_MT_041618 - dna_dnase: 'yes' - dna_isolate_meth: phenol/chloroform extraction - dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - dna_project_contact: John Jones - dna_samp_id: '187654' - dna_sample_format: 10 mM Tris-HCl - dna_sample_name: JGI_pond_041618 - dna_seq_project: '1191234' - dna_seq_project_name: JGI Pond metagenomics - dna_seq_project_pi: Jane Johnson - dna_volume: 25 - dnase_rna: 'yes' - door_comp_type: revolving - door_cond: damaged - door_direct: inward - door_loc: north - door_mat: aluminum - door_move: collapsible - door_size: - has_raw_value: xxx - door_type: composite - door_type_metal: collapsible - door_type_wood: battened - door_water_mold: - has_raw_value: xxx - down_par: - has_raw_value: xxx - - drawings: operation - - efficiency_percent: - has_raw_value: xxx - - elevator: - has_raw_value: xxx - embargoed: true - emsl_biosample_identifiers: - - generic:xxx - emulsions: - - has_raw_value: xxx - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! - escalator: - has_raw_value: xxx - ethylbenzene: - has_raw_value: xxx - exp_duct: - has_raw_value: xxx - exp_pipe: - has_raw_value: xxx - - experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' - ext_door: - has_raw_value: xxx - ext_wall_orient: north - ext_window_orient: north - - fertilizer_regm: - - has_raw_value: xxx - field: - has_raw_value: xxx - filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point - filter_type: - - HEPA - fireplace_type: - has_raw_value: xxx - - floor_age: - has_raw_value: xxx - floor_area: - has_raw_value: xxx - floor_cond: new - floor_count: - has_raw_value: xxx - floor_finish_mat: tile - floor_struc: balcony - floor_thermal_mass: - has_raw_value: xxx - floor_water_mold: condensation - fluor: - has_raw_value: xxx - freq_clean: - has_raw_value: xxx - freq_cook: - has_raw_value: xxx - fungicide_regm: - - has_raw_value: xxx - furniture: cabinet - - gaseous_substances: - - has_raw_value: xxx - gender_restroom: female - genetic_mod: - has_raw_value: xxx - geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' - glucosidase_act: - has_raw_value: 5 mol per liter per hour - gold_biosample_identifiers: - - gold:Gb123456789 - - gold:Gb90909090 - gravidity: - has_raw_value: xxx - gravity: - - has_raw_value: xxx - - growth_habit: erect - growth_hormone_regm: - - has_raw_value: xxx - - hall_count: - has_raw_value: xxx - handidness: ambidexterity - hc_produced: Oil - hcr: Shale - hcr_fw_salinity: - has_raw_value: xxx - hcr_geol_age: Archean - hcr_pressure: - has_raw_value: xxx - hcr_temp: - has_raw_value: xxx - heat_cool_type: - - radiant system - heat_deliv_loc: north - heat_sys_deliv_meth: xxx - heat_system_id: - has_raw_value: xxx - heavy_metals: - - has_raw_value: mercury;0.09 micrograms per gram - - has_raw_value: arsenic;0.09 micrograms per gram - heavy_metals_meth: - - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x - height_carper_fiber: - has_raw_value: xxx - herbicide_regm: - - has_raw_value: xxx - horizon_meth: - has_raw_value: xxx - host_age: - has_raw_value: xxx - host_body_habitat: - has_raw_value: xxx - host_body_product: - has_raw_value: xxx - host_body_site: - has_raw_value: xxx - host_body_temp: - has_raw_value: xxx - host_color: - has_raw_value: xxx - host_common_name: - has_raw_value: xxx - host_diet: - - has_raw_value: xxx - host_dry_mass: - has_raw_value: xxx - host_family_relation: - - xxx - host_genotype: - has_raw_value: xxx - host_growth_cond: - has_raw_value: xxx - host_height: - has_raw_value: xxx - host_last_meal: - - has_raw_value: xxx - host_length: - has_raw_value: xxx - host_life_stage: - has_raw_value: xxx - - host_phenotype: - has_raw_value: xxx - host_sex: female - host_shape: - has_raw_value: xxx - host_subject_id: - has_raw_value: xxx - host_subspecf_genlin: - - xxx - host_substrate: - has_raw_value: xxx - host_symbiont: - - xxx - host_tot_mass: - has_raw_value: xxx - host_wet_mass: - has_raw_value: xxx - humidity: - has_raw_value: xxx - - id: nmdc:bsm-99-dtTMNb - igsn_biosample_identifiers: - - any:curie_1 - - any:curie_2 - img_identifiers: - - img.taxon:abc123 - indoor_space: bedroom - indoor_surf: cabinet - indust_eff_percent: - has_raw_value: xxx - inorg_particles: - - has_raw_value: xxx - insdc_biosample_identifiers: - - biosample:SAMN123456789 - - biosample:SAMN000 - inside_lux: - has_raw_value: xxx - int_wall_cond: new - isotope_exposure: 13C glucose - iw_bt_date_well: - has_raw_value: xxx - iwf: - has_raw_value: xxx - last_clean: - has_raw_value: xxx - lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 - lbc_thirty: - has_raw_value: 543 mg/kg - lbceq: - has_raw_value: 1575 mg/kg - light_intensity: - has_raw_value: xxx - - light_type: - - none - - lithology: Basement - - manganese: - has_raw_value: 24.7 mg/kg - max_occup: - has_raw_value: xxx - - mech_struc: subway - mechanical_damage: - - has_raw_value: xxx - methane: - has_raw_value: xxx - micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 - micro_biomass_meth: xxx - micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 - microbial_biomass: - has_raw_value: xxx - microbial_biomass_c: 0.05 ug C/g dry soil - microbial_biomass_n: 0.05 ug N/g dry soil - mineral_nutr_regm: - - has_raw_value: xxx - - name: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. - - nitrite_nitrogen: - has_raw_value: 1.2 mg/kg - nitro: - has_raw_value: xxx - non_microb_biomass: insect 0.23 ug; plant 1g - non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 - non_min_nutr_regm: - - xxx - nucl_acid_amp: - has_raw_value: xxx - nucl_acid_ext: - has_raw_value: xxx - number_pets: - has_raw_value: xxx - number_plants: - has_raw_value: xxx - number_resident: - has_raw_value: xxx - occup_density_samp: - has_raw_value: xxx - occup_document: estimate - occup_samp: - has_raw_value: xxx - org_carb: - has_raw_value: xxx - org_count_qpcr_info: xxx - - org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 - org_particles: - - has_raw_value: xxx - other_treatment: unconstrained text - owc_tvdss: - has_raw_value: xxx - oxygen: - has_raw_value: xxx - part_of: - - nmdc:sty-00-987654 - - nmdc:sty-00-qwerty - part_org_nitro: - has_raw_value: xxx - particle_class: - - has_raw_value: xxx - pcr_cond: - has_raw_value: xxx - pcr_primers: - has_raw_value: xxx - permeability: - has_raw_value: xxx - - pesticide_regm: - - has_raw_value: xxx - - - ph_regm: - - has_raw_value: xxx - - photon_flux: - has_raw_value: xxx - plant_growth_med: - has_raw_value: xxx - plant_product: - has_raw_value: xxx - plant_sex: Androdioecious - plant_struc: - has_raw_value: xxx - pollutants: - - has_raw_value: xxx - - porosity: - has_raw_value: xxx - - pour_point: - has_raw_value: xxx - pre_treatment: - has_raw_value: xxx - pres_animal_insect: cat;3 - - prev_land_use_meth: xxx - previous_land_use: - has_raw_value: xxx - primary_prod: - has_raw_value: xxx - primary_treatment: - has_raw_value: xxx - prod_rate: - has_raw_value: xxx - prod_start_date: - has_raw_value: xxx - - project_id: no example from MIxS - - proposal_dna: '504000' - proposal_rna: '504000' - quad_pos: North side - radiation_regm: - - has_raw_value: xxx - rainfall_regm: - - has_raw_value: xxx - reactor_type: - has_raw_value: xxx - - rel_air_humidity: - has_raw_value: xxx - rel_humidity_out: - has_raw_value: xxx - rel_samp_loc: edge of car - # rel_to_oxygen: aerobe - replicate_number: '1' - reservoir: - has_raw_value: xxx - resins_pc: - has_raw_value: xxx - rna_absorb1: 2.02 - rna_absorb2: 2.02 - rna_collect_site: untreated pond water - rna_concentration: 100 - #rna_cont_type: plate - #rna_cont_well: C2 - rna_container_id: Pond_MT_041618 - rna_isolate_meth: phenol/chloroform extraction - rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - rna_project_contact: John Jones - rna_samp_id: '187654' - rna_sample_format: 10 mM Tris-HCl - rna_sample_name: JGI_pond_041618 - rna_seq_project: '1191234' - rna_seq_project_name: JGI Pond metagenomics - rna_seq_project_pi: Jane Johnson - rna_volume: 25 - room_air_exch_rate: - has_raw_value: xxx - room_architec_elem: xxx - room_condt: new - room_connected: attic - room_count: - has_raw_value: xxx - room_dim: - has_raw_value: xxx - room_door_dist: - has_raw_value: xxx - room_door_share: - has_raw_value: xxx - room_hallway: - has_raw_value: xxx - room_loc: corner room - room_moist_dam_hist: 123 - room_net_area: - has_raw_value: xxx - room_occup: - has_raw_value: xxx - room_samp_pos: north corner - room_type: attic - room_vol: - has_raw_value: xxx - room_wall_share: - has_raw_value: xxx - room_window_count: 123 - root_cond: - has_raw_value: xxx - root_med_carbon: - has_raw_value: xxx - root_med_macronutr: - has_raw_value: xxx - root_med_micronutr: - has_raw_value: xxx - root_med_ph: - has_raw_value: xxx - root_med_regl: - has_raw_value: xxx - root_med_solid: - has_raw_value: xxx - root_med_suppl: - has_raw_value: xxx - - salt_regm: - - has_raw_value: xxx - samp_capt_status: other - samp_collec_device: xxx - - samp_collect_point: well - samp_dis_stage: dissemination - samp_floor: basement - samp_loc_corr_rate: - has_raw_value: xxx - - samp_md: - has_raw_value: xxx - samp_name: see also name - samp_preserv: - has_raw_value: xxx - samp_room_id: - has_raw_value: xxx - - samp_sort_meth: - - has_raw_value: xxx - - samp_subtype: biofilm - - samp_time_out: - has_raw_value: xxx - samp_transport_cond: - has_raw_value: xxx - samp_tvdss: - has_raw_value: xxx - samp_type: - has_raw_value: xxx - - samp_weather: cloudy - samp_well_name: - has_raw_value: xxx - - sample_link: - - IGSN:DSJ0284 - - any:curie - sample_shipped: 15 g - sample_type: soil - water extract - saturates_pc: - has_raw_value: xxx - season: - has_raw_value: xxx - season_environment: - - has_raw_value: xxx - - season_use: Spring - secondary_treatment: - has_raw_value: xxx - sediment_type: biogenous - seq_meth: - has_raw_value: xxx - seq_quality_check: - has_raw_value: xxx - sewage_type: - has_raw_value: xxx - shad_dev_water_mold: xxx - shading_device_cond: damaged - shading_device_loc: - has_raw_value: xxx - shading_device_mat: - has_raw_value: xxx - shading_device_type: tree - - silicate: - has_raw_value: xxx - size_frac: - has_raw_value: xxx - - sludge_retent_time: - has_raw_value: xxx - - soil_horizon: O horizon - soil_text_measure: - has_raw_value: xxx - soil_texture_meth: xxx - - solar_irradiance: - has_raw_value: xxx - soluble_inorg_mat: - - has_raw_value: xxx - - soluble_org_mat: - - has_raw_value: xxx - soluble_react_phosp: - has_raw_value: xxx - - space_typ_state: - has_raw_value: xxx - specific: operation - specific_humidity: - has_raw_value: xxx - sr_dep_env: Lacustine - sr_geol_age: Archean - sr_kerog_type: other - sr_lithology: Clastic - standing_water_regm: - - has_raw_value: xxx - start_date_inc: '2023-01-27' - start_time_inc: 13:42+0000 - - substructure_type: - - basement - - sulfate_fw: - has_raw_value: xxx - - surf_air_cont: - - dust - surf_humidity: - has_raw_value: xxx - surf_material: adobe - surf_moisture: - has_raw_value: xxx - surf_moisture_ph: 123 - surf_temp: - has_raw_value: xxx - suspend_part_matter: - has_raw_value: xxx - suspend_solids: - - has_raw_value: xxx - tan: - has_raw_value: xxx - target_gene: - has_raw_value: xxx - target_subfragment: - has_raw_value: xxx - technical_reps: '2' - - temp_out: - has_raw_value: xxx - tertiary_treatment: - has_raw_value: xxx - - tiss_cult_growth_med: - has_raw_value: xxx - toluene: - has_raw_value: xxx - - tot_inorg_nitro: - has_raw_value: xxx - tot_iron: - has_raw_value: xxx - tot_nitro: - has_raw_value: xxx - - tot_part_carb: - has_raw_value: xxx - - tot_phosphate: - has_raw_value: xxx - tot_sulfur: - has_raw_value: xxx - train_line: red - train_stat_loc: south station above ground - train_stop_loc: end - turbidity: - has_raw_value: xxx - tvdss_of_hcr_press: - has_raw_value: xxx - tvdss_of_hcr_temp: - has_raw_value: xxx - typ_occup_density: 123 - type: nmdc:Biosample. change this to require a class name or an enumeration - ventilation_rate: - has_raw_value: xxx - ventilation_type: - has_raw_value: xxx - vfa: - has_raw_value: xxx - vfa_fw: - has_raw_value: xxx - vis_media: photos - viscosity: - has_raw_value: xxx - volatile_org_comp: - - has_raw_value: xxx - wall_area: - has_raw_value: xxx - wall_const_type: frame construction - wall_finish_mat: plaster - wall_height: - has_raw_value: xxx - wall_loc: north - wall_surf_treatment: painted - wall_texture: knockdown - wall_thermal_mass: - has_raw_value: xxx - wall_water_mold: - has_raw_value: xxx - wastewater_type: - has_raw_value: xxx - water_cont_soil_meth: MIxS doesn't provide an example - water_content: - - MIxS doesn't provide an example 1 - - MIxS doesn't provide an example 2 - water_current: - has_raw_value: xxx - water_cut: - has_raw_value: xxx - water_feat_size: - has_raw_value: xxx - water_feat_type: fountain - water_prod_rate: - has_raw_value: xxx - water_temp_regm: - - has_raw_value: xxx - watering_regm: - - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - weekday: Monday - win: - has_raw_value: xxx - wind_direction: - has_raw_value: xxx - wind_speed: - has_raw_value: xxx - window_cond: damaged - window_cover: blinds - window_horiz_pos: left - window_loc: north - window_mat: fiberglass - window_open_freq: - has_raw_value: xxx - window_size: - has_raw_value: xxx - window_status: - has_raw_value: xxx - window_type: single-hung sash window - window_vert_pos: bottom - window_water_mold: - has_raw_value: xxx - xylene: - has_raw_value: xxx - zinc: - has_raw_value: 2.5 mg/kg - host_taxid: - has_raw_value: "NCBITaxon:9606" - term: - id: NCBITaxon:9606 - diff --git a/src/schema/core.yaml b/src/schema/core.yaml index f13520ca50..bcb8fa1608 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -28,12 +28,6 @@ default_prefix: nmdc default_range: string -subsets: - environment: { } - investigation: { } - nucleic acid sequence source: { } - sequencing: { } - types: bytes: diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index a9b59f1bd8..9553939f51 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -17,50 +17,45 @@ prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ - MIXS_yaml: - prefix_prefix: MIXS_yaml - prefix_reference: https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/ + xsd: + prefix_prefix: xsd + prefix_reference: http://www.w3.org/2001/XMLSchema# + shex: + prefix_prefix: shex + prefix_reference: http://www.w3.org/ns/shex# + schema: + prefix_prefix: schema + prefix_reference: http://schema.org/ default_prefix: MIXS -subsets: - mixs_environmental_triad: - title: MIxS Environmental Triad - mixs extension: {} - checklist: - description: A MIxS checklist. These can be combined with packages - from_schema: http://w3id.org/mixs/terms - package: - description: A MIxS package. These can be combined with checklists - from_schema: http://w3id.org/mixs/terms - checklist_package_combination: - description: A combination of a checklist and a package - from_schema: http://w3id.org/mixs/terms enums: - arch_struc_enum: - from_schema: http://w3id.org/mixs/terms + AERO_STRUC_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + glider: {} + plane: {} + ARCH_STRUC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: building: {} - shed: {} home: {} - biol_stat_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - wild: {} - natural: {} - semi-natural: {} - inbred line: {} - breeder's line: {} - hybrid: {} - clonal selection: {} - mutant: {} - biotic_relationship_enum: - from_schema: http://w3id.org/mixs/terms + shed: {} + BIOTIC_RELATIONSHIP_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + commensalism: {} free living: {} - parasite: {} - commensal: {} - symbiont: {} - build_docs_enum: - from_schema: http://w3id.org/mixs/terms + mutualism: {} + parasitism: {} + symbiotic: {} + BUILDING_SETTING_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + exurban: {} + rural: {} + suburban: {} + urban: {} + BUILD_DOCS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: building information model: {} commissioning report: {} @@ -75,251 +70,89 @@ enums: submittals: {} ventilation system: {} windows: {} - build_occup_type_enum: - from_schema: http://w3id.org/mixs/terms + BUILD_OCCUP_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - office: {} + airport: {} + commercial: {} + health care: {} + high rise: {} + low rise: {} market: {} - restaurant: {} + office: {} residence: {} - school: {} residential: {} - commercial: {} - low rise: {} - high rise: {} - wood framed: {} - health care: {} - airport: {} + restaurant: {} + school: {} sports complex: {} - building_setting_enum: - from_schema: http://w3id.org/mixs/terms + wood framed: {} + BUILT_STRUC_SET_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - urban: {} - suburban: {} - exurban: {} rural: {} - ceil_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - ceil_finish_mat_enum: - from_schema: http://w3id.org/mixs/terms + urban: {} + CEIL_FINISH_MAT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + PVC: {} drywall: {} + fiberglass: {} + metal: {} mineral fibre: {} - tiles: {} - PVC: {} + mineral wool/calcium silicate: {} plasterboard: {} - metal: {} - fiberglass: {} stucco: {} - mineral wool/calcium silicate: {} + tiles: {} wood: {} - ceil_texture_enum: - from_schema: http://w3id.org/mixs/terms + CEIL_STRUC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - crows feet: {} - crows-foot stomp: {} - double skip: {} - hawk and trowel: {} - knockdown: {} - popcorn: {} - orange peel: {} - rosebud stomp: {} - Santa-Fe texture: {} - skip trowel: {} - smooth: {} - stomp knockdown: {} - swirl: {} - ceil_type_enum: - from_schema: http://w3id.org/mixs/terms + concrete: {} + wood frame: {} + CEIL_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - cathedral: {} - dropped: {} - concave: {} barrel-shaped: {} + cathedral: {} coffered: {} + concave: {} cove: {} + dropped: {} stretched: {} - cur_land_use_enum: - from_schema: http://w3id.org/mixs/terms + DEPOS_ENV_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - badlands: {} - cities: {} - conifers: - annotations: - originally: conifers (e.g. pine,spruce,fir,cypress) - examples: - - value: cypress - - value: fir - - value: pine - - value: spruce - crop trees: - annotations: - originally: crop trees (nuts,fruit,christmas trees,nursery trees) - examples: - - value: christmas trees - - value: fruit - - value: nursery trees - - value: nuts - farmstead: {} - gravel: {} - hardwoods: - annotations: - originally: hardwoods (e.g. oak,hickory,elm,aspen) - examples: - - value: aspen - - value: elm - - value: hickory - - value: oak - hayland: {} - horticultural plants: - annotations: - originally: horticultural plants (e.g. tulips) - examples: - - value: tulips - industrial areas: {} - intermixed hardwood and conifers: {} - marshlands: - annotations: - originally: marshlands (grass,sedges,rushes) - examples: - - value: grass - - value: rushes - - value: sedgees - meadows: - annotations: - originally: meadows (grasses,alfalfa,fescue,bromegrass,timothy) - examples: - - value: alfalfa - - value: bromegrass - - value: fescue - - value: grasses - - value: timothy - mines/quarries: {} - mudflats: {} - oil waste areas: {} - pastureland: - annotations: - originally: pastureland (grasslands used for livestock grazing) - comments: - - grasslands used for livestock grazing - permanent snow or ice: {} - rainforest: - annotations: - originally: rainforest (evergreen forest receiving greater than 406 cm annual rainfall) - comments: - - evergreen forest receiving greater than 406 cm annual rainfall - rangeland: {} - roads/railroads: {} - rock: {} - row crops: {} - saline seeps: {} - salt flats: {} - sand: {} - shrub crops: - annotations: - originally: shrub crops (blueberries,nursery ornamentals,filberts) - examples: - - value: blueberries - - value: filberts - - value: nursery ornamentals - shrub land: - annotations: - originally: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus) - examples: - - value: creosote bush - - value: eucalyptus - - value: mesquite - - value: sage-brush - - value: shrub oak - small grains: {} - successional shrub land: - annotations: - originally: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries) - examples: - - value: blackberries - - value: chokecherry - - value: hazels - - value: shrub dogwoods - - value: sumacs - - value: tree saplings - swamp: - annotations: - originally: swamp (permanent or semi-permanent water body dominated by woody plants) - comments: - - permanent or semi-permanent water body dominated by woody plants - tropical: - annotations: - originally: tropical (e.g. mangrove,palms) - examples: - - value: mangrove - - value: palms - tundra: - annotations: - originally: tundra (mosses,lichens) - examples: - - value: lichens - - value: mosses - vegetable crops: {} - vine crops: - annotations: - originally: vine crops (grapes) - examples: - - value: grapes - depos_env_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Continental - Alluvial: {} Continental - Aeolian: {} + Continental - Alluvial: {} Continental - Fluvial: {} Continental - Lacustrine: {} - Transitional - Deltaic: {} - Transitional - Tidal: {} - Transitional - Lagoonal: {} - Transitional - Beach: {} - Transitional - Lake: {} - Marine - Shallow: {} Marine - Deep: {} Marine - Reef: {} + Marine - Shallow: {} Other - Evaporite: {} Other - Glacial: {} Other - Volcanic: {} + Transitional - Beach: {} + Transitional - Deltaic: {} + Transitional - Lagoonal: {} + Transitional - Lake: {} + Transitional - Tidal: {} other: {} - door_comp_type_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_COMP_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: metal covered: {} revolving: {} sliding: {} telescopic: {} - door_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - door_direct_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_DIRECT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: inward: {} outward: {} sideways: {} - door_loc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - door_mat_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_MAT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: aluminum: {} cellular PVC: {} @@ -331,8 +164,8 @@ enums: vinyl: {} wood: {} wood/plastic composite: {} - door_move_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_MOVE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: collapsible: {} folding: {} @@ -340,77 +173,42 @@ enums: rolling shutter: {} sliding: {} swinging: {} - door_type_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: composite: {} metal: {} wooden: {} - door_type_metal_enum: - from_schema: http://w3id.org/mixs/terms + DOOR_TYPE_METAL_ENUM: + from_schema: https://w3id.org/mixs permissible_values: collapsible: {} corrugated steel: {} hollow: {} rolling shutters: {} steel plate: {} - door_type_wood_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - bettened and ledged: {} - battened: {} - ledged and braced: {} - ledged and framed: {} - ledged, braced and frame: {} - framed and paneled: {} - glashed or sash: {} - flush: {} - louvered: {} - wire gauged: {} - drainage_class_enum: - from_schema: http://w3id.org/mixs/terms + DRAINAGE_CLASS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - very poorly: {} + excessively drained: {} + moderately well: {} poorly: {} somewhat poorly: {} - moderately well: {} + very poorly: {} well: {} - excessively drained: {} - drawings_enum: - from_schema: http://w3id.org/mixs/terms + DRAWINGS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - operation: {} as built: {} - construction: {} bid: {} - design: {} building navigation map: {} + construction: {} + design: {} diagram: {} + operation: {} sketch: {} - ext_wall_orient_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - northeast: {} - southeast: {} - southwest: {} - northwest: {} - ext_window_orient_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - northeast: {} - southeast: {} - southwest: {} - northwest: {} - fao_class_enum: - from_schema: http://w3id.org/mixs/terms + FAO_CLASS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: Acrisols: {} Andosols: {} @@ -438,83 +236,59 @@ enums: Solonetz: {} Vertisols: {} Yermosols: {} - filter_type_enum: - from_schema: http://w3id.org/mixs/terms + FILTER_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - particulate air filter: {} - chemical air filter: {} - low-MERV pleated media: {} HEPA: {} + chemical air filter: {} electrostatic: {} gas-phase or ultraviolet air treatments: {} - floor_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - floor_finish_mat_enum: - from_schema: http://w3id.org/mixs/terms + low-MERV pleated media: {} + particulate air filter: {} + FIREPLACE_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - tile: {} - wood strip or parquet: {} - carpet: {} - rug: {} - laminate wood: {} - lineoleum: {} - vinyl composition tile: {} - sheet vinyl: {} - stone: {} - bamboo: {} - cork: {} - terrazo: {} - concrete: {} - none: {} - sealed: {} - clear finish: {} - paint: {} - none or unfinished: {} - floor_struc_enum: - from_schema: http://w3id.org/mixs/terms + gas burning: {} + wood burning: {} + FLOOR_STRUC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: balcony: {} + concrete: {} floating floor: {} glass floor: {} raised floor: {} sprung floor: {} wood-framed: {} - concrete: {} - floor_water_mold_enum: - from_schema: http://w3id.org/mixs/terms + FLOOR_WATER_MOLD_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - mold odor: {} - wet floor: {} - water stains: {} - wall discoloration: {} - floor discoloration: {} - ceiling discoloration: {} - peeling paint or wallpaper: {} bulging walls: {} + ceiling discoloration: {} condensation: {} - freq_clean_enum: - from_schema: http://w3id.org/mixs/terms + floor discoloration: {} + mold odor: {} + peeling paint or wallpaper: {} + wall discoloration: {} + water stains: {} + wet floor: {} + FREQ_CLEAN_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + Annually: {} Daily: {} - Weekly: {} Monthly: {} Quarterly: {} - Annually: {} + Weekly: {} other: {} - furniture_enum: - from_schema: http://w3id.org/mixs/terms + FURNITURE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: cabinet: {} chair: {} desks: {} - gender_restroom_enum: - from_schema: http://w3id.org/mixs/terms + GENDER_RESTROOM_ENUM: + from_schema: https://w3id.org/mixs permissible_values: all gender: {} female: {} @@ -522,96 +296,66 @@ enums: male: {} male and female: {} unisex: {} - growth_habit_enum: - from_schema: http://w3id.org/mixs/terms + GROWTH_HABIT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: erect: {} + prostrate: {} semi-erect: {} spreading: {} - prostrate: {} - handidness_enum: - from_schema: http://w3id.org/mixs/terms + HANDIDNESS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: ambidexterity: {} left handedness: {} mixed-handedness: {} right handedness: {} - hc_produced_enum: - from_schema: http://w3id.org/mixs/terms + HCR_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - Oil: {} - Gas-Condensate: {} - Gas: {} - Bitumen: {} - Coalbed Methane: {} - other: {} - hcr_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Oil Reservoir: {} + Coalbed: {} Gas Reservoir: {} + Oil Reservoir: {} Oil Sand: {} - Coalbed: {} Shale: {} - Tight Oil Reservoir: {} Tight Gas Reservoir: {} + Tight Oil Reservoir: {} other: {} - hcr_geol_age_enum: - from_schema: http://w3id.org/mixs/terms + HC_PRODUCED_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - Archean: {} - Cambrian: {} - Carboniferous: {} - Cenozoic: {} - Cretaceous: {} - Devonian: {} - Jurassic: {} - Mesozoic: {} - Neogene: {} - Ordovician: {} - Paleogene: {} - Paleozoic: {} - Permian: {} - Precambrian: {} - Proterozoic: {} - Silurian: {} - Triassic: {} + Bitumen: {} + Coalbed Methane: {} + Gas: {} + Gas-Condensate: {} + Oil: {} other: {} - heat_cool_type_enum: - from_schema: http://w3id.org/mixs/terms + HEAT_COOL_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - radiant system: {} - heat pump: {} forced air system: {} + heat pump: {} + radiant system: {} steam forced heat: {} wood stove: {} - heat_deliv_loc_enum: - from_schema: http://w3id.org/mixs/terms + HEAT_SYS_DELIV_METH_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - north: {} - south: {} - east: {} - west: {} - host_sex_enum: - from_schema: http://w3id.org/mixs/terms + conductive: {} + radiant: {} + INDOOR_SPACE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - female: {} - hermaphrodite: {} - male: {} - neuter: {} - indoor_space_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - bedroom: {} - office: {} bathroom: {} + bedroom: {} + elevator: {} foyer: {} + hallway: {} kitchen: {} locker room: {} - hallway: {} - elevator: {} - indoor_surf_enum: - from_schema: http://w3id.org/mixs/terms + office: {} + INDOOR_SURF_ENUM: + from_schema: https://w3id.org/mixs permissible_values: cabinet: {} ceiling: {} @@ -619,26 +363,18 @@ enums: door: {} shelving: {} vent cover: {} - window: {} wall: {} - int_wall_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - light_type_enum: - from_schema: http://w3id.org/mixs/terms + window: {} + LIGHT_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - natural light: {} - electric light: {} desk lamp: {} + electric light: {} flourescent lights: {} + natural light: {} none: {} - lithology_enum: - from_schema: http://w3id.org/mixs/terms + LITHOLOGY_ENUM: + from_schema: https://w3id.org/mixs permissible_values: Basement: {} Chalk: {} @@ -653,56 +389,38 @@ enums: Siltstone: {} Volcanic: {} other: {} - mech_struc_enum: - from_schema: http://w3id.org/mixs/terms + MECH_STRUC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - subway: {} - coach: {} + boat: {} + bus: {} + car: {} carriage: {} + coach: {} elevator: {} escalator: {} - boat: {} + subway: {} train: {} - car: {} - bus: {} - occup_document_enum: - from_schema: http://w3id.org/mixs/terms + OCCUP_DOCUMENT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: automated count: {} estimate: {} manual count: {} videos: {} - organism_count_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - ATP: {} - MPN: {} - other: {} - oxy_stat_samp_enum: - from_schema: http://w3id.org/mixs/terms + OXY_STAT_SAMP_ENUM: + from_schema: https://w3id.org/mixs permissible_values: aerobic: {} anaerobic: {} other: {} - plant_growth_med_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - other artificial liquid medium: {} - other artificial solid medium: {} - peat moss: {} - perlite: {} - pumice: {} - sand: {} - soil: {} - vermiculite: {} - water: {} - plant_sex_enum: - from_schema: http://w3id.org/mixs/terms + PLANT_SEX_ENUM: + from_schema: https://w3id.org/mixs permissible_values: Androdioecious: {} Androecious: {} - Androgynous: {} Androgynomonoecious: {} + Androgynous: {} Andromonoecious: {} Bisexual: {} Dichogamous: {} @@ -728,38 +446,38 @@ enums: Trimonoecious: {} Trioecious: {} Unisexual: {} - profile_position_enum: - from_schema: http://w3id.org/mixs/terms + PROFILE_POSITION_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - summit: {} - shoulder: {} backslope: {} footslope: {} + shoulder: {} + summit: {} toeslope: {} - quad_pos_enum: - from_schema: http://w3id.org/mixs/terms + QUAD_POS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - North side: {} - West side: {} - South side: {} East side: {} - rel_samp_loc_enum: - from_schema: http://w3id.org/mixs/terms + North side: {} + South side: {} + West side: {} + REL_SAMP_LOC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - edge of car: {} center of car: {} + edge of car: {} under a seat: {} - room_condt_enum: - from_schema: http://w3id.org/mixs/terms + ROOM_CONDT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - new: {} - visible wear: {} - needs repair: {} damaged: {} + needs repair: {} + new: {} rupture: {} visible signs of mold/mildew: {} - room_connected_enum: - from_schema: http://w3id.org/mixs/terms + visible wear: {} + ROOM_CONNECTED_ENUM: + from_schema: https://w3id.org/mixs permissible_values: attic: {} bathroom: {} @@ -772,138 +490,97 @@ enums: mail room: {} office: {} stairwell: {} - room_loc_enum: - from_schema: http://w3id.org/mixs/terms + ROOM_LOC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: corner room: {} - interior room: {} exterior wall: {} - room_samp_pos_enum: - from_schema: http://w3id.org/mixs/terms + interior room: {} + ROOM_SAMP_POS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - north corner: {} - south corner: {} - west corner: {} + center: {} east corner: {} + north corner: {} northeast corner: {} northwest corner: {} + south corner: {} southeast corner: {} southwest corner: {} - center: {} - room_type_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - attic: {} - bathroom: {} - closet: {} - conference room: {} - elevator: {} - examining room: {} - hallway: {} - kitchen: {} - mail room: {} - private office: {} - open office: {} - stairwell: {} - ',restroom': {} - lobby: {} - vestibule: {} - mechanical or electrical room: {} - data center: {} - laboratory_wet: {} - laboratory_dry: {} - gymnasium: {} - natatorium: {} - auditorium: {} - lockers: {} - cafe: {} - warehouse: {} - samp_capt_status_enum: - from_schema: http://w3id.org/mixs/terms + west corner: {} + SAMP_CAPT_STATUS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: active surveillance in response to an outbreak: {} active surveillance not initiated by an outbreak: {} farm sample: {} market sample: {} other: {} - samp_collect_point_enum: - from_schema: http://w3id.org/mixs/terms + SAMP_COLLECT_POINT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - well: {} - test well: {} drilling rig: {} - wellhead: {} + other: {} separator: {} storage tank: {} - other: {} - samp_dis_stage_enum: - from_schema: http://w3id.org/mixs/terms + test well: {} + well: {} + wellhead: {} + SAMP_DIS_STAGE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: dissemination: {} growth and reproduction: {} infection: {} inoculation: {} - penetration: {} other: {} - samp_floor_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - 1st floor: {} - 2nd floor: {} - basement: {} - lobby: {} - samp_md_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - DF: {} - RT: {} - KB: {} - MSL: {} - other: {} - samp_subtype_enum: - from_schema: http://w3id.org/mixs/terms + penetration: {} + SAMP_SUBTYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - oil phase: {} - water phase: {} biofilm: {} not applicable: {} + oil phase: {} other: {} - samp_weather_enum: - from_schema: http://w3id.org/mixs/terms + water phase: {} + SAMP_WEATHER_ENUM: + from_schema: https://w3id.org/mixs permissible_values: clear sky: {} cloudy: {} foggy: {} hail: {} rain: {} - snow: {} sleet: {} + snow: {} sunny: {} windy: {} - season_use_enum: - from_schema: http://w3id.org/mixs/terms + SEASON_USE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + Fall: {} Spring: {} Summer: {} - Fall: {} Winter: {} - sediment_type_enum: - from_schema: http://w3id.org/mixs/terms + SEDIMENT_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: biogenous: {} cosmogenous: {} hydrogenous: {} lithogenous: {} - shading_device_cond_enum: - from_schema: http://w3id.org/mixs/terms + SEQ_QUALITY_CHECK_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - shading_device_type_enum: - from_schema: http://w3id.org/mixs/terms + manually edited: {} + none: {} + SHADING_DEVICE_LOC_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + exterior: {} + interior: {} + SHADING_DEVICE_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: bahama shutters: {} exterior roll blind: {} @@ -917,36 +594,56 @@ enums: tree: {} trellis: {} venetian awning: {} - soil_horizon_enum: - from_schema: http://w3id.org/mixs/terms + SHARED_ENUM_0: + from_schema: https://w3id.org/mixs permissible_values: - O horizon: {} - A horizon: {} - E horizon: {} - B horizon: {} - C horizon: {} - R layer: {} - Permafrost: {} - M horizon: {} - specific_enum: - from_schema: http://w3id.org/mixs/terms + east: {} + north: {} + northeast: {} + northwest: {} + south: {} + southeast: {} + southwest: {} + west: {} + SHARED_ENUM_1: + from_schema: https://w3id.org/mixs permissible_values: - operation: {} - as built: {} - construction: {} - bid: {} - design: {} - photos: {} - sr_dep_env_enum: - from_schema: http://w3id.org/mixs/terms + no presence of mold visible: {} + presence of mold visible: {} + SHARED_ENUM_2: + from_schema: https://w3id.org/mixs permissible_values: - Lacustine: {} - Fluvioldeltaic: {} - Fluviomarine: {} - Marine: {} - other: {} - sr_geol_age_enum: - from_schema: http://w3id.org/mixs/terms + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + SHARED_ENUM_3: + from_schema: https://w3id.org/mixs + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + SHARED_ENUM_4: + from_schema: https://w3id.org/mixs + permissible_values: + Santa-Fe texture: {} + crows feet: {} + crows-foot stomp: {} + double skip: {} + hawk and trowel: {} + knockdown: {} + orange peel: {} + popcorn: {} + rosebud stomp: {} + skip trowel: {} + smooth: {} + stomp knockdown: {} + swirl: {} + SHARED_ENUM_5: + from_schema: https://w3id.org/mixs permissible_values: Archean: {} Cambrian: {} @@ -966,48 +663,81 @@ enums: Silurian: {} Triassic: {} other: {} - sr_kerog_type_enum: - from_schema: http://w3id.org/mixs/terms + SOIL_HORIZON_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + A horizon: {} + B horizon: {} + C horizon: {} + E horizon: {} + O horizon: {} + Permafrost: {} + R layer: {} + M horizon: {} + SPACE_TYP_STATE_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + typically occupied: {} + typically unoccupied: {} + SPECIFIC_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + as built: {} + bid: {} + construction: {} + design: {} + operation: {} + photos: {} + SR_DEP_ENV_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + Fluvioldeltaic: {} + Fluviomarine: {} + Lacustine: {} + Marine: {} + other: {} + SR_KEROG_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: Type I: {} Type II: {} Type III: {} Type IV: {} other: {} - sr_lithology_enum: - from_schema: http://w3id.org/mixs/terms + SR_LITHOLOGY_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - Clastic: {} + Biosilicieous: {} Carbonate: {} + Clastic: {} Coal: {} - Biosilicieous: {} other: {} - substructure_type_enum: - from_schema: http://w3id.org/mixs/terms + SUBSTRUCTURE_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + basement: {} crawlspace: {} slab on grade: {} - basement: {} - surf_air_cont_enum: - from_schema: http://w3id.org/mixs/terms + SURF_AIR_CONT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + biocides: {} + biological contaminants: {} dust: {} + nutrients: {} organic matter: {} particulate matter: {} - volatile organic compounds: {} - biological contaminants: {} radon: {} - nutrients: {} - biocides: {} - surf_material_enum: - from_schema: http://w3id.org/mixs/terms + volatile organic compounds: {} + SURF_MATERIAL_ENUM: + from_schema: https://w3id.org/mixs permissible_values: adobe: {} carpet: {} cinder blocks: {} concrete: {} - hay bales: {} glass: {} + hay bales: {} metal: {} paint: {} plastic: {} @@ -1017,10264 +747,7659 @@ enums: tile: {} vinyl: {} wood: {} - tidal_stage_enum: - from_schema: http://w3id.org/mixs/terms + TIDAL_STAGE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - low tide: {} ebb tide: {} flood tide: {} high tide: {} - tillage_enum: - from_schema: http://w3id.org/mixs/terms + low tide: {} + TILLAGE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - drill: {} + chisel: {} cutting disc: {} + disc plough: {} + drill: {} + mouldboard: {} ridge till: {} strip tillage: {} - zonal tillage: {} - chisel: {} tined: {} - mouldboard: {} - disc plough: {} - train_line_enum: - from_schema: http://w3id.org/mixs/terms + zonal tillage: {} + TRAIN_LINE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - red: {} green: {} orange: {} - train_stat_loc_enum: - from_schema: http://w3id.org/mixs/terms + red: {} + TRAIN_STAT_LOC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - south station above ground: {} - south station underground: {} - south station amtrak: {} forest hills: {} riverside: {} - train_stop_loc_enum: - from_schema: http://w3id.org/mixs/terms + south station above ground: {} + south station amtrak: {} + south station underground: {} + TRAIN_STOP_LOC_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + downtown: {} end: {} mid: {} - downtown: {} - vis_media_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - photos: {} - videos: {} - commonly of the building: {} - site context (adjacent buildings, vegetation, terrain, streets): {} - interiors: {} - equipment: {} - 3D scans: {} - wall_const_type_enum: - from_schema: http://w3id.org/mixs/terms + WALL_CONST_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: + fire resistive: {} frame construction: {} joisted masonry: {} light noncombustible: {} masonry noncombustible: {} modified fire resistive: {} - fire resistive: {} - wall_finish_mat_enum: - from_schema: http://w3id.org/mixs/terms + WALL_FINISH_MAT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - plaster: {} - gypsum plaster: {} - veneer plaster: {} + acoustical treatment: {} gypsum board: {} - tile: {} - terrazzo: {} + gypsum plaster: {} + masonry: {} + metal: {} + plaster: {} stone facing: {} - acoustical treatment: {} + terrazzo: {} + tile: {} + veneer plaster: {} wood: {} - metal: {} - masonry: {} - wall_loc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - wall_surf_treatment_enum: - from_schema: http://w3id.org/mixs/terms + WALL_SURF_TREATMENT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - painted: {} - wall paper: {} + fabric: {} no treatment: {} + painted: {} paneling: {} stucco: {} - fabric: {} - wall_texture_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - crows feet: {} - crows-foot stomp: {} - '': {} - double skip: {} - hawk and trowel: {} - knockdown: {} - popcorn: {} - orange peel: {} - rosebud stomp: {} - Santa-Fe texture: {} - skip trowel: {} - smooth: {} - stomp knockdown: {} - swirl: {} - water_feat_type_enum: - from_schema: http://w3id.org/mixs/terms + wall paper: {} + WATER_FEAT_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: fountain: {} pool: {} standing feature: {} stream: {} waterfall: {} - weekday_enum: - from_schema: http://w3id.org/mixs/terms + WEEKDAY_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - Monday: {} - Tuesday: {} - Wednesday: {} - Thursday: {} Friday: {} + Monday: {} Saturday: {} Sunday: {} - window_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - window_cover_enum: - from_schema: http://w3id.org/mixs/terms + Thursday: {} + Tuesday: {} + Wednesday: {} + WINDOW_COVER_ENUM: + from_schema: https://w3id.org/mixs permissible_values: blinds: {} curtains: {} none: {} - window_horiz_pos_enum: - from_schema: http://w3id.org/mixs/terms + WINDOW_HORIZ_POS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: left: {} middle: {} right: {} - window_loc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - window_mat_enum: - from_schema: http://w3id.org/mixs/terms + WINDOW_MAT_ENUM: + from_schema: https://w3id.org/mixs permissible_values: clad: {} fiberglass: {} metal: {} vinyl: {} wood: {} - window_type_enum: - from_schema: http://w3id.org/mixs/terms + WINDOW_STATUS_ENUM: + from_schema: https://w3id.org/mixs + permissible_values: + closed: {} + open: {} + WINDOW_TYPE_ENUM: + from_schema: https://w3id.org/mixs permissible_values: - single-hung sash window: {} - horizontal sash window: {} fixed window: {} - window_vert_pos_enum: - from_schema: http://w3id.org/mixs/terms + horizontal sash window: {} + single-hung sash window: {} + WINDOW_VERT_POS_ENUM: + from_schema: https://w3id.org/mixs permissible_values: bottom: {} + high: {} + low: {} middle: {} top: {} - low: {} - high: {} + cur_land_use_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + badlands: {} + cities: {} + conifers: + annotations: + originally: conifers (e.g. pine,spruce,fir,cypress) + examples: + - value: cypress + - value: fir + - value: pine + - value: spruce + crop trees: + annotations: + originally: crop trees (nuts,fruit,christmas trees,nursery trees) + examples: + - value: christmas trees + - value: fruit + - value: nursery trees + - value: nuts + farmstead: {} + gravel: {} + hardwoods: + annotations: + originally: hardwoods (e.g. oak,hickory,elm,aspen) + examples: + - value: aspen + - value: elm + - value: hickory + - value: oak + hayland: {} + horticultural plants: + annotations: + originally: horticultural plants (e.g. tulips) + examples: + - value: tulips + industrial areas: {} + intermixed hardwood and conifers: {} + marshlands: + annotations: + originally: marshlands (grass,sedges,rushes) + examples: + - value: grass + - value: rushes + - value: sedgees + meadows: + annotations: + originally: meadows (grasses,alfalfa,fescue,bromegrass,timothy) + examples: + - value: alfalfa + - value: bromegrass + - value: fescue + - value: grasses + - value: timothy + mines/quarries: {} + mudflats: {} + oil waste areas: {} + pastureland: + annotations: + originally: pastureland (grasslands used for livestock grazing) + comments: + - grasslands used for livestock grazing + permanent snow or ice: {} + rainforest: + annotations: + originally: rainforest (evergreen forest receiving greater than 406 cm annual rainfall) + comments: + - evergreen forest receiving greater than 406 cm annual rainfall + rangeland: {} + roads/railroads: {} + rock: {} + row crops: {} + saline seeps: {} + salt flats: {} + sand: {} + shrub crops: + annotations: + originally: shrub crops (blueberries,nursery ornamentals,filberts) + examples: + - value: blueberries + - value: filberts + - value: nursery ornamentals + shrub land: + annotations: + originally: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus) + examples: + - value: creosote bush + - value: eucalyptus + - value: mesquite + - value: sage-brush + - value: shrub oak + small grains: {} + successional shrub land: + annotations: + originally: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries) + examples: + - value: blackberries + - value: chokecherry + - value: hazels + - value: shrub dogwoods + - value: sumacs + - value: tree saplings + swamp: + annotations: + originally: swamp (permanent or semi-permanent water body dominated by woody plants) + comments: + - permanent or semi-permanent water body dominated by woody plants + tropical: + annotations: + originally: tropical (e.g. mangrove,palms) + examples: + - value: mangrove + - value: palms + tundra: + annotations: + originally: tundra (mosses,lichens) + examples: + - value: lichens + - value: mosses + vegetable crops: {} + vine crops: + annotations: + originally: vine crops (grapes) + examples: + - value: grapes slots: abs_air_humidity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per gram, kilogram per kilogram, kilogram, pound - occurrence: - tag: occurrence - value: '1' description: Actual mass of water vapor - mh20 - present in the air water vapor mixture title: absolute air humidity examples: - value: 9 gram per gram - from_schema: http://w3id.org/mixs/terms - aliases: - - absolute air humidity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - absolute + - air + - humidity slot_uri: MIXS:0000122 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true add_recov_method: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration;timestamp - occurrence: - tag: occurrence - value: '1' description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field title: secondary and tertiary recovery methods and start date examples: - value: Polymer Addition;2018-06-21T14:30Z - from_schema: http://w3id.org/mixs/terms - aliases: - - secondary and tertiary recovery methods and start date - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - date + - method + - recover + - secondary + - start + string_serialization: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other];{timestamp}' slot_uri: MIXS:0001009 - multivalued: false - range: TextValue additional_info: - annotations: - expected_value: - tag: expected_value - value: text - occurrence: - tag: occurrence - value: '1' description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary title: additional info - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - additional info - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - information slot_uri: MIXS:0000300 - multivalued: false range: TextValue address: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: value - occurrence: - tag: occurrence - value: '1' - description: The street name and building number where the sampling occurred. + description: The street name and building number where the sampling occurred title: address - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - address - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{integer}{text}' slot_uri: MIXS:0000218 - multivalued: false - range: TextValue adj_room: - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' description: List of rooms (room number, room name) immediately adjacent to the sampling room title: adjacent rooms - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - adjacent rooms - is_a: core field - string_serialization: '{text};{integer}' + from_schema: https://w3id.org/mixs + keywords: + - adjacent + - room slot_uri: MIXS:0000219 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true aero_struc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together title: aerospace structure examples: - value: plane - from_schema: http://w3id.org/mixs/terms - aliases: - - aerospace structure - is_a: core field - string_serialization: '[plane|glider]' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000773 - multivalued: false - range: TextValue + range: AERO_STRUC_ENUM agrochem_addition: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: agrochemical name;agrochemical amount;timestamp - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Addition of fertilizers, pesticides, etc. - amount and time of applications title: history/agrochemical additions examples: - value: roundup;5 milligram per liter;2018-06-21 - from_schema: http://w3id.org/mixs/terms - aliases: - - history/agrochemical additions - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - history string_serialization: '{text};{float} {unit};{timestamp}' slot_uri: MIXS:0000639 + domain_of: + - Agriculture + - Soil multivalued: true range: TextValue air_PM_concen: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: particulate matter name;measurement value - preferred_unit: - tag: preferred_unit - value: micrograms per cubic meter - occurrence: - tag: occurrence - value: m description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM title: air particulate matter concentration examples: - value: PM2.5;10 microgram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: - - air particulate matter concentration - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - air + - concentration + - particle + - particulate string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000108 multivalued: true - range: TextValue air_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Temperature of the air at the time of sampling title: air temperature - examples: - - value: 20 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - air temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - air + - temperature slot_uri: MIXS:0000124 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true air_temp_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: temperature value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: m description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens title: air temperature regimen examples: - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - air temperature regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - air + - regimen + - temperature string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 multivalued: true range: TextValue al_sat: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: Aluminum saturation (esp. For tropical soils) title: extreme_unusual_properties/Al saturation - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - extreme_unusual_properties/Al saturation - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - extreme + - properties + - saturation + - unusual slot_uri: MIXS:0000607 - multivalued: false - range: QuantityValue + domain_of: + - Soil + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true al_sat_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or URL - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining Al saturation title: extreme_unusual_properties/Al saturation method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - extreme_unusual_properties/Al saturation method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - extreme + - method + - properties + - saturation + - unusual slot_uri: MIXS:0000324 - multivalued: false + domain_of: + - Soil range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true alkalinity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milliequivalent per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate title: alkalinity examples: - value: 50 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - alkalinity - is_a: core field slot_uri: MIXS:0000421 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true alkalinity_method: - annotations: - expected_value: - tag: expected_value - value: description of method - occurrence: - tag: occurrence - value: '1' description: Method used for alkalinity measurement title: alkalinity method examples: - value: titration - from_schema: http://w3id.org/mixs/terms - aliases: - - alkalinity method - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - alkalinity + - method slot_uri: MIXS:0000298 - multivalued: false range: TextValue alkyl_diethers: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: mole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of alkyl diethers title: alkyl diethers examples: - value: 0.005 mole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - alkyl diethers - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000490 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true alt: annotations: - expected_value: - tag: expected_value - value: measurement value - description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + Preferred_unit: + tag: Preferred_unit + value: meter + description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air title: altitude examples: - value: 100 meter - from_schema: http://w3id.org/mixs/terms - aliases: - - altitude - is_a: environment field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000094 - multivalued: false - domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true aminopept_act: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: mole per liter per hour - occurrence: - tag: occurrence - value: '1' description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - value: 0.269 mole per liter per hour - from_schema: http://w3id.org/mixs/terms - aliases: - - aminopeptidase activity - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000172 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ammonium: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of ammonium in the sample title: ammonium examples: - value: 1.5 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - ammonium - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000427 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true amount_light: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: lux, lumens per square meter - occurrence: - tag: occurrence - value: '1' description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area - title: amount of light - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - amount of light - is_a: core field + title: amount of light + from_schema: https://w3id.org/mixs + keywords: + - light slot_uri: MIXS:0000140 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ances_data: - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) title: ancestral data examples: - value: A/3*B - from_schema: http://w3id.org/mixs/terms - aliases: - - ancestral data - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000247 - multivalued: false range: TextValue annual_precpt: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter - occurrence: - tag: occurrence - value: '1' - description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps title: mean annual precipitation - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - mean annual precipitation - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mean slot_uri: MIXS:0000644 - multivalued: false - range: QuantityValue + domain_of: + - Agriculture + - Soil + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true annual_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Mean annual temperature title: mean annual temperature examples: - value: 12.5 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - mean annual temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mean + - temperature slot_uri: MIXS:0000642 - multivalued: false - range: QuantityValue + domain_of: + - Agriculture + - Soil + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true antibiotic_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: antibiotic name;antibiotic amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram - occurrence: - tag: occurrence - value: m description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens title: antibiotic regimen examples: - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - antibiotic regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - regimen string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000553 multivalued: true range: TextValue api: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degrees API - occurrence: - tag: occurrence - value: '1' - description: 'API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)' + description: 'API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1 API)' title: API gravity examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - API gravity - is_a: core field + - value: 31.1 API + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000157 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true arch_struc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: An architectural structure is a human-made, free-standing, immobile outdoor construction title: architectural structure examples: - value: shed - from_schema: http://w3id.org/mixs/terms - aliases: - - architectural structure - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000774 - multivalued: false - range: arch_struc_enum + range: ARCH_STRUC_ENUM aromatics_pc: annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: aromatics wt% - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - aromatics wt% - is_a: core field - string_serialization: '{text};{float} {unit}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000133 - multivalued: false range: TextValue + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true asphaltenes_pc: annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: asphaltenes wt% - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - asphaltenes wt% - is_a: core field - string_serialization: '{text};{float} {unit}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000135 - multivalued: false range: TextValue + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true atmospheric_data: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: atmospheric data name;measurement value - occurrence: - tag: occurrence - value: m description: Measurement of atmospheric data; can include multiple data title: atmospheric data examples: - value: wind speed;9 knots - from_schema: http://w3id.org/mixs/terms - aliases: - - atmospheric data - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0001097 multivalued: true range: TextValue avg_dew_point: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day title: average dew point examples: - value: 25.5 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - average dew point - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - average slot_uri: MIXS:0000141 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true avg_occup: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' - description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. + description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room title: average daily occupancy - examples: - - value: '2' - from_schema: http://w3id.org/mixs/terms - aliases: - - average daily occupancy - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - average slot_uri: MIXS:0000775 - multivalued: false range: TextValue avg_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day title: average temperature examples: - value: 12.5 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - average temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - average + - temperature slot_uri: MIXS:0000142 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true bac_prod: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per cubic meter per day - occurrence: - tag: occurrence - value: '1' description: Bacterial production in the water column measured by isotope uptake title: bacterial production examples: - value: 5 milligram per cubic meter per day - from_schema: http://w3id.org/mixs/terms - aliases: - - bacterial production - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - production slot_uri: MIXS:0000683 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true bac_resp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per cubic meter per day, micromole oxygen per liter per hour - occurrence: - tag: occurrence - value: '1' description: Measurement of bacterial respiration in the water column title: bacterial respiration examples: - value: 300 micromole oxygen per liter per hour - from_schema: http://w3id.org/mixs/terms - aliases: - - bacterial respiration - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000684 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true bacteria_carb_prod: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: nanogram per hour - occurrence: - tag: occurrence - value: '1' description: Measurement of bacterial carbon production title: bacterial carbon production examples: - value: 2.53 microgram per liter per hour - from_schema: http://w3id.org/mixs/terms - aliases: - - bacterial carbon production - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - production slot_uri: MIXS:0000173 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true barometric_press: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millibar - occurrence: - tag: occurrence - value: '1' description: Force per unit area exerted against a surface by the weight of air above that surface title: barometric pressure examples: - value: 5 millibar - from_schema: http://w3id.org/mixs/terms - aliases: - - barometric pressure - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - pressure slot_uri: MIXS:0000096 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true basin: - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' description: Name of the basin (e.g. Campos) title: basin name examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - basin name - is_a: core field - string_serialization: '{text}' + - value: Campos + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000290 - multivalued: false range: TextValue bathroom_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of bathrooms in the building title: bathroom count examples: - value: '1' - from_schema: http://w3id.org/mixs/terms - aliases: - - bathroom count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count slot_uri: MIXS:0000776 - multivalued: false range: TextValue bedroom_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of bedrooms in the building title: bedroom count examples: - value: '2' - from_schema: http://w3id.org/mixs/terms - aliases: - - bedroom count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count slot_uri: MIXS:0000777 - multivalued: false range: TextValue benzene: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of benzene in the sample title: benzene - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - benzene - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000153 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true biochem_oxygen_dem: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period title: biochemical oxygen demand - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - biochemical oxygen demand - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - oxygen slot_uri: MIXS:0000653 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true biocide: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: name;name;timestamp - occurrence: - tag: occurrence - value: '1' description: List of biocides (commercial name of product and supplier) and date of administration title: biocide administration examples: - value: ALPHA 1427;Baker Hughes;2008-01-23 - from_schema: http://w3id.org/mixs/terms - aliases: - - biocide administration - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - administration string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001011 - multivalued: false - range: TextValue + recommended: true biocide_admin_method: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;frequency;duration;duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) title: biocide administration method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - biocide administration method - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - administration + - method string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' slot_uri: MIXS:0000456 - multivalued: false + recommended: true range: TextValue biol_stat: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The level of genome modification. + description: The level of genome modification title: biological status examples: - value: natural - from_schema: http://w3id.org/mixs/terms - aliases: - - biological status - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - status + string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal selection|mutant]' slot_uri: MIXS:0000858 - multivalued: false - range: biol_stat_enum biomass: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: biomass type;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: ton, kilogram, gram - occurrence: - tag: occurrence - value: m description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements title: biomass examples: - value: total;20 gram - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - biomass - is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 multivalued: true range: TextValue biotic_regm: - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi title: biotic regimen examples: - value: sample inoculated with Rhizobium spp. Culture - from_schema: http://w3id.org/mixs/terms - aliases: - - biotic regimen - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - regimen slot_uri: MIXS:0001038 - multivalued: false range: TextValue + multivalued: true biotic_relationship: - annotations: - expected_value: - tag: expected_value - value: enumeration description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object title: observed biotic relationship examples: - value: free living - from_schema: http://w3id.org/mixs/terms - aliases: - - observed biotic relationship - is_a: nucleic acid sequence source field + from_schema: https://w3id.org/mixs + keywords: + - observed + - relationship slot_uri: MIXS:0000028 - multivalued: false - range: biotic_relationship_enum + range: BIOTIC_RELATIONSHIP_ENUM bishomohopanol: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, microgram per gram - occurrence: - tag: occurrence - value: '1' description: Concentration of bishomohopanol title: bishomohopanol examples: - value: 14 microgram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - bishomohopanol - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000175 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true blood_press_diast: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter mercury - occurrence: - tag: occurrence - value: '1' description: Resting diastolic blood pressure, measured as mm mercury title: host blood pressure diastolic - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - host blood pressure diastolic - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - pressure slot_uri: MIXS:0000258 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true blood_press_syst: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter mercury - occurrence: - tag: occurrence - value: '1' description: Resting systolic blood pressure, measured as mm mercury title: host blood pressure systolic - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - host blood pressure systolic - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - pressure slot_uri: MIXS:0000259 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true bromide: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of bromide title: bromide examples: - value: 0.05 parts per million - from_schema: http://w3id.org/mixs/terms - aliases: - - bromide - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000176 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true build_docs: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The building design, construction and operation documents title: design, construction, and operation documents examples: - value: maintenance plans - from_schema: http://w3id.org/mixs/terms - aliases: - - design, construction, and operation documents - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - documents slot_uri: MIXS:0000787 - multivalued: false - range: build_docs_enum + range: BUILD_DOCS_ENUM build_occup_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: The primary function for which a building or discrete part of a building is intended to be used title: building occupancy type examples: - value: market - from_schema: http://w3id.org/mixs/terms - aliases: - - building occupancy type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type slot_uri: MIXS:0000761 + range: BUILD_OCCUP_TYPE_ENUM multivalued: true - range: build_occup_type_enum building_setting: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: A location (geography) where a building is set title: building setting examples: - value: rural - from_schema: http://w3id.org/mixs/terms - aliases: - - building setting - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000768 - multivalued: false - range: building_setting_enum + range: BUILDING_SETTING_ENUM built_struc_age: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: year - occurrence: - tag: occurrence - value: '1' description: The age of the built structure since construction title: built structure age examples: - - value: '15' - from_schema: http://w3id.org/mixs/terms - aliases: - - built structure age - is_a: core field + - value: 15 years + from_schema: https://w3id.org/mixs + keywords: + - age slot_uri: MIXS:0000145 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true built_struc_set: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The characterization of the location of the built structure as high or low human density title: built structure setting examples: - value: rural - from_schema: http://w3id.org/mixs/terms - aliases: - - built structure setting - is_a: core field - string_serialization: '[urban|rural]' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000778 - multivalued: false - range: TextValue + range: BUILT_STRUC_SET_ENUM built_struc_type: - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads title: built structure type - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - built structure type - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - type slot_uri: MIXS:0000721 - multivalued: false range: TextValue calcium: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of calcium in the sample title: calcium examples: - value: 0.2 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - calcium - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000432 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true carb_dioxide: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Carbon dioxide (gas) amount or concentration at the time of sampling title: carbon dioxide examples: - value: 410 parts per million - from_schema: http://w3id.org/mixs/terms - aliases: - - carbon dioxide - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon slot_uri: MIXS:0000097 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true carb_monoxide: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Carbon monoxide (gas) amount or concentration at the time of sampling title: carbon monoxide examples: - value: 0.1 parts per million - from_schema: http://w3id.org/mixs/terms - aliases: - - carbon monoxide - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon slot_uri: MIXS:0000098 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true carb_nitro_ratio: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value - occurrence: - tag: occurrence - value: '1' description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - value: '0.417361111' - from_schema: http://w3id.org/mixs/terms - aliases: - - carbon/nitrogen ratio - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - nitrogen + - ratio + string_serialization: '{float}:{float}' slot_uri: MIXS:0000310 - multivalued: false range: QuantityValue ceil_area: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The area of the ceiling space within the room title: ceiling area examples: - value: 25 square meter - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling area - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - area + - ceiling slot_uri: MIXS:0000148 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ceil_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: ceiling condition examples: - value: damaged - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ceiling + - condition slot_uri: MIXS:0000779 - multivalued: false - range: ceil_cond_enum + range: SHARED_ENUM_3 ceil_finish_mat: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of material used to finish a ceiling title: ceiling finish material examples: - value: stucco - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling finish material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ceiling + - material slot_uri: MIXS:0000780 - multivalued: false - range: ceil_finish_mat_enum + range: CEIL_FINISH_MAT_ENUM ceil_struc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The construction format of the ceiling title: ceiling structure examples: - value: concrete - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling structure - is_a: core field - string_serialization: '[wood frame|concrete]' + from_schema: https://w3id.org/mixs + keywords: + - ceiling slot_uri: MIXS:0000782 - multivalued: false - range: TextValue + range: CEIL_STRUC_ENUM ceil_texture: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The feel, appearance, or consistency of a ceiling surface title: ceiling texture examples: - value: popcorn - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling texture - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ceiling + - texture slot_uri: MIXS:0000783 - multivalued: false - range: ceil_texture_enum + range: SHARED_ENUM_4 ceil_thermal_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow title: ceiling thermal mass - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling thermal mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ceiling + - mass slot_uri: MIXS:0000143 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ceil_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of ceiling according to the ceiling's appearance or construction title: ceiling type examples: - value: coffered - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ceiling + - type slot_uri: MIXS:0000784 - multivalued: false - range: ceil_type_enum + range: CEIL_TYPE_ENUM ceil_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Signs of the presence of mold or mildew on the ceiling title: ceiling signs of water/mold examples: - value: presence of mold visible - from_schema: http://w3id.org/mixs/terms - aliases: - - ceiling signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' + from_schema: https://w3id.org/mixs + keywords: + - ceiling slot_uri: MIXS:0000781 - multivalued: false - range: TextValue + range: SHARED_ENUM_1 chem_administration: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: CHEBI;timestamp - occurrence: - tag: occurrence - value: m description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi title: chemical administration examples: - value: agar [CHEBI:2509];2018-05-11T20:00Z - from_schema: http://w3id.org/mixs/terms - aliases: - - chemical administration - is_a: core field - string_serialization: '{termLabel} {[termID]};{timestamp}' + from_schema: https://w3id.org/mixs + keywords: + - administration + string_serialization: '{termLabel} [{termID}];{timestamp}' slot_uri: MIXS:0000751 multivalued: true range: ControlledTermValue chem_mutagen: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: mutagen name;mutagen amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: m description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens title: chemical mutagen examples: - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - chemical mutagen - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000555 multivalued: true range: TextValue chem_oxygen_dem: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite title: chemical oxygen demand - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - chemical oxygen demand - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - oxygen slot_uri: MIXS:0000656 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true chem_treat_method: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;frequency;duration;duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) title: chemical treatment method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - chemical treatment method - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - method + - treatment string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' slot_uri: MIXS:0000457 - multivalued: false range: string chem_treatment: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: name;name;timestamp - occurrence: - tag: occurrence - value: '1' description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included title: chemical treatment examples: - value: ACCENT 1125;DOW;2010-11-17 - from_schema: http://w3id.org/mixs/terms - aliases: - - chemical treatment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - treatment string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001012 - multivalued: false - range: TextValue chimera_check: - annotations: - expected_value: - tag: expected_value - value: name and version of software, parameters used - description: Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences. + description: Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences title: chimera check software examples: - value: uchime;v4.1;default parameters - from_schema: http://w3id.org/mixs/terms - aliases: - - chimera check software - is_a: sequencing field - string_serialization: '{software};{version};{parameters}' + from_schema: https://w3id.org/mixs + keywords: + - software slot_uri: MIXS:0000052 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true chloride: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of chloride in the sample title: chloride examples: - value: 5000 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - chloride - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000429 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true chlorophyll: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per cubic meter, microgram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of chlorophyll title: chlorophyll examples: - value: 5 milligram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: - - chlorophyll - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000177 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true climate_environment: - annotations: - expected_value: - tag: expected_value - value: climate name;treatment interval and duration - occurrence: - tag: occurrence - value: m description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates title: climate environment examples: - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - climate environment - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - environment slot_uri: MIXS:0001040 - multivalued: true range: TextValue + multivalued: true collection_date: - annotations: - expected_value: - tag: expected_value - value: date and time description: 'The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' title: collection date examples: - - value: 2018-05-11T10:00:00+01:00; 2018-05-11 - from_schema: http://w3id.org/mixs/terms - aliases: - - collection date - is_a: environment field + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs + keywords: + - date slot_uri: MIXS:0000011 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + - SymbiontAssociated range: TimestampValue conduc: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milliSiemens per centimeter - occurrence: - tag: occurrence - value: '1' description: Electrical conductivity of water title: conductivity examples: - value: 10 milliSiemens per centimeter - from_schema: http://w3id.org/mixs/terms - aliases: - - conductivity - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000692 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true cool_syst_id: - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' description: The cooling system identifier title: cooling system identifier examples: - value: '12345' - from_schema: http://w3id.org/mixs/terms - aliases: - - cooling system identifier - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - identifier slot_uri: MIXS:0000785 - multivalued: false range: TextValue crop_rotation: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: crop rotation status;schedule - occurrence: - tag: occurrence - value: '1' description: Whether or not crop is rotated, and if yes, rotation schedule title: history/crop rotation examples: - value: yes;R2/2017-01-01/2018-12-31/P6M - from_schema: http://w3id.org/mixs/terms - aliases: - - history/crop rotation - is_a: core field - string_serialization: '{boolean};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - history slot_uri: MIXS:0000318 - multivalued: false - range: TextValue cult_root_med: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: name, PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. + description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors title: culture rooting medium examples: - value: http://himedialabs.com/TD/PT158.pdf - from_schema: http://w3id.org/mixs/terms - aliases: - - culture rooting medium - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - culture string_serialization: '{text}|{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001041 - multivalued: false - range: TextValue cur_land_use: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: Present state of sample site title: current land use examples: - value: conifers - from_schema: http://w3id.org/mixs/terms - aliases: - - current land use - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - land + - use + string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]' slot_uri: MIXS:0001080 - multivalued: false - range: cur_land_use_enum + domain_of: + - Agriculture + - Soil cur_vegetation: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: current vegetation type - occurrence: - tag: occurrence - value: '1' description: Vegetation classification from one or more standard classification systems, or agricultural crop title: current vegetation - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - current vegetation - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - vegetation string_serialization: '{text}' slot_uri: MIXS:0000312 - multivalued: false range: TextValue cur_vegetation_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in vegetation classification title: current vegetation method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - current vegetation method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - method + - vegetation slot_uri: MIXS:0000314 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true date_last_rain: - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' description: The date of the last time it rained title: date last rain examples: - - value: 2018-05-11:T14:30Z - from_schema: http://w3id.org/mixs/terms - aliases: - - date last rain - is_a: core field + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs + keywords: + - date + - rain slot_uri: MIXS:0000786 - multivalued: false range: TimestampValue density: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per cubic meter, gram per cubic centimeter - occurrence: - tag: occurrence - value: '1' description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) title: density examples: - value: 1000 kilogram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - density - is_a: core field slot_uri: MIXS:0000435 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true depos_env: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field title: depositional environment - examples: - - value: Continental - Alluvial - from_schema: http://w3id.org/mixs/terms - aliases: - - depositional environment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - environment slot_uri: MIXS:0000992 - multivalued: false - range: depos_env_enum + range: DEPOS_ENV_ENUM + recommended: true depth: annotations: - expected_value: - tag: expected_value - value: measurement value - description: The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. + Preferred_unit: + tag: Preferred_unit + value: meter + description: The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples title: depth - examples: - - value: 10 meter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - depth - is_a: environment field slot_uri: MIXS:0000018 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true dew_point: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. + description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water title: dew point examples: - value: 22 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - dew point - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000129 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diether_lipids: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: diether lipid name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: nanogram per liter - occurrence: - tag: occurrence - value: m description: Concentration of diether lipids; can include multiple types of diether lipids title: diether lipids examples: - value: 0.2 nanogram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - diether lipids - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 multivalued: true range: TextValue diss_carb_dioxide: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample title: dissolved carbon dioxide examples: - value: 5 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved carbon dioxide - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - dissolved slot_uri: MIXS:0000436 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_hydrogen: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - value: 0.3 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved hydrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved slot_uri: MIXS:0000179 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_inorg_carb: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter title: dissolved inorganic carbon examples: - value: 2059 micromole per kilogram - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved inorganic carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - dissolved + - inorganic slot_uri: MIXS:0000434 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_inorg_nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved inorganic nitrogen title: dissolved inorganic nitrogen examples: - value: 761 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved inorganic nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - inorganic + - nitrogen slot_uri: MIXS:0000698 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_inorg_phosp: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - value: 56.5 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved inorganic phosphorus - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - inorganic + - phosphorus slot_uri: MIXS:0000106 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_iron: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved iron in the sample title: dissolved iron - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved iron - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved slot_uri: MIXS:0000139 - multivalued: false range: QuantityValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_org_carb: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid title: dissolved organic carbon examples: - value: 197 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved organic carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - dissolved + - organic slot_uri: MIXS:0000433 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_org_nitro: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - value: 0.05 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved organic nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - nitrogen + - organic slot_uri: MIXS:0000162 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_oxygen: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per kilogram, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of dissolved oxygen title: dissolved oxygen examples: - value: 175 micromole per kilogram - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved oxygen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - oxygen slot_uri: MIXS:0000119 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true diss_oxygen_fluid: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per kilogram, milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). + description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic) title: dissolved oxygen in fluids - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - dissolved oxygen in fluids - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - oxygen slot_uri: MIXS:0000438 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true door_comp_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The composite type of the door title: door type, composite examples: - value: revolving - from_schema: http://w3id.org/mixs/terms - aliases: - - door type, composite - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - type slot_uri: MIXS:0000795 - multivalued: false - range: door_comp_type_enum + range: DOOR_COMP_TYPE_ENUM door_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The phsical condition of the door title: door condition examples: - value: new - from_schema: http://w3id.org/mixs/terms - aliases: - - door condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - door slot_uri: MIXS:0000788 - multivalued: false - range: door_cond_enum + range: SHARED_ENUM_2 door_direct: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The direction the door opens title: door direction of opening examples: - value: inward - from_schema: http://w3id.org/mixs/terms - aliases: - - door direction of opening - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - direction + - door slot_uri: MIXS:0000789 - multivalued: false - range: door_direct_enum + range: DOOR_DIRECT_ENUM door_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The relative location of the door in the room title: door location examples: - value: north - from_schema: http://w3id.org/mixs/terms - aliases: - - door location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - location slot_uri: MIXS:0000790 - multivalued: false - range: door_loc_enum + range: SHARED_ENUM_0 door_mat: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The material the door is composed of title: door material examples: - value: wood - from_schema: http://w3id.org/mixs/terms - aliases: - - door material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - material slot_uri: MIXS:0000791 - multivalued: false - range: door_mat_enum + range: DOOR_MAT_ENUM door_move: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of movement of the door title: door movement examples: - value: swinging - from_schema: http://w3id.org/mixs/terms - aliases: - - door movement - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door slot_uri: MIXS:0000792 - multivalued: false - range: door_move_enum + range: DOOR_MOVE_ENUM door_size: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The size of the door title: door area or size examples: - value: 2.5 square meter - from_schema: http://w3id.org/mixs/terms - aliases: - - door area or size - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - area + - door + - size slot_uri: MIXS:0000158 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true door_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of door material title: door type examples: - value: wooden - from_schema: http://w3id.org/mixs/terms - aliases: - - door type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - type slot_uri: MIXS:0000794 - multivalued: false - range: door_type_enum + range: DOOR_TYPE_ENUM door_type_metal: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of metal door title: door type, metal examples: - value: hollow - from_schema: http://w3id.org/mixs/terms - aliases: - - door type, metal - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - type slot_uri: MIXS:0000796 - multivalued: false - range: door_type_metal_enum + range: DOOR_TYPE_METAL_ENUM door_type_wood: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of wood door title: door type, wood examples: - value: battened - from_schema: http://w3id.org/mixs/terms - aliases: - - door type, wood - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - door + - type + string_serialization: '[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]' slot_uri: MIXS:0000797 - multivalued: false - range: door_type_wood_enum door_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Signs of the presence of mold or mildew on a door title: door signs of water/mold examples: - value: presence of mold visible - from_schema: http://w3id.org/mixs/terms - aliases: - - door signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' + from_schema: https://w3id.org/mixs + keywords: + - door slot_uri: MIXS:0000793 - multivalued: false - range: TextValue + range: SHARED_ENUM_1 down_par: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microEinstein per square meter per second, microEinstein per square centimeter per second - occurrence: - tag: occurrence - value: '1' description: Visible waveband radiance and irradiance measurements in the water column title: downward PAR examples: - value: 28.71 microEinstein per square meter per second - from_schema: http://w3id.org/mixs/terms - aliases: - - downward PAR - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000703 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true drainage_class: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Drainage classification from a standard system such as the USDA system title: drainage classification examples: - value: well - from_schema: http://w3id.org/mixs/terms - aliases: - - drainage classification - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - classification slot_uri: MIXS:0001085 - multivalued: false - range: drainage_class_enum + range: DRAINAGE_CLASS_ENUM drawings: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents title: drawings examples: - value: sketch - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - drawings - is_a: core field slot_uri: MIXS:0000798 - multivalued: false - range: drawings_enum + range: DRAWINGS_ENUM efficiency_percent: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Percentage of volatile solids removed from the anaerobic digestor title: efficiency percent - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - efficiency percent - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - percent slot_uri: MIXS:0000657 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true elev: annotations: - expected_value: - tag: expected_value - value: measurement value - description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit. + Preferred_unit: + tag: Preferred_unit + value: meter + description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit title: elevation examples: - value: 100 meter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - elevation - is_a: environment field slot_uri: MIXS:0000093 - multivalued: false range: float + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true elevator: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of elevators within the built structure title: elevator count examples: - value: '2' - from_schema: http://w3id.org/mixs/terms - aliases: - - elevator count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count slot_uri: MIXS:0000799 - multivalued: false range: TextValue emulsions: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: emulsion name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per liter - occurrence: - tag: occurrence - value: m description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types title: emulsions - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - emulsions - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000660 multivalued: true range: TextValue env_broad_scale: - annotations: - expected_value: - tag: expected_value - value: The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes. - tooltip: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - description: 'Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' + description: 'Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' title: broad-scale environmental context examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean - from_schema: http://w3id.org/mixs/terms - aliases: - - broad-scale environmental context - is_a: environment field - string_serialization: '{termLabel} {[termID]}' + - value: rangeland biome [ENVO:01000247] + from_schema: https://w3id.org/mixs + keywords: + - context + - environmental slot_uri: MIXS:0000012 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig range: ControlledIdentifiedTermValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + annotations: + tooltip: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context env_local_scale: annotations: - expected_value: - tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + Expected_value: + tag: Expected_value + value: Environmental entities having causal influences upon the entity at time of sampling tooltip: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - description: 'Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.' + description: 'Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' title: local environmental context examples: - - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336].' - from_schema: http://w3id.org/mixs/terms - aliases: - - local environmental context - is_a: environment field - string_serialization: '{termLabel} {[termID]}' + - value: hillside [ENVO:01000333] + from_schema: https://w3id.org/mixs + keywords: + - context + - environmental + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000013 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig range: ControlledIdentifiedTermValue env_medium: - annotations: - expected_value: - tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. - tooltip: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - description: 'Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).' + description: 'Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)' title: environmental medium examples: - - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]' - from_schema: http://w3id.org/mixs/terms - aliases: - - environmental medium - is_a: environment field - string_serialization: '{termLabel} {[termID]}' + - value: bluegrass field soil [ENVO:00005789] + from_schema: https://w3id.org/mixs + keywords: + - environmental slot_uri: MIXS:0000014 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig range: ControlledIdentifiedTermValue - escalator: + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' + tooltip: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure + escalator: description: The number of escalators within the built structure title: escalator count examples: - value: '4' - from_schema: http://w3id.org/mixs/terms - aliases: - - escalator count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count slot_uri: MIXS:0000800 - multivalued: false range: TextValue ethylbenzene: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of ethylbenzene in the sample title: ethylbenzene - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - ethylbenzene - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000155 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true exp_duct: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The amount of exposed ductwork in the room title: exposed ductwork - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - exposed ductwork - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000144 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true exp_pipe: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The number of exposed pipes in the room title: exposed pipes - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - exposed pipes - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - pipes slot_uri: MIXS:0000220 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true experimental_factor: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: text or EFO and/or OBI - description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI + description: Variable aspects of an experiment design that can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI) title: experimental factor examples: - - value: time series design [EFO:EFO_0001779] - from_schema: http://w3id.org/mixs/terms - aliases: - - experimental factor - is_a: investigation field - string_serialization: '{termLabel} {[termID]}|{text}' + - value: time series design [EFO:0001779] + from_schema: https://w3id.org/mixs + keywords: + - experimental + - factor + string_serialization: '{termLabel} [{termID}]|{text}' slot_uri: MIXS:0000008 - multivalued: false range: ControlledTermValue + multivalued: false + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ ext_door: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of exterior doors in the built structure title: exterior door count - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - exterior door count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - door + - exterior slot_uri: MIXS:0000170 - multivalued: false range: TextValue ext_wall_orient: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The orientation of the exterior wall title: orientations of exterior wall examples: - value: northwest - from_schema: http://w3id.org/mixs/terms - aliases: - - orientations of exterior wall - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - exterior + - wall slot_uri: MIXS:0000817 - multivalued: false - range: ext_wall_orient_enum + range: SHARED_ENUM_0 ext_window_orient: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The compass direction the exterior window of the room is facing title: orientations of exterior window examples: - value: southwest - from_schema: http://w3id.org/mixs/terms - aliases: - - orientations of exterior window - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - exterior + - window slot_uri: MIXS:0000818 - multivalued: false - range: ext_window_orient_enum + range: SHARED_ENUM_0 extreme_event: - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' description: Unusual physical events that may have affected microbial populations title: history/extreme events - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - history/extreme events - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - event + - history slot_uri: MIXS:0000320 - multivalued: false range: string fao_class: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups title: soil_taxonomic/FAO classification examples: - value: Luvisols - from_schema: http://w3id.org/mixs/terms - aliases: - - soil_taxonomic/FAO classification - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - classification slot_uri: MIXS:0001083 - multivalued: false - range: fao_class_enum + range: FAO_CLASS_ENUM fertilizer_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: fertilizer name;fertilizer amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens title: fertilizer regimen examples: - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - fertilizer regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - regimen string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000556 multivalued: true range: TextValue field: - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' description: Name of the hydrocarbon field (e.g. Albacora) title: field name - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - field name - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000291 - multivalued: false range: TextValue + recommended: true filter_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: A device which removes solid particulates or airborne molecular contaminants title: filter type examples: - value: HEPA - from_schema: http://w3id.org/mixs/terms - aliases: - - filter type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - filter + - type slot_uri: MIXS:0000765 + range: FILTER_TYPE_ENUM multivalued: true - range: filter_type_enum fire: - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' description: Historical and/or physical evidence of fire title: history/fire - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - history/fire - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - history slot_uri: MIXS:0001086 - multivalued: false range: string fireplace_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: A firebox with chimney title: fireplace type examples: - value: wood burning - from_schema: http://w3id.org/mixs/terms - aliases: - - fireplace type - is_a: core field - string_serialization: '[gas burning|wood burning]' + from_schema: https://w3id.org/mixs + keywords: + - type slot_uri: MIXS:0000802 - multivalued: false - range: TextValue + range: FIREPLACE_TYPE_ENUM flooding: - annotations: - expected_value: - tag: expected_value - value: date - occurrence: - tag: occurrence - value: '1' description: Historical and/or physical evidence of flooding title: history/flooding - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - history/flooding - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - history slot_uri: MIXS:0000319 - multivalued: false range: string floor_age: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: years, weeks, days - occurrence: - tag: occurrence - value: '1' description: The time period since installment of the carpet or flooring title: floor age - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - floor age - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - age + - floor slot_uri: MIXS:0000164 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true floor_area: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The area of the floor space within the room title: floor area - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - floor area - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - area + - floor slot_uri: MIXS:0000165 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true floor_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: floor condition examples: - value: new - from_schema: http://w3id.org/mixs/terms - aliases: - - floor condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - floor slot_uri: MIXS:0000803 - multivalued: false - range: floor_cond_enum + range: SHARED_ENUM_3 floor_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of floors in the building, including basements and mechanical penthouse title: floor count - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - floor count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - floor slot_uri: MIXS:0000225 - multivalued: false range: TextValue floor_finish_mat: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: The floor covering type; the finished surface that is walked on title: floor finish material examples: - value: carpet - from_schema: http://w3id.org/mixs/terms - aliases: - - floor finish material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - floor + - material + string_serialization: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint]' slot_uri: MIXS:0000804 - multivalued: false - range: floor_finish_mat_enum floor_struc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Refers to the structural elements and subfloor upon which the finish flooring is installed title: floor structure examples: - value: concrete - from_schema: http://w3id.org/mixs/terms - aliases: - - floor structure - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - floor slot_uri: MIXS:0000806 - multivalued: false - range: floor_struc_enum + range: FLOOR_STRUC_ENUM floor_thermal_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' description: The ability of the floor to provide inertia against temperature fluctuations title: floor thermal mass - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - floor thermal mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - floor + - mass slot_uri: MIXS:0000166 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true floor_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Signs of the presence of mold or mildew in a room title: floor signs of water/mold examples: - value: ceiling discoloration - from_schema: http://w3id.org/mixs/terms - aliases: - - floor signs of water/mold - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - floor slot_uri: MIXS:0000805 - multivalued: false - range: floor_water_mold_enum + range: FLOOR_WATER_MOLD_ENUM fluor: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram chlorophyll a per cubic meter, volts - occurrence: - tag: occurrence - value: '1' description: Raw or converted fluorescence of water title: fluorescence examples: - value: 2.5 volts - from_schema: http://w3id.org/mixs/terms - aliases: - - fluorescence - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000704 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true freq_clean: - annotations: - expected_value: - tag: expected_value - value: enumeration or {text} - occurrence: - tag: occurrence - value: '1' - description: The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually. + description: The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually title: frequency of cleaning examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - frequency of cleaning - is_a: core field + - value: Daily + from_schema: https://w3id.org/mixs + keywords: + - frequency slot_uri: MIXS:0000226 - multivalued: false range: QuantityValue freq_cook: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The number of times a meal is cooked per week title: frequency of cooking - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - frequency of cooking - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - frequency slot_uri: MIXS:0000227 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true fungicide_regm: annotations: - expected_value: - tag: expected_value - value: fungicide name;fungicide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens title: fungicide regimen examples: - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - fungicide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen slot_uri: MIXS:0000557 - multivalued: true range: TextValue + multivalued: true furniture: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The types of furniture present in the sampled room title: furniture examples: - value: chair - from_schema: http://w3id.org/mixs/terms - aliases: - - furniture - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000807 - multivalued: false - range: furniture_enum + range: FURNITURE_ENUM gaseous_environment: annotations: - expected_value: - tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: m description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens title: gaseous environment examples: - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - gaseous environment - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - environment slot_uri: MIXS:0000558 - multivalued: true range: TextValue + multivalued: true gaseous_substances: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: gaseous substance name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: m description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances title: gaseous substances - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - gaseous substances - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000661 multivalued: true range: TextValue gender_restroom: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The gender type of the restroom title: gender of restroom examples: - value: male - from_schema: http://w3id.org/mixs/terms - aliases: - - gender of restroom - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000808 - multivalued: false - range: gender_restroom_enum + range: GENDER_RESTROOM_ENUM genetic_mod: annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' + Expected_value: + tag: Expected_value + value: PMID, DOI, URL or text description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection title: genetic modification examples: - value: aox1A transgenic - from_schema: http://w3id.org/mixs/terms - aliases: - - genetic modification - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' + from_schema: https://w3id.org/mixs + string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000859 - multivalued: false - range: TextValue geo_loc_name: - annotations: - expected_value: - tag: expected_value - value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name' description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ) title: geographic location (country and/or sea,region) examples: - value: 'USA: Maryland, Bethesda' - from_schema: http://w3id.org/mixs/terms - aliases: - - geographic location (country and/or sea,region) - is_a: environment field - string_serialization: '{term}: {term}, {text}' + from_schema: https://w3id.org/mixs + keywords: + - geographic + - location slot_uri: MIXS:0000010 - multivalued: false - range: TextValue + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + - SymbiontAssociated + range: TextValue + pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' + structured_pattern: + syntax: '^{text}: {text}, {text}$' + interpolated: true + partial_match: true glucosidase_act: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: mol per liter per hour - occurrence: - tag: occurrence - value: '1' description: Measurement of glucosidase activity title: glucosidase activity examples: - value: 5 mol per liter per hour - from_schema: http://w3id.org/mixs/terms - aliases: - - glucosidase activity - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000137 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true gravidity: - annotations: - expected_value: - tag: expected_value - value: gravidity status;timestamp - occurrence: - tag: occurrence - value: '1' description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used title: gravidity examples: - value: yes;due date:2018-05-11 - from_schema: http://w3id.org/mixs/terms - aliases: - - gravidity - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{boolean};{timestamp}' slot_uri: MIXS:0000875 - multivalued: false range: TextValue gravity: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: gravity factor value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter per square second, g - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments title: gravity examples: - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - gravity - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000559 multivalued: true range: TextValue growth_facil: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: free text or CO - occurrence: - tag: occurrence - value: '1' description: 'Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' title: growth facility examples: - value: Growth chamber [CO_715:0000189] - from_schema: http://w3id.org/mixs/terms - aliases: - - growth facility - is_a: core field - string_serialization: '{text}|{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - facility + - growth + string_serialization: '{text}|{termLabel} [{termID}]' slot_uri: MIXS:0001043 - multivalued: false range: ControlledTermValue growth_habit: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Characteristic shape, appearance or growth form of a plant species title: growth habit examples: - value: spreading - from_schema: http://w3id.org/mixs/terms - aliases: - - growth habit - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - growth slot_uri: MIXS:0001044 - multivalued: false - range: growth_habit_enum + range: GROWTH_HABIT_ENUM growth_hormone_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: growth hormone name;growth hormone amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens title: growth hormone regimen examples: - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - growth hormone regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - growth + - regimen string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000560 multivalued: true range: TextValue hall_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The total count of hallways and cooridors in the built structure title: hallway/corridor count - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - hallway/corridor count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - corridor + - count + - hallway slot_uri: MIXS:0000228 - multivalued: false range: TextValue handidness: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The handidness of the individual sampled title: handidness examples: - value: right handedness - from_schema: http://w3id.org/mixs/terms - aliases: - - handidness - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000809 - multivalued: false - range: handidness_enum + range: HANDIDNESS_ENUM hc_produced: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field title: hydrocarbon type produced examples: - value: Gas - from_schema: http://w3id.org/mixs/terms - aliases: - - hydrocarbon type produced - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - hydrocarbon + - type slot_uri: MIXS:0000989 - multivalued: false - range: hc_produced_enum + range: HC_PRODUCED_ENUM hcr: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field title: hydrocarbon resource type examples: - value: Oil Sand - from_schema: http://w3id.org/mixs/terms - aliases: - - hydrocarbon resource type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - hydrocarbon + - resource + - type slot_uri: MIXS:0000988 - multivalued: false - range: hcr_enum + range: HCR_ENUM hcr_fw_salinity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS title: formation water salinity - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - formation water salinity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - salinity + - water slot_uri: MIXS:0000406 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true hcr_geol_age: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' title: hydrocarbon resource geological age examples: - value: Silurian - from_schema: http://w3id.org/mixs/terms - aliases: - - hydrocarbon resource geological age - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - age + - hydrocarbon + - resource slot_uri: MIXS:0000993 - multivalued: false - range: hcr_geol_age_enum + range: SHARED_ENUM_5 + recommended: true hcr_pressure: annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: atmosphere, kilopascal - occurrence: - tag: occurrence - value: '1' description: Original pressure of the hydrocarbon resource title: hydrocarbon resource original pressure - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - hydrocarbon resource original pressure - is_a: core field - string_serialization: '{float} - {float} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - hydrocarbon + - pressure + - resource slot_uri: MIXS:0000395 - multivalued: false range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true hcr_temp: annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Original temperature of the hydrocarbon resource title: hydrocarbon resource original temperature examples: - value: 150-295 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - hydrocarbon resource original temperature - is_a: core field - string_serialization: '{float} - {float} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - hydrocarbon + - resource + - temperature slot_uri: MIXS:0000393 - multivalued: false range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true heat_cool_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: Methods of conditioning or heating a room or building title: heating and cooling system type examples: - value: heat pump - from_schema: http://w3id.org/mixs/terms - aliases: - - heating and cooling system type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type slot_uri: MIXS:0000766 + range: HEAT_COOL_TYPE_ENUM multivalued: true - range: heat_cool_type_enum heat_deliv_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The location of heat delivery within the room title: heating delivery locations examples: - value: north - from_schema: http://w3id.org/mixs/terms - aliases: - - heating delivery locations - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - delivery + - location + - locations slot_uri: MIXS:0000810 - multivalued: false - range: heat_deliv_loc_enum + range: SHARED_ENUM_0 heat_sys_deliv_meth: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The method by which the heat is delivered through the system title: heating system delivery method examples: - value: radiant - from_schema: http://w3id.org/mixs/terms - aliases: - - heating system delivery method - is_a: core field - string_serialization: '[conductive|radiant]' + from_schema: https://w3id.org/mixs + keywords: + - delivery + - method slot_uri: MIXS:0000812 - multivalued: false range: string heat_system_id: - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' description: The heating system identifier title: heating system identifier - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - heating system identifier - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - identifier slot_uri: MIXS:0000833 - multivalued: false range: TextValue heavy_metals: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: heavy metal name;measurement value unit - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per gram - occurrence: - tag: occurrence - value: m - description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field. + description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field title: extreme_unusual_properties/heavy metals examples: - value: mercury;0.09 micrograms per gram - from_schema: http://w3id.org/mixs/terms - aliases: - - extreme_unusual_properties/heavy metals - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - extreme + - properties + - unusual string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000652 + domain_of: + - Soil multivalued: true range: TextValue heavy_metals_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining heavy metals title: extreme_unusual_properties/heavy metals method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - extreme_unusual_properties/heavy metals method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - extreme + - method + - properties + - unusual slot_uri: MIXS:0000343 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true height_carper_fiber: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: centimeter - occurrence: - tag: occurrence - value: '1' description: The average carpet fiber height in the indoor environment title: height carpet fiber mat - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - height carpet fiber mat - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - height slot_uri: MIXS:0000167 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true herbicide_regm: annotations: - expected_value: - tag: expected_value - value: herbicide name;herbicide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: herbicide regimen examples: - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - herbicide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen slot_uri: MIXS:0000561 - multivalued: true range: TextValue + multivalued: true horizon_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining the horizon - title: soil horizon method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil horizon method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + title: horizon method + from_schema: https://w3id.org/mixs + keywords: + - horizon + - method slot_uri: MIXS:0000321 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true host_age: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: year, day, hour - occurrence: - tag: occurrence - value: '1' description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees title: host age - examples: - - value: 10 days - from_schema: http://w3id.org/mixs/terms - aliases: - - host age - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - age + - host + - host. slot_uri: MIXS:0000255 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_body_habitat: - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' description: Original body habitat where the sample was obtained from title: host body habitat - examples: - - value: nasopharynx - from_schema: http://w3id.org/mixs/terms - aliases: - - host body habitat - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - body + - habitat + - host + - host. slot_uri: MIXS:0000866 - multivalued: false range: TextValue host_body_product: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: FMA or UBERON - occurrence: - tag: occurrence - value: '1' - description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon + description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. Use terms from the foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) title: host body product examples: - - value: Portion of mucus [fma66938] - from_schema: http://w3id.org/mixs/terms - aliases: - - host body product - is_a: core field - string_serialization: '{termLabel} {[termID]}' + - value: mucus [FMA:66938] + from_schema: https://w3id.org/mixs + keywords: + - body + - host + - host. + - product + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000888 - multivalued: false range: ControlledTermValue host_body_site: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: FMA or UBERON - occurrence: - tag: occurrence - value: '1' - description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON + description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). Use terms from the foundational model of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON) title: host body site - examples: - - value: gill [UBERON:0002535] - from_schema: http://w3id.org/mixs/terms - aliases: - - host body site - is_a: core field - string_serialization: '{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - body + - host + - host. + - site + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000867 - multivalued: false range: ControlledTermValue host_body_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Core body temperature of the host when sample was collected title: host body temperature - examples: - - value: 15 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - host body temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - body + - host + - host. + - temperature slot_uri: MIXS:0000274 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_color: - annotations: - expected_value: - tag: expected_value - value: color - occurrence: - tag: occurrence - value: '1' description: The color of host title: host color - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - host color - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. slot_uri: MIXS:0000260 - multivalued: false range: TextValue host_common_name: annotations: - expected_value: - tag: expected_value - value: common name - occurrence: - tag: occurrence - value: '1' - description: Common name of the host. + Preferred_unit: + tag: Preferred_unit + value: '' + description: Common name of the host title: host common name - examples: - - value: human - from_schema: http://w3id.org/mixs/terms - aliases: - - host common name - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. slot_uri: MIXS:0000248 - multivalued: false range: TextValue host_diet: - annotations: - expected_value: - tag: expected_value - value: diet type - occurrence: - tag: occurrence - value: m description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types title: host diet - examples: - - value: herbivore - from_schema: http://w3id.org/mixs/terms - aliases: - - host diet - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - diet + - host + - host. slot_uri: MIXS:0000869 - multivalued: true - range: TextValue - host_disease_stat: - annotations: - expected_value: - tag: expected_value - value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text - title: host disease status - examples: - - value: rabies [DOID:11260] - from_schema: http://w3id.org/mixs/terms - aliases: - - host disease status - is_a: nucleic acid sequence source field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000031 - multivalued: false range: TextValue + multivalued: true host_dry_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: kilogram, gram - occurrence: - tag: occurrence - value: '1' description: Measurement of dry mass title: host dry mass examples: - value: 500 gram - from_schema: http://w3id.org/mixs/terms - aliases: - - host dry mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dry + - host + - host. + - mass slot_uri: MIXS:0000257 - multivalued: false range: QuantityValue - host_family_relation: - annotations: - expected_value: - tag: expected_value - value: relationship type;arbitrary identifier - occurrence: - tag: occurrence - value: m - description: Familial relationships to other hosts in the same study; can include multiple relationships - title: host family relationship - examples: - - value: offspring;Mussel25 - from_schema: http://w3id.org/mixs/terms - aliases: - - host family relationship - is_a: core field - string_serialization: '{text};{text}' - slot_uri: MIXS:0000872 - multivalued: true - range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_genotype: - annotations: - expected_value: - tag: expected_value - value: genotype - occurrence: - tag: occurrence - value: '1' description: Observed genotype title: host genotype - examples: - - value: C57BL/6 - from_schema: http://w3id.org/mixs/terms - aliases: - - host genotype - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. slot_uri: MIXS:0000365 - multivalued: false range: TextValue host_growth_cond: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' description: Literature reference giving growth conditions of the host title: host growth conditions examples: - value: https://academic.oup.com/icesjms/article/68/2/349/617247 - from_schema: http://w3id.org/mixs/terms - aliases: - - host growth conditions - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' + from_schema: https://w3id.org/mixs + keywords: + - condition + - growth + - host + - host. slot_uri: MIXS:0000871 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true host_height: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: centimeter, millimeter, meter - occurrence: - tag: occurrence - value: '1' description: The height of subject title: host height - examples: - - value: 0.1 meter - from_schema: http://w3id.org/mixs/terms - aliases: - - host height - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - height + - host + - host. slot_uri: MIXS:0000264 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_last_meal: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: content;duration - occurrence: - tag: occurrence - value: m description: Content of last meal and time since feeding; can include multiple values title: host last meal - examples: - - value: corn feed;P2H - from_schema: http://w3id.org/mixs/terms - aliases: - - host last meal - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. string_serialization: '{text};{duration}' slot_uri: MIXS:0000870 multivalued: true - range: TextValue host_length: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: centimeter, millimeter, meter - occurrence: - tag: occurrence - value: '1' description: The length of subject title: host length examples: - value: 1 meter - from_schema: http://w3id.org/mixs/terms - aliases: - - host length - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - length slot_uri: MIXS:0000256 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_life_stage: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: stage - occurrence: - tag: occurrence - value: '1' description: Description of life stage of host title: host life stage - examples: - - value: adult - from_schema: http://w3id.org/mixs/terms - aliases: - - host life stage - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - life string_serialization: '{text}' slot_uri: MIXS:0000251 - multivalued: false range: TextValue host_phenotype: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: PATO or HP - occurrence: - tag: occurrence - value: '1' - description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP + description: Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP) title: host phenotype - examples: - - value: elongated [PATO:0001154] - from_schema: http://w3id.org/mixs/terms - aliases: - - host phenotype - is_a: core field - string_serialization: '{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000874 - multivalued: false range: ControlledTermValue host_sex: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Gender or physical sex of the host. + description: Gender or physical sex of the host title: host sex - examples: - - value: non-binary - from_schema: http://w3id.org/mixs/terms - aliases: - - host sex - is_a: core field + comments: + - example of non-binary from Excel sheets does not match any of the enumerated values + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender (female to male)|transgender (male to female) + + |undeclared]' slot_uri: MIXS:0000811 - multivalued: false - range: host_sex_enum host_shape: - annotations: - expected_value: - tag: expected_value - value: shape - occurrence: - tag: occurrence - value: '1' description: Morphological shape of host title: host shape examples: - value: round - from_schema: http://w3id.org/mixs/terms - aliases: - - host shape - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. slot_uri: MIXS:0000261 - multivalued: false range: TextValue host_subject_id: - annotations: - expected_value: - tag: expected_value - value: unique identifier - occurrence: - tag: occurrence - value: '1' - description: A unique identifier by which each subject can be referred to, de-identified. + description: A unique identifier by which each subject can be referred to, de-identified title: host subject id - examples: - - value: MPI123 - from_schema: http://w3id.org/mixs/terms - aliases: - - host subject id - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - identifier slot_uri: MIXS:0000861 - multivalued: false range: TextValue host_subspecf_genlin: annotations: - expected_value: - tag: expected_value - value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar. - occurrence: - tag: occurrence - value: m - description: Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. + Expected_value: + tag: Expected_value + value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar + description: Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123 title: host subspecific genetic lineage examples: - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' - from_schema: http://w3id.org/mixs/terms - aliases: - - host subspecific genetic lineage - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - lineage string_serialization: '{rank name}:{text}' slot_uri: MIXS:0001318 multivalued: true range: string host_substrate: - annotations: - expected_value: - tag: expected_value - value: substrate name - occurrence: - tag: occurrence - value: '1' - description: The growth substrate of the host. + description: The growth substrate of the host title: host substrate examples: - value: rock - from_schema: http://w3id.org/mixs/terms - aliases: - - host substrate - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - host + - host. slot_uri: MIXS:0000252 - multivalued: false range: TextValue host_symbiont: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: species name or common name - occurrence: - tag: occurrence - value: m - description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. + description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite) title: observed host symbionts - examples: - - value: flukeworms - from_schema: http://w3id.org/mixs/terms - aliases: - - observed host symbionts - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - observed + - symbiosis string_serialization: '{text}' slot_uri: MIXS:0001298 multivalued: true range: string host_taxid: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: NCBI taxon identifier - occurrence: - tag: occurrence - value: '1' description: NCBI taxon id of the host, e.g. 9606 title: host taxid - from_schema: http://w3id.org/mixs/terms - aliases: - - host taxid - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - taxon slot_uri: MIXS:0000250 - multivalued: false - range: ControlledIdentifiedTermValue comments: - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value + range: ControlledIdentifiedTermValue host_tot_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: kilogram, gram - occurrence: - tag: occurrence - value: '1' description: Total mass of the host at collection, the unit depends on host title: host total mass - examples: - - value: 2500 gram - from_schema: http://w3id.org/mixs/terms - aliases: - - host total mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - mass + - total slot_uri: MIXS:0000263 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true host_wet_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: kilogram, gram - occurrence: - tag: occurrence - value: '1' description: Measurement of wet mass title: host wet mass examples: - value: 1500 gram - from_schema: http://w3id.org/mixs/terms - aliases: - - host wet mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - host + - host. + - mass + - wet slot_uri: MIXS:0000567 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true humidity: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: gram per cubic meter - occurrence: - tag: occurrence - value: '1' description: Amount of water vapour in the air, at the time of sampling title: humidity - examples: - - value: 25 gram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - humidity - is_a: core field slot_uri: MIXS:0000100 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true humidity_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: humidity value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per cubic meter - occurrence: - tag: occurrence - value: m description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: humidity regimen examples: - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - humidity regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - humidity + - regimen string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 multivalued: true range: TextValue indoor_space: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used title: indoor space examples: - value: foyer - from_schema: http://w3id.org/mixs/terms - aliases: - - indoor space - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - indoor slot_uri: MIXS:0000763 - multivalued: false - range: indoor_space_enum + range: INDOOR_SPACE_ENUM indoor_surf: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Type of indoor surface title: indoor surface examples: - value: wall - from_schema: http://w3id.org/mixs/terms - aliases: - - indoor surface - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - indoor + - surface slot_uri: MIXS:0000764 - multivalued: false - range: indoor_surf_enum + range: INDOOR_SURF_ENUM indust_eff_percent: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: Percentage of industrial effluents received by wastewater treatment plant title: industrial effluent percent - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - industrial effluent percent - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - percent slot_uri: MIXS:0000662 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true inorg_particles: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: inorganic particle name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles title: inorganic particles - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - inorganic particles - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - inorganic + - particle string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000664 multivalued: true range: TextValue inside_lux: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: kilowatt per square metre - occurrence: - tag: occurrence - value: '1' description: The recorded value at sampling time (power density) title: inside lux light - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - inside lux light - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - inside + - light slot_uri: MIXS:0000168 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true int_wall_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: interior wall condition examples: - value: damaged - from_schema: http://w3id.org/mixs/terms - aliases: - - interior wall condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - interior + - wall slot_uri: MIXS:0000813 - multivalued: false - range: int_wall_cond_enum + range: SHARED_ENUM_3 iw_bt_date_well: - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' description: Injection water breakthrough date per well following a secondary and/or tertiary recovery title: injection water breakthrough date of specific well examples: - - value: '2018-05-11' - from_schema: http://w3id.org/mixs/terms - aliases: - - injection water breakthrough date of specific well - is_a: core field + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs + keywords: + - date + - water slot_uri: MIXS:0001010 - multivalued: false range: TimestampValue iwf: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) title: injection water fraction + comments: + - pattern was "[0-9]*\\.?[0-9]+ ?%" + - percent or float? examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - injection water fraction - is_a: core field + - value: '0.79' + from_schema: https://w3id.org/mixs + keywords: + - fraction + - water slot_uri: MIXS:0000455 - multivalued: false - range: QuantityValue + range: float + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true last_clean: - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' description: The last time the floor was cleaned (swept, mopped, vacuumed) title: last time swept/mopped/vacuumed examples: - - value: 2018-05-11:T14:30Z - from_schema: http://w3id.org/mixs/terms - aliases: - - last time swept/mopped/vacuumed - is_a: core field + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs + keywords: + - time slot_uri: MIXS:0000814 - multivalued: false range: TimestampValue lat_lon: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: decimal degrees, limit to 8 decimal points description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system title: geographic location (latitude and longitude) examples: - value: 50.586825 6.408977 - from_schema: http://w3id.org/mixs/terms - aliases: - - geographic location (latitude and longitude) - is_a: environment field + from_schema: https://w3id.org/mixs + keywords: + - geographic + - location string_serialization: '{float} {float}' slot_uri: MIXS:0000009 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + - SymbiontAssociated + pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$ + structured_pattern: + syntax: ^{lat} {lon}$ + interpolated: true + partial_match: true range: GeolocationValue light_intensity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: lux - occurrence: - tag: occurrence - value: '1' description: Measurement of light intensity title: light intensity examples: - value: 0.3 lux - from_schema: http://w3id.org/mixs/terms - aliases: - - light intensity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - intensity + - light slot_uri: MIXS:0000706 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true light_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: exposure type;light intensity;light quality - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: lux; micrometer, nanometer, angstrom - occurrence: - tag: occurrence - value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + description: Information about treatment(s) involving exposure to light, including both light intensity and quality title: light regimen examples: - value: incandescant light;10 lux;450 nanometer - from_schema: http://w3id.org/mixs/terms - aliases: - - light regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - light + - regimen string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 - multivalued: false range: TextValue light_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light title: light type examples: - value: desk lamp - from_schema: http://w3id.org/mixs/terms - aliases: - - light type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - light + - type slot_uri: MIXS:0000769 + range: LIGHT_TYPE_ENUM multivalued: true - range: light_type_enum link_addit_analys: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Link to additional analysis results performed on the sample title: links to additional analysis - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - links to additional analysis - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - link slot_uri: MIXS:0000340 - multivalued: false + domain_of: + - Soil range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true link_class_info: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Link to digitized soil maps or other soil classification information title: link to classification information - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - link to classification information - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - classification + - information + - link + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000329 - multivalued: false - range: TextValue + domain_of: + - Agriculture + - Soil link_climate_info: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Link to climate resource title: link to climate information - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - link to climate information - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - information + - link slot_uri: MIXS:0000328 - multivalued: false - range: TextValue + domain_of: + - Agriculture + - Soil + range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true lithology: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field' title: lithology examples: - value: Volcanic - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - lithology - is_a: core field slot_uri: MIXS:0000990 - multivalued: false - range: lithology_enum + range: LITHOLOGY_ENUM + recommended: true local_class: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: local classification name - occurrence: - tag: occurrence - value: '1' description: Soil classification based on local soil classification system title: soil_taxonomic/local classification - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil_taxonomic/local classification - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - classification string_serialization: '{text}' slot_uri: MIXS:0000330 - multivalued: false - range: TextValue local_class_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining the local soil classification title: soil_taxonomic/local classification method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil_taxonomic/local classification method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - classification + - method slot_uri: MIXS:0000331 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true magnesium: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: mole per liter, milligram per liter, parts per million, micromole per kilogram - occurrence: - tag: occurrence - value: '1' description: Concentration of magnesium in the sample title: magnesium examples: - value: 52.8 micromole per kilogram - from_schema: http://w3id.org/mixs/terms - aliases: - - magnesium - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000431 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true max_occup: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The maximum amount of people allowed in the indoor environment title: maximum occupancy - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - maximum occupancy - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - maximum slot_uri: MIXS:0000229 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true mean_frict_vel: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter per second - occurrence: - tag: occurrence - value: '1' description: Measurement of mean friction velocity title: mean friction velocity examples: - value: 0.5 meter per second - from_schema: http://w3id.org/mixs/terms - aliases: - - mean friction velocity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mean + - velocity slot_uri: MIXS:0000498 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true mean_peak_frict_vel: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter per second - occurrence: - tag: occurrence - value: '1' description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - value: 1 meter per second - from_schema: http://w3id.org/mixs/terms - aliases: - - mean peak friction velocity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mean + - peak + - velocity slot_uri: MIXS:0000502 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true mech_struc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'mechanical structure: a moving structure' title: mechanical structure examples: - value: elevator - from_schema: http://w3id.org/mixs/terms - aliases: - - mechanical structure - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000815 - multivalued: false - range: mech_struc_enum + range: MECH_STRUC_ENUM mechanical_damage: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: damage type;body site - occurrence: - tag: occurrence - value: m description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites title: mechanical damage examples: - value: pruning;bark - from_schema: http://w3id.org/mixs/terms - aliases: - - mechanical damage - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{text}' slot_uri: MIXS:0001052 multivalued: true - range: TextValue methane: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, parts per billion, parts per million - occurrence: - tag: occurrence - value: '1' description: Methane (gas) amount or concentration at the time of sampling title: methane - examples: - - value: 1800 parts per billion - from_schema: http://w3id.org/mixs/terms - aliases: - - methane - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000101 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true micro_biomass_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining microbial biomass title: microbial biomass method + comments: + - slot name/scn was microbial_biomass_meth examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - microbial biomass method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021 + from_schema: https://w3id.org/mixs + keywords: + - biomass + - method + - microbial slot_uri: MIXS:0000339 - multivalued: false range: string microbial_biomass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: ton, kilogram, gram per kilogram soil - occurrence: - tag: occurrence - value: '1' description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units title: microbial biomass - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - microbial biomass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - biomass + - microbial slot_uri: MIXS:0000650 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true mineral_nutr_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: mineral nutrient name;mineral nutrient amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens title: mineral nutrient regimen examples: - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - mineral nutrient regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mineral + - nutrient + - regimen string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000570 multivalued: true range: TextValue misc_param: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: parameter name;measurement value - occurrence: - tag: occurrence - value: m description: Any other measurement performed or parameter collected, that is not listed here title: miscellaneous parameter examples: - value: Bicarbonate ion concentration;2075 micromole per kilogram - from_schema: http://w3id.org/mixs/terms - aliases: - - miscellaneous parameter - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - parameter string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 + domain_of: + - Agriculture + - Air + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + - HostAssociated + - HumanAssociated + - HumanGut + - HumanOral + - HumanSkin + - HumanVaginal + - HydrocarbonResourcesCores + - HydrocarbonResourcesFluidsSwabs + - MicrobialMatBiofilm + - MiscellaneousNaturalOrArtificialEnvironment + - PlantAssociated + - Sediment + - Soil + - SymbiontAssociated + - WastewaterSludge + - Water multivalued: true range: TextValue n_alkanes: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: n-alkane name;measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: m description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - value: n-hexadecane;100 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - n-alkanes - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 multivalued: true range: TextValue nitrate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of nitrate in the sample title: nitrate examples: - value: 65 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - nitrate - is_a: core field slot_uri: MIXS:0000425 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true nitrite: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of nitrite in the sample title: nitrite examples: - value: 0.5 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - nitrite - is_a: core field slot_uri: MIXS:0000426 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of nitrogen (total) title: nitrogen examples: - value: 4.2 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - nitrogen - is_a: core field slot_uri: MIXS:0000504 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true non_min_nutr_regm: annotations: - expected_value: - tag: expected_value - value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens title: non-mineral nutrient regimen examples: - - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - non-mineral nutrient regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ + from_schema: https://w3id.org/mixs + keywords: + - non-mineral + - nutrient + - regimen slot_uri: MIXS:0000571 - multivalued: true range: string + multivalued: true nucl_acid_amp: - annotations: - expected_value: - tag: expected_value - value: PMID, DOI or URL description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids title: nucleic acid amplification examples: - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ - from_schema: http://w3id.org/mixs/terms - aliases: - - nucleic acid amplification - is_a: sequencing field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000038 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true nucl_acid_ext: - annotations: - expected_value: - tag: expected_value - value: PMID, DOI or URL description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample title: nucleic acid extraction examples: - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf - from_schema: http://w3id.org/mixs/terms - aliases: - - nucleic acid extraction - is_a: sequencing field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000037 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true number_pets: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The number of pets residing in the sampled space title: number of pets - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - number of pets - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - number slot_uri: MIXS:0000231 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true number_plants: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The number of plant(s) in the sampling space title: number of houseplants - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - number of houseplants - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - number slot_uri: MIXS:0000230 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true number_resident: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: The number of individuals currently occupying in the sampling location title: number of residents - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - number of residents - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - number slot_uri: MIXS:0000232 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true occup_density_samp: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: Average number of occupants at time of sampling per square footage title: occupant density at sampling examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - occupant density at sampling - is_a: core field + - value: '0.1' + from_schema: https://w3id.org/mixs + keywords: + - density slot_uri: MIXS:0000217 - multivalued: false range: QuantityValue occup_document: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of documentation of occupancy title: occupancy documentation examples: - value: estimate - from_schema: http://w3id.org/mixs/terms - aliases: - - occupancy documentation - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - documentation slot_uri: MIXS:0000816 - multivalued: false - range: occup_document_enum + range: OCCUP_DOCUMENT_ENUM occup_samp: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: Number of occupants present at time of sample within the given space title: occupancy at sampling examples: - value: '10' - from_schema: http://w3id.org/mixs/terms - aliases: - - occupancy at sampling - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000772 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true org_carb: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of organic carbon title: organic carbon examples: - value: 1.5 microgram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - organic carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - organic slot_uri: MIXS:0000508 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true org_count_qpcr_info: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: number of cells per gram (or ml or cm^2) - occurrence: - tag: occurrence - value: '1' description: 'If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)' title: organism count qPCR information - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - organism count qPCR information - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - information + - organism string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles' slot_uri: MIXS:0000099 - multivalued: false range: string org_matter: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of organic matter title: organic matter examples: - value: 1.75 milligram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: - - organic matter - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - organic slot_uri: MIXS:0000204 - multivalued: false - range: QuantityValue + domain_of: + - MicrobialMatBiofilm + - MiscellaneousNaturalOrArtificialEnvironment + - Sediment + - Soil + - Water + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true org_nitro: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of organic nitrogen title: organic nitrogen examples: - value: 4 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - organic nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - nitrogen + - organic slot_uri: MIXS:0000205 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true org_particles: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: particle name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per liter - occurrence: - tag: occurrence - value: m - description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc title: organic particles - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - organic particles - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - organic + - particle string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000665 multivalued: true range: TextValue organism_count: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: organism name;measurement value;enumeration - preferred_unit: - tag: preferred_unit - value: number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter - occurrence: - tag: occurrence - value: m description: 'Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' title: organism count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - from_schema: http://w3id.org/mixs/terms - aliases: - - organism count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - organism + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' slot_uri: MIXS:0000103 multivalued: true range: QuantityValue owc_tvdss: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) title: oil water contact depth - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - oil water contact depth - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - oil + - water slot_uri: MIXS:0000405 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true oxy_stat_samp: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Oxygenation status of sample title: oxygenation status of sample examples: - value: aerobic - from_schema: http://w3id.org/mixs/terms - aliases: - - oxygenation status of sample - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - oxygen + - sample + - status slot_uri: MIXS:0000753 - multivalued: false - range: oxy_stat_samp_enum + range: OXY_STAT_SAMP_ENUM oxygen: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Oxygen (gas) amount or concentration at the time of sampling title: oxygen examples: - value: 600 parts per million - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - oxygen - is_a: core field slot_uri: MIXS:0000104 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true part_org_carb: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of particulate organic carbon title: particulate organic carbon examples: - value: 1.92 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - particulate organic carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - organic + - particle + - particulate slot_uri: MIXS:0000515 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true part_org_nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of particulate organic nitrogen title: particulate organic nitrogen examples: - value: 0.3 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - particulate organic nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - nitrogen + - organic + - particle + - particulate slot_uri: MIXS:0000719 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true particle_class: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: particle name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micrometer - occurrence: - tag: occurrence - value: m description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values title: particle classification - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - particle classification - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - classification + - particle string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000206 multivalued: true range: TextValue pcr_cond: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' title: pcr conditions examples: - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 - from_schema: http://w3id.org/mixs/terms - aliases: - - pcr conditions - is_a: sequencing field + from_schema: https://w3id.org/mixs + keywords: + - condition + - pcr string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles slot_uri: MIXS:0000049 - multivalued: false - range: TextValue pcr_primers: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: 'FWD: forward primer sequence;REV:reverse primer sequence' description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters title: pcr primers examples: - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT - from_schema: http://w3id.org/mixs/terms - aliases: - - pcr primers - is_a: sequencing field + from_schema: https://w3id.org/mixs + keywords: + - pcr string_serialization: FWD:{dna};REV:{dna} slot_uri: MIXS:0000046 - multivalued: false - range: TextValue permeability: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: mD - occurrence: - tag: occurrence - value: '1' description: 'Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' title: permeability - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - permeability - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{integer} - {integer} {unit}' slot_uri: MIXS:0000404 - multivalued: false range: TextValue perturbation: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: perturbation type name;perturbation interval and duration - occurrence: - tag: occurrence - value: m description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types title: perturbation examples: - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - perturbation - is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 multivalued: true range: TextValue pesticide_regm: annotations: - expected_value: - tag: expected_value - value: pesticide name;pesticide amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens title: pesticide regimen examples: - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - pesticide regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen slot_uri: MIXS:0000573 - multivalued: true range: TextValue + multivalued: true petroleum_hydrocarb: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - value: 0.05 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - petroleum hydrocarbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - hydrocarbon + - petroleum slot_uri: MIXS:0000516 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ph: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid title: pH examples: - value: '7.2' - from_schema: http://w3id.org/mixs/terms - aliases: - - pH - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ph slot_uri: MIXS:0001001 - multivalued: false - range: double + range: float ph_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining ph + description: Reference or method used in determining pH title: pH method examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - pH method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + from_schema: https://w3id.org/mixs + keywords: + - method + - ph slot_uri: MIXS:0001106 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true ph_regm: - annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - occurrence: - tag: occurrence - value: m description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen title: pH regimen examples: - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - pH regimen - is_a: core field - string_serialization: '{float};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - ph + - regimen slot_uri: MIXS:0001056 - multivalued: true range: TextValue + multivalued: true phaeopigments: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: phaeopigment name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per cubic meter - occurrence: - tag: occurrence - value: m description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - value: 2.5 milligram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: - - phaeopigments - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 multivalued: true range: TextValue phosphate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of phosphate title: phosphate examples: - value: 0.7 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - phosphate - is_a: core field slot_uri: MIXS:0000505 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true phosplipid_fatt_acid: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: phospholipid fatty acid name;measurement value - preferred_unit: - tag: preferred_unit - value: mole per gram, mole per liter - occurrence: - tag: occurrence - value: m description: Concentration of phospholipid fatty acids; can include multiple values title: phospholipid fatty acid examples: - value: 2.98 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - phospholipid fatty acid - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 multivalued: true range: TextValue photon_flux: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: number of photons per second per unit area - occurrence: - tag: occurrence - value: '1' description: Measurement of photon flux title: photon flux examples: - value: 3.926 micromole photons per second per square meter - from_schema: http://w3id.org/mixs/terms - aliases: - - photon flux - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000725 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true plant_growth_med: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: EO or enumeration - occurrence: - tag: occurrence - value: '1' description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary title: plant growth medium - examples: - - value: hydroponic plant culture media [EO:0007067] - from_schema: http://w3id.org/mixs/terms - aliases: - - plant growth medium - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - growth + - plant + string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' slot_uri: MIXS:0001057 - multivalued: false range: ControlledTermValue plant_product: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: product name - occurrence: - tag: occurrence - value: '1' description: Substance produced by the plant, where the sample was obtained from title: plant product examples: - value: xylem sap [PO:0025539] - from_schema: http://w3id.org/mixs/terms - aliases: - - plant product - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - plant + - product string_serialization: '{text}' slot_uri: MIXS:0001058 - multivalued: false - range: TextValue plant_sex: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite title: plant sex examples: - value: Hermaphroditic - from_schema: http://w3id.org/mixs/terms - aliases: - - plant sex - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - plant slot_uri: MIXS:0001059 - multivalued: false - range: plant_sex_enum + range: PLANT_SEX_ENUM plant_struc: - annotations: - expected_value: - tag: expected_value - value: PO - occurrence: - tag: occurrence - value: '1' - description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. + description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here title: plant structure examples: - value: epidermis [PO:0005679] - from_schema: http://w3id.org/mixs/terms - aliases: - - plant structure - is_a: core field - string_serialization: '{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - plant slot_uri: MIXS:0001060 - multivalued: false range: ControlledTermValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true pollutants: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: pollutant name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, mole per liter, milligram per liter, microgram per cubic meter - occurrence: - tag: occurrence - value: m description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant title: pollutants examples: - value: lead;0.15 microgram per cubic meter - from_schema: http://w3id.org/mixs/terms - aliases: - - pollutants - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000107 multivalued: true range: TextValue pool_dna_extracts: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: pooling status;number of pooled extracts - occurrence: - tag: occurrence - value: '1' + Preferred_unit: + tag: Preferred_unit + value: gram, milliliter, microliter description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given title: pooling of DNA extracts (if done) examples: - - value: yes;5 - from_schema: http://w3id.org/mixs/terms - aliases: - - pooling of DNA extracts (if done) - is_a: core field - string_serialization: '{boolean};{integer}' + - value: yes, 5 + from_schema: https://w3id.org/mixs + keywords: + - dna + - pooling slot_uri: MIXS:0000325 - multivalued: false - range: TextValue porosity: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value or range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: Porosity of deposited sediment is volume of voids divided by the total volume of sample title: porosity - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - porosity - is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000211 - multivalued: false range: TextValue potassium: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of potassium in the sample title: potassium examples: - value: 463 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - potassium - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000430 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true pour_point: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' - description: 'Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' + description: 'Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' title: pour point - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - pour point - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000127 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true pre_treatment: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: pre-treatment type - occurrence: - tag: occurrence - value: '1' description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater title: pre-treatment - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - pre-treatment - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text}' slot_uri: MIXS:0000348 - multivalued: false - range: TextValue pres_animal_insect: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration;count - occurrence: - tag: occurrence - value: '1' - description: The type and number of animals or insects present in the sampling space. + description: The type and number of animals or insects present in the sampling space title: presence of pets, animals, or insects examples: - value: cat;5 - from_schema: http://w3id.org/mixs/terms - aliases: - - presence of pets, animals, or insects - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - animal + - presence + string_serialization: '[cat|dog|rodent|snake|other];{integer}' slot_uri: MIXS:0000819 - multivalued: false range: string - pattern: ^(cat|dog|rodent|snake|other);\d+$ pressure: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: atmosphere - occurrence: - tag: occurrence - value: '1' description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - value: 50 atmosphere - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - pressure - is_a: core field slot_uri: MIXS:0000412 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true prev_land_use_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining previous land use and dates title: history/previous land use method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - history/previous land use method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - history + - land + - method + - use slot_uri: MIXS:0000316 - multivalued: false range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true previous_land_use: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: land use name;date - occurrence: - tag: occurrence - value: '1' description: Previous land use and dates title: history/previous land use examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - history/previous land use - is_a: core field + - value: fallow; 2018-05-11:T14:30Z + from_schema: https://w3id.org/mixs + keywords: + - history + - land + - use string_serialization: '{text};{timestamp}' slot_uri: MIXS:0000315 - multivalued: false - range: TextValue primary_prod: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per cubic meter per day, gram per square meter per day - occurrence: - tag: occurrence - value: '1' description: Measurement of primary production, generally measured as isotope uptake title: primary production examples: - value: 100 milligram per cubic meter per day - from_schema: http://w3id.org/mixs/terms - aliases: - - primary production - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - primary + - production slot_uri: MIXS:0000728 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true primary_treatment: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: primary treatment type - occurrence: - tag: occurrence - value: '1' description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed title: primary treatment - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - primary treatment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - primary + - treatment string_serialization: '{text}' slot_uri: MIXS:0000349 - multivalued: false - range: TextValue prod_rate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cubic meter per day - occurrence: - tag: occurrence - value: '1' description: Oil and/or gas production rates per well (e.g. 524 m3 / day) title: production rate - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - production rate - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - production + - rate slot_uri: MIXS:0000452 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true prod_start_date: - annotations: - expected_value: - tag: expected_value - value: timestamp - occurrence: - tag: occurrence - value: '1' description: Date of field's first production title: production start date examples: - - value: '2018-05-11' - from_schema: http://w3id.org/mixs/terms - aliases: - - production start date - is_a: core field + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs + keywords: + - date + - production + - start slot_uri: MIXS:0001008 - multivalued: false range: TimestampValue + recommended: true profile_position: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas title: profile position examples: - value: summit - from_schema: http://w3id.org/mixs/terms - aliases: - - profile position - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0001084 - multivalued: false - range: profile_position_enum + range: PROFILE_POSITION_ENUM quad_pos: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The quadrant position of the sampling room within the building title: quadrant position examples: - value: West side - from_schema: http://w3id.org/mixs/terms - aliases: - - quadrant position - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000820 - multivalued: false - range: quad_pos_enum + range: QUAD_POS_ENUM radiation_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: radiation type name;radiation amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: rad, gray - occurrence: - tag: occurrence - value: m description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens title: radiation regimen examples: - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - radiation regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - regimen string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000575 multivalued: true range: TextValue rainfall_regm: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter - occurrence: - tag: occurrence - value: m description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: rainfall regimen examples: - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - rainfall regimen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - rain + - regimen string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000576 multivalued: true range: TextValue reactor_type: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: reactor type name - occurrence: - tag: occurrence - value: '1' description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage title: reactor type - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - reactor type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type string_serialization: '{text}' slot_uri: MIXS:0000350 - multivalued: false - range: TextValue redox_potential: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millivolt - occurrence: - tag: occurrence - value: '1' description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential title: redox potential examples: - value: 300 millivolt - from_schema: http://w3id.org/mixs/terms - aliases: - - redox potential - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000182 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true rel_air_humidity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air title: relative air humidity + comments: + - percent or float? examples: - - value: 80% - from_schema: http://w3id.org/mixs/terms - aliases: - - relative air humidity - is_a: core field + - value: '0.8' + from_schema: https://w3id.org/mixs + keywords: + - air + - humidity + - relative slot_uri: MIXS:0000121 - multivalued: false - range: QuantityValue + range: float + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true rel_humidity_out: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram of air, kilogram of air - occurrence: - tag: occurrence - value: '1' description: The recorded outside relative humidity value at the time of sampling title: outside relative humidity examples: - value: 12 per kilogram of air - from_schema: http://w3id.org/mixs/terms - aliases: - - outside relative humidity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - humidity + - relative slot_uri: MIXS:0000188 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true rel_samp_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The sampling location within the train car title: relative sampling location examples: - value: center of car - from_schema: http://w3id.org/mixs/terms - aliases: - - relative sampling location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - relative slot_uri: MIXS:0000821 - multivalued: false - range: rel_samp_loc_enum + range: REL_SAMP_LOC_ENUM reservoir: - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' description: Name of the reservoir (e.g. Carapebus) title: reservoir name - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - reservoir name - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000303 - multivalued: false range: TextValue + recommended: true resins_pc: annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: resins wt% - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - resins wt% - is_a: core field - string_serialization: '{text};{float} {unit}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000134 - multivalued: false range: TextValue + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true room_air_exch_rate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: liter per hour - occurrence: - tag: occurrence - value: '1' description: The rate at which outside air replaces indoor air in a given space title: room air exchange rate - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room air exchange rate - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - air + - rate + - room slot_uri: MIXS:0000169 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true room_architec_elem: - annotations: - expected_value: - tag: expected_value - value: free text - occurrence: - tag: occurrence - value: '1' description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure title: room architectural elements - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room architectural elements - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - room slot_uri: MIXS:0000233 - multivalued: false range: string room_condt: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The condition of the room at the time of sampling title: room condition examples: - value: new - from_schema: http://w3id.org/mixs/terms - aliases: - - room condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - room slot_uri: MIXS:0000822 - multivalued: false - range: room_condt_enum + range: ROOM_CONDT_ENUM room_connected: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: List of rooms connected to the sampling room by a doorway title: rooms connected by a doorway examples: - value: office - from_schema: http://w3id.org/mixs/terms - aliases: - - rooms connected by a doorway - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - doorway + - room slot_uri: MIXS:0000826 - multivalued: false - range: room_connected_enum + range: ROOM_CONNECTED_ENUM room_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The total count of rooms in the built structure including all room types title: room count - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - room slot_uri: MIXS:0000234 - multivalued: false range: TextValue room_dim: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: The length, width and height of sampling room title: room dimensions examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room dimensions - is_a: core field + - value: 4 meter x 4 meter x 4 meter + from_schema: https://w3id.org/mixs + keywords: + - dimensions + - room string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' slot_uri: MIXS:0000192 - multivalued: false range: TextValue room_door_dist: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms title: room door distance - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room door distance - is_a: core field - string_serialization: '{integer} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - distance + - door + - room slot_uri: MIXS:0000193 - multivalued: false range: TextValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true room_door_share: - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' description: List of room(s) (room number, room name) sharing a door with the sampling room title: rooms that share a door with sampling room - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - rooms that share a door with sampling room - is_a: core field - string_serialization: '{text};{integer}' + from_schema: https://w3id.org/mixs + keywords: + - door + - room slot_uri: MIXS:0000242 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true room_hallway: - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' description: List of room(s) (room number, room name) located in the same hallway as sampling room title: rooms that are on the same hallway - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - rooms that are on the same hallway - is_a: core field - string_serialization: '{text};{integer}' + from_schema: https://w3id.org/mixs + keywords: + - hallway + - room slot_uri: MIXS:0000238 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true room_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The position of the room within the building title: room location in building examples: - value: interior room - from_schema: http://w3id.org/mixs/terms - aliases: - - room location in building - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - room slot_uri: MIXS:0000823 - multivalued: false - range: room_loc_enum + range: ROOM_LOC_ENUM room_moist_dam_hist: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed title: room moisture damage or mold history - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room moisture damage or mold history - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - history + - moisture + - room slot_uri: MIXS:0000235 - multivalued: false range: integer room_net_area: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square feet, square meter - occurrence: - tag: occurrence - value: '1' description: The net floor area of sampling room. Net area excludes wall thicknesses title: room net area - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room net area - is_a: core field - string_serialization: '{integer} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - area + - room slot_uri: MIXS:0000194 - multivalued: false range: TextValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true room_occup: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: Count of room occupancy at time of sampling title: room occupancy - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room occupancy - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - room slot_uri: MIXS:0000236 - multivalued: false range: QuantityValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true room_samp_pos: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The horizontal sampling position in the room relative to architectural elements title: room sampling position examples: - value: south corner - from_schema: http://w3id.org/mixs/terms - aliases: - - room sampling position - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - room slot_uri: MIXS:0000824 - multivalued: false - range: room_samp_pos_enum + range: ROOM_SAMP_POS_ENUM room_type: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure title: room type examples: - value: bathroom - from_schema: http://w3id.org/mixs/terms - aliases: - - room type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - room + - type + string_serialization: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' slot_uri: MIXS:0000825 - multivalued: false - range: room_type_enum room_vol: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cubic feet, cubic meter - occurrence: - tag: occurrence - value: '1' description: Volume of sampling room title: room volume - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room volume - is_a: core field - string_serialization: '{integer} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - room + - volume slot_uri: MIXS:0000195 - multivalued: false range: TextValue + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true room_wall_share: - annotations: - expected_value: - tag: expected_value - value: room name;room number - occurrence: - tag: occurrence - value: '1' description: List of room(s) (room number, room name) sharing a wall with the sampling room title: rooms that share a wall with sampling room - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - rooms that share a wall with sampling room - is_a: core field - string_serialization: '{text};{integer}' + from_schema: https://w3id.org/mixs + keywords: + - room + - wall slot_uri: MIXS:0000243 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true room_window_count: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: Number of windows in the room title: room window count - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - room window count - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - count + - room + - window slot_uri: MIXS:0000237 - multivalued: false range: integer root_cond: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' - description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container title: rooting conditions examples: - value: http://himedialabs.com/TD/PT158.pdf - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting conditions - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' + from_schema: https://w3id.org/mixs + keywords: + - condition slot_uri: MIXS:0001061 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true root_med_carbon: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: carbon source name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + description: Source of organic carbon in the culture rooting medium; e.g. sucrose title: rooting medium carbon examples: - value: sucrose - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000577 - multivalued: false range: TextValue root_med_macronutr: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: macronutrient name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). + description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L) title: rooting medium macronutrients examples: - - value: KH2PO4;170¬†milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium macronutrients - is_a: core field + - value: KH2PO4;170 milligram per liter + from_schema: https://w3id.org/mixs + keywords: + - macronutrients string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000578 - multivalued: false range: TextValue root_med_micronutr: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: micronutrient name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). + description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L) title: rooting medium micronutrients examples: - - value: H3BO3;6.2¬†milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium micronutrients - is_a: core field + - value: H3BO3;6.2 milligram per liter + from_schema: https://w3id.org/mixs + keywords: + - micronutrients string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000579 - multivalued: false range: TextValue root_med_ph: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: pH measurement of the culture rooting medium; e.g. 5.5. + description: pH measurement of the culture rooting medium; e.g. 5.5 title: rooting medium pH examples: - value: '7.5' - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium pH - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - ph slot_uri: MIXS:0001062 - multivalued: false range: QuantityValue root_med_regl: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: regulator name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. + description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA title: rooting medium regulators examples: - value: abscisic acid;0.75 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium regulators - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000581 - multivalued: false range: TextValue root_med_solid: - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' - description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + description: Specification of the solidifying agent in the culture rooting medium; e.g. agar title: rooting medium solidifier examples: - value: agar - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium solidifier - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0001063 - multivalued: false range: TextValue root_med_suppl: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: supplement name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). + description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L) title: rooting medium organic supplements examples: - value: nicotinic acid;0.5 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - rooting medium organic supplements - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - organic string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000580 - multivalued: false range: TextValue salinity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: practical salinity unit, percentage - occurrence: - tag: occurrence - value: '1' - description: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. + description: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater title: salinity examples: - value: 25 practical salinity unit - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - salinity - is_a: core field slot_uri: MIXS:0000183 - multivalued: false - range: QuantityValue - salinity_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining salinity - title: salinity method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - salinity method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000341 - multivalued: false range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true salt_regm: annotations: - expected_value: - tag: expected_value - value: salt name;salt amount;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, microgram, mole per liter, gram per liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens title: salt regimen examples: - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - salt regimen - is_a: core field - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen + - salt slot_uri: MIXS:0000582 - multivalued: true range: TextValue + multivalued: true samp_capt_status: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Reason for the sample title: sample capture status examples: - value: farm sample - from_schema: http://w3id.org/mixs/terms - aliases: - - sample capture status - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sample + - status slot_uri: MIXS:0000860 - multivalued: false - range: samp_capt_status_enum - samp_collec_device: - annotations: - expected_value: - tag: expected_value - value: device name - description: The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). - title: sample collection device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - from_schema: http://w3id.org/mixs/terms - aliases: - - sample collection device - is_a: nucleic acid sequence source field - string_serialization: '{termLabel} {[termID]}|{text}' - slot_uri: MIXS:0000002 - multivalued: false - range: string - samp_collec_method: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url , or text - description: The method employed for collecting the sample. - title: sample collection method - examples: - - value: swabbing - from_schema: http://w3id.org/mixs/terms - aliases: - - sample collection method - is_a: nucleic acid sequence source field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' - slot_uri: MIXS:0001225 - multivalued: false - range: string + range: SAMP_CAPT_STATUS_ENUM samp_collect_point: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field title: sample collection point examples: - value: well - from_schema: http://w3id.org/mixs/terms - aliases: - - sample collection point - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sample slot_uri: MIXS:0001015 - multivalued: false - range: samp_collect_point_enum + range: SAMP_COLLECT_POINT_ENUM samp_dis_stage: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. + description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen title: sample disease stage examples: - value: infection - from_schema: http://w3id.org/mixs/terms - aliases: - - sample disease stage - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - disease + - sample slot_uri: MIXS:0000249 - multivalued: false - range: samp_dis_stage_enum + range: SAMP_DIS_STAGE_ENUM samp_floor: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: The floor of the building, where the sampling room is located title: sampling floor examples: - value: 4th floor - from_schema: http://w3id.org/mixs/terms - aliases: - - sampling floor - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - floor + string_serialization: '[1st floor|2nd floor|{integer} floor|basement|lobby]' slot_uri: MIXS:0000828 - multivalued: false - range: samp_floor_enum samp_loc_corr_rate: annotations: - expected_value: - tag: expected_value - value: measurement value range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter per year - occurrence: - tag: occurrence - value: '1' description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays title: corrosion rate at sample location - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - corrosion rate at sample location - is_a: core field - string_serialization: '{float} - {float} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - location + - rate + - sample slot_uri: MIXS:0000136 - multivalued: false range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true samp_mat_process: - annotations: - expected_value: - tag: expected_value - value: text - description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. + description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed title: sample material processing examples: - value: filtering of seawater, storing samples in ethanol - from_schema: http://w3id.org/mixs/terms - aliases: - - sample material processing - is_a: nucleic acid sequence source field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - material + - process + - sample slot_uri: MIXS:0000016 - multivalued: false range: ControlledTermValue samp_md: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;enumeration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field title: sample measured depth examples: - value: 1534 meter;MSL - from_schema: http://w3id.org/mixs/terms - aliases: - - sample measured depth - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - measurement + - sample + string_serialization: '{float} {unit};[GL|DF|RT|KB|MSL|other]' slot_uri: MIXS:0000413 - multivalued: false range: QuantityValue samp_name: annotations: - expected_value: - tag: expected_value - value: text - description: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name. + Preferred_unit: + tag: Preferred_unit + value: '' + description: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name title: sample name examples: - value: ISDsoil1 - from_schema: http://w3id.org/mixs/terms - aliases: - - sample name - is_a: investigation field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - sample slot_uri: MIXS:0001107 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig + - Air + - BuiltEnvironment + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + - HostAssociated + - HumanAssociated + - HumanGut + - HumanOral + - HumanSkin + - HumanVaginal + - HydrocarbonResourcesCores + - HydrocarbonResourcesFluidsSwabs + - MicrobialMatBiofilm + - MiscellaneousNaturalOrArtificialEnvironment + - PlantAssociated + - Sediment + - Soil + - SymbiontAssociated + - WastewaterSludge + - Water range: string samp_preserv: annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milliliter - occurrence: - tag: occurrence - value: '1' description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) title: preservative added to sample - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - preservative added to sample - is_a: core field - string_serialization: '{text};{float} {unit}' + from_schema: https://w3id.org/mixs + keywords: + - sample slot_uri: MIXS:0000463 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true samp_room_id: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: Sampling room number. This ID should be consistent with the designations on the building floor plans title: sampling room ID or name - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sampling room ID or name - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - identifier + - room slot_uri: MIXS:0000244 - multivalued: false range: TextValue samp_size: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millliter, gram, milligram, liter - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected title: amount or size of sample collected examples: - value: 5 liter - from_schema: http://w3id.org/mixs/terms - aliases: - - amount or size of sample collected - is_a: nucleic acid sequence source field + from_schema: https://w3id.org/mixs + keywords: + - sample + - size slot_uri: MIXS:0000001 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true samp_sort_meth: - annotations: - expected_value: - tag: expected_value - value: description of method - occurrence: - tag: occurrence - value: m - description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. + description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor title: sample size sorting method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sample size sorting method - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - method + - sample + - size slot_uri: MIXS:0000216 - multivalued: true range: TextValue + multivalued: true samp_store_dur: - annotations: - expected_value: - tag: expected_value - value: duration - occurrence: - tag: occurrence - value: '1' - description: Duration for which the sample was stored + description: Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format title: sample storage duration examples: - value: P1Y6M - from_schema: http://w3id.org/mixs/terms - aliases: - - sample storage duration - is_a: core field - string_serialization: '{duration}' + from_schema: https://w3id.org/mixs + keywords: + - duration + - period + - sample + - storage slot_uri: MIXS:0000116 - multivalued: false range: TextValue + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true samp_store_loc: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: location name - occurrence: - tag: occurrence - value: '1' description: Location at which sample was stored, usually name of a specific freezer/room title: sample storage location examples: - value: Freezer no:5 - from_schema: http://w3id.org/mixs/terms - aliases: - - sample storage location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - sample + - storage string_serialization: '{text}' slot_uri: MIXS:0000755 - multivalued: false - range: TextValue samp_store_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Temperature at which sample was stored, e.g. -80 degree Celsius title: sample storage temperature examples: - value: -80 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - sample storage temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sample + - storage + - temperature slot_uri: MIXS:0000110 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true samp_subtype: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field title: sample subtype examples: - value: biofilm - from_schema: http://w3id.org/mixs/terms - aliases: - - sample subtype - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sample slot_uri: MIXS:0000999 - multivalued: false - range: samp_subtype_enum + range: SAMP_SUBTYPE_ENUM + recommended: true samp_taxon_id: - annotations: - expected_value: - tag: expected_value - value: Taxonomy ID - description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome’ for mock community/positive controls, or 'blank sample' for negative controls. - title: Taxonomy ID of DNA sample - from_schema: http://w3id.org/mixs/terms - aliases: - - Taxonomy ID of DNA sample - is_a: investigation field + description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome for mock community/positive controls, or 'blank sample' for negative controls + title: taxonomy ID of DNA sample + from_schema: https://w3id.org/mixs + keywords: + - dna + - identifier + - sample + - taxon slot_uri: MIXS:0001320 - multivalued: false + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig range: ControlledIdentifiedTermValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$ + structured_pattern: + syntax: ^{text} \[{NCBItaxon_id}\]$ + interpolated: true + partial_match: true comments: - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value samp_time_out: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: time - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: hour - occurrence: - tag: occurrence - value: '1' description: The recent and long term history of outside sampling title: sampling time outside - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sampling time outside - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - time + string_serialization: '{float}' slot_uri: MIXS:0000196 - multivalued: false range: TextValue samp_transport_cond: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: days;degree Celsius - occurrence: - tag: occurrence - value: '1' - description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) + description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 C) title: sample transport conditions examples: - value: 5 days;-20 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - sample transport conditions - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - sample + - transport string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 - multivalued: false range: TextValue samp_tvdss: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value or measurement value range - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m title: sample true vertical depth subsea - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sample true vertical depth subsea - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - sample string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000409 - multivalued: false + recommended: true range: TextValue samp_type: - annotations: - expected_value: - tag: expected_value - value: GENEPIO:0001246 - occurrence: - tag: occurrence - value: '1' - description: The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246). + description: The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246) title: sample type examples: - value: built environment sample [GENEPIO:0001248] - from_schema: http://w3id.org/mixs/terms - aliases: - - sample type - is_a: core field - string_serialization: '{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - sample + - type slot_uri: MIXS:0000998 - multivalued: false range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true samp_vol_we_dna_ext: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: millliter, gram, milligram, square centimeter - description: 'Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).' + Preferred_unit: + tag: Preferred_unit + value: milliliter, gram, milligram, square centimeter + description: 'Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)' title: sample volume or weight for DNA extraction examples: - value: 1500 milliliter - from_schema: http://w3id.org/mixs/terms - aliases: - - sample volume or weight for DNA extraction - is_a: nucleic acid sequence source field + from_schema: https://w3id.org/mixs + keywords: + - dna + - sample + - volume + - weight slot_uri: MIXS:0000111 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true samp_weather: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The weather on the sampling day title: sampling day weather examples: - value: foggy - from_schema: http://w3id.org/mixs/terms - aliases: - - sampling day weather - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - day + - weather slot_uri: MIXS:0000827 - multivalued: false - range: samp_weather_enum + range: SAMP_WEATHER_ENUM samp_well_name: - annotations: - expected_value: - tag: expected_value - value: name - occurrence: - tag: occurrence - value: '1' description: Name of the well (e.g. BXA1123) where sample was taken title: sample well name - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sample well name - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - sample slot_uri: MIXS:0000296 - multivalued: false range: TextValue + recommended: true saturates_pc: annotations: - expected_value: - tag: expected_value - value: name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' - description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: saturates wt% - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - saturates wt% - is_a: core field - string_serialization: '{text};{float} {unit}' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000131 - multivalued: false range: TextValue + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true season: annotations: - expected_value: - tag: expected_value - value: NCIT:C94729 - occurrence: - tag: occurrence - value: '1' - description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). + Expected_value: + tag: Expected_value + value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter [NCIT:C94730] + description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729) title: season + comments: + - autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$ + - would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$ examples: - value: autumn [NCIT:C94733] - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - season - is_a: core field - string_serialization: '{termLabel} {[termID]}' + string_serialization: '{termLabel} [{termID}]' slot_uri: MIXS:0000829 - multivalued: false range: TextValue + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$ season_environment: - annotations: - expected_value: - tag: expected_value - value: seasonal environment name;treatment interval and duration - occurrence: - tag: occurrence - value: m description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment title: seasonal environment examples: - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - seasonal environment - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - environment + - season slot_uri: MIXS:0001068 - multivalued: true range: TextValue + multivalued: true season_precpt: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: millimeter - occurrence: - tag: occurrence - value: '1' - description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. + description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps title: mean seasonal precipitation examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - mean seasonal precipitation - is_a: core field + - value: 75 millimeters + from_schema: https://w3id.org/mixs + keywords: + - mean + - season slot_uri: MIXS:0000645 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true season_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Mean seasonal temperature title: mean seasonal temperature examples: - value: 18 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - mean seasonal temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mean + - season + - temperature slot_uri: MIXS:0000643 - multivalued: false - range: QuantityValue + domain_of: + - Agriculture + - FoodFarmEnvironment + - Soil + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true season_use: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The seasons the space is occupied title: seasonal use examples: - value: Winter - from_schema: http://w3id.org/mixs/terms - aliases: - - seasonal use - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - season + - use slot_uri: MIXS:0000830 - multivalued: false - range: season_use_enum + range: SEASON_USE_ENUM secondary_treatment: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: secondary treatment type - occurrence: - tag: occurrence - value: '1' description: The process for substantially degrading the biological content of the sewage title: secondary treatment - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - secondary treatment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - secondary + - treatment string_serialization: '{text}' slot_uri: MIXS:0000351 - multivalued: false - range: TextValue sediment_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Information about the sediment type based on major constituents title: sediment type examples: - value: biogenous - from_schema: http://w3id.org/mixs/terms - aliases: - - sediment type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sediment + - type slot_uri: MIXS:0001078 - multivalued: false - range: sediment_type_enum + range: SEDIMENT_TYPE_ENUM seq_meth: - annotations: - expected_value: - tag: expected_value - value: Text or OBI - description: Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103). + description: Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103) title: sequencing method examples: - value: 454 Genome Sequencer FLX [OBI:0000702] - from_schema: http://w3id.org/mixs/terms - aliases: - - sequencing method - is_a: sequencing field - string_serialization: '{termLabel} {[termID]}|{text}' + from_schema: https://w3id.org/mixs + keywords: + - method slot_uri: MIXS:0000050 - multivalued: false - range: TextValue + domain_of: + - MigsBa + - MigsEu + - MigsOrg + - MigsPl + - MigsVi + - Mimag + - MimarksC + - MimarksS + - Mims + - Misag + - Miuvig + - Agriculture + - FoodAnimalAndAnimalFeed + - FoodFarmEnvironment + - FoodFoodProductionFacility + - FoodHumanFoods + range: TextValue + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true seq_quality_check: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: none or manually edited description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA title: sequence quality check examples: - value: none - from_schema: http://w3id.org/mixs/terms - aliases: - - sequence quality check - is_a: sequencing field - string_serialization: '[none|manually edited]' + from_schema: https://w3id.org/mixs + keywords: + - quality slot_uri: MIXS:0000051 - multivalued: false - range: TextValue + range: SEQ_QUALITY_CHECK_ENUM sewage_type: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: sewage type name - occurrence: - tag: occurrence - value: '1' description: Type of wastewater treatment plant as municipial or industrial title: sewage type - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sewage type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type string_serialization: '{text}' slot_uri: MIXS:0000215 - multivalued: false - range: TextValue shad_dev_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Signs of the presence of mold or mildew on the shading device title: shading device signs of water/mold examples: - value: no presence of mold visible - from_schema: http://w3id.org/mixs/terms - aliases: - - shading device signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' + from_schema: https://w3id.org/mixs + keywords: + - device slot_uri: MIXS:0000834 - multivalued: false range: string shading_device_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The physical condition of the shading device at the time of sampling title: shading device condition examples: - value: new - from_schema: http://w3id.org/mixs/terms - aliases: - - shading device condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - device slot_uri: MIXS:0000831 - multivalued: false - range: shading_device_cond_enum + range: SHARED_ENUM_2 shading_device_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The location of the shading device in relation to the built structure title: shading device location examples: - value: exterior - from_schema: http://w3id.org/mixs/terms - aliases: - - shading device location - is_a: core field - string_serialization: '[exterior|interior]' + from_schema: https://w3id.org/mixs + keywords: + - device + - location slot_uri: MIXS:0000832 - multivalued: false - range: TextValue + range: SHADING_DEVICE_LOC_ENUM shading_device_mat: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: material name - occurrence: - tag: occurrence - value: '1' description: The material the shading device is composed of title: shading device material - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - shading device material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - device + - material string_serialization: '{text}' slot_uri: MIXS:0000245 - multivalued: false - range: TextValue shading_device_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of shading device title: shading device type examples: - - value: slatted aluminum awning - from_schema: http://w3id.org/mixs/terms - aliases: - - shading device type - is_a: core field + - value: slatted aluminum + description: was slatted aluminum awning + from_schema: https://w3id.org/mixs + keywords: + - device + - type slot_uri: MIXS:0000835 - multivalued: false - range: shading_device_type_enum + range: SHADING_DEVICE_TYPE_ENUM sieving: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: design name and/or size;amount - occurrence: - tag: occurrence - value: '1' description: Collection design of pooled samples and/or sieve size and amount of sample sieved - title: composite design/sieving - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - composite design/sieving - is_a: core field - string_serialization: '{{text}|{float} {unit}};{float} {unit}' + title: sieving + from_schema: https://w3id.org/mixs + string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000322 - multivalued: false range: TextValue silicate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of silicate title: silicate examples: - value: 0.05 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - silicate - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000184 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true size_frac: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: filter size value range description: Filtering pore size used in sample preparation title: size fraction selected examples: - value: 0-0.22 micrometer - from_schema: http://w3id.org/mixs/terms - aliases: - - size fraction selected - is_a: nucleic acid sequence source field + from_schema: https://w3id.org/mixs + keywords: + - fraction + - size string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 - multivalued: false range: TextValue size_frac_low: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micrometer - occurrence: - tag: occurrence - value: '1' description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample title: size-fraction lower threshold examples: - value: 0.2 micrometer - from_schema: http://w3id.org/mixs/terms - aliases: - - size-fraction lower threshold - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - lower slot_uri: MIXS:0000735 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true size_frac_up: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micrometer - occurrence: - tag: occurrence - value: '1' - description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample + description: Mesh or pore size of the device used to retain the sample. Materials smaller than the size threshold are excluded from the sample title: size-fraction upper threshold examples: - value: 20 micrometer - from_schema: http://w3id.org/mixs/terms - aliases: - - size-fraction upper threshold - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - upper slot_uri: MIXS:0000736 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true slope_aspect: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree - occurrence: - tag: occurrence - value: '1' - description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration title: slope aspect - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - slope aspect - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - slope slot_uri: MIXS:0000647 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true slope_gradient: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer title: slope gradient - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - slope gradient - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - slope slot_uri: MIXS:0000646 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true sludge_retent_time: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: hours - occurrence: - tag: occurrence - value: '1' description: The time activated sludge remains in reactor title: sludge retention time - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sludge retention time - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - time slot_uri: MIXS:0000669 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true sodium: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Sodium concentration in the sample title: sodium examples: - value: 10.5 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - sodium - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000428 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true soil_horizon: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath title: soil horizon examples: - value: A horizon - from_schema: http://w3id.org/mixs/terms - aliases: - - soil horizon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - horizon + - soil slot_uri: MIXS:0001082 - multivalued: false - range: soil_horizon_enum - soil_text_measure: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' - description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. - title: soil texture measurement - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil texture measurement - is_a: core field - slot_uri: MIXS:0000335 - multivalued: false - range: QuantityValue + range: SOIL_HORIZON_ENUM soil_texture_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining soil texture title: soil texture method examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil texture method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf + from_schema: https://w3id.org/mixs + keywords: + - method + - soil + - texture slot_uri: MIXS:0000336 - multivalued: false + domain_of: + - Agriculture + - FoodFarmEnvironment + - Soil range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true soil_type: annotations: - expected_value: - tag: expected_value - value: ENVO_00001998 - occurrence: - tag: occurrence - value: '1' - description: Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes. + Expected_value: + tag: Expected_value + value: ENVO:00001998 + description: Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes title: soil type examples: - value: plinthosol [ENVO:00002250] - from_schema: http://w3id.org/mixs/terms - aliases: - - soil type - is_a: core field - string_serialization: '{termLabel} {[termID]}' + from_schema: https://w3id.org/mixs + keywords: + - soil + - type slot_uri: MIXS:0000332 - multivalued: false - range: TextValue soil_type_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining soil series name or other lower-level classification title: soil type method examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soil type method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf + from_schema: https://w3id.org/mixs + keywords: + - method + - soil + - type slot_uri: MIXS:0000334 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true solar_irradiance: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: kilowatts per square meter per day, ergs per square centimeter per second - occurrence: - tag: occurrence - value: '1' description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval title: solar irradiance examples: - value: 1.36 kilowatts per square meter per day - from_schema: http://w3id.org/mixs/terms - aliases: - - solar irradiance - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000112 - multivalued: false range: QuantityValue + multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true soluble_inorg_mat: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: soluble inorganic material name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, microgram, mole per liter, gram per liter, parts per million - occurrence: - tag: occurrence - value: m - description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc title: soluble inorganic material - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soluble inorganic material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - inorganic + - material + - soluble string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000672 multivalued: true range: TextValue soluble_org_mat: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: soluble organic material name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, microgram, mole per liter, gram per liter, parts per million - occurrence: - tag: occurrence - value: m - description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc title: soluble organic material - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - soluble organic material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - material + - organic + - soluble string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000673 multivalued: true range: TextValue soluble_react_phosp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of soluble reactive phosphorus title: soluble reactive phosphorus examples: - value: 0.1 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - soluble reactive phosphorus - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - phosphorus + - soluble slot_uri: MIXS:0000738 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true source_mat_id: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: 'for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer' - description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). + description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2) title: source material identifiers examples: - value: MPI012345 - from_schema: http://w3id.org/mixs/terms - aliases: - - source material identifiers - is_a: nucleic acid sequence source field + from_schema: https://w3id.org/mixs + keywords: + - identifier + - material + - source string_serialization: '{text}' slot_uri: MIXS:0000026 multivalued: false range: TextValue space_typ_state: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Customary or normal state of the space title: space typical state examples: - value: typically occupied - from_schema: http://w3id.org/mixs/terms - aliases: - - space typical state - is_a: core field - string_serialization: '[typically occupied|typically unoccupied]' + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000770 - multivalued: false - range: TextValue + range: SPACE_TYP_STATE_ENUM specific: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' title: specifications examples: - value: construction - from_schema: http://w3id.org/mixs/terms - aliases: - - specifications - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000836 - multivalued: false - range: specific_enum + range: SPECIFIC_ENUM specific_humidity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram of air, kilogram of air - occurrence: - tag: occurrence - value: '1' - description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. + description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound title: specific humidity examples: - value: 15 per kilogram of air - from_schema: http://w3id.org/mixs/terms - aliases: - - specific humidity - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - humidity slot_uri: MIXS:0000214 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true sr_dep_env: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field title: source rock depositional environment examples: - value: Marine - from_schema: http://w3id.org/mixs/terms - aliases: - - source rock depositional environment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - environment + - source slot_uri: MIXS:0000996 - multivalued: false - range: sr_dep_env_enum + range: SR_DEP_ENV_ENUM sr_geol_age: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' title: source rock geological age examples: - value: Silurian - from_schema: http://w3id.org/mixs/terms - aliases: - - source rock geological age - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - age + - source slot_uri: MIXS:0000997 - multivalued: false - range: sr_geol_age_enum + range: SHARED_ENUM_5 sr_kerog_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field' title: source rock kerogen type examples: - value: Type IV - from_schema: http://w3id.org/mixs/terms - aliases: - - source rock kerogen type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - source + - type slot_uri: MIXS:0000994 - multivalued: false - range: sr_kerog_type_enum + range: SR_KEROG_TYPE_ENUM sr_lithology: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field title: source rock lithology examples: - value: Coal - from_schema: http://w3id.org/mixs/terms - aliases: - - source rock lithology - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - lithology + - source slot_uri: MIXS:0000995 - multivalued: false - range: sr_lithology_enum + range: SR_LITHOLOGY_ENUM standing_water_regm: - annotations: - expected_value: - tag: expected_value - value: standing water type;treatment interval and duration - occurrence: - tag: occurrence - value: m description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: standing water regimen examples: - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - standing water regimen - is_a: core field - string_serialization: '{text};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen + - water slot_uri: MIXS:0001069 - multivalued: true range: TextValue + multivalued: true store_cond: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: storage condition type;duration - occurrence: - tag: occurrence - value: '1' - description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). + description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) title: storage conditions examples: - value: -20 degree Celsius freezer;P2Y10D - from_schema: http://w3id.org/mixs/terms - aliases: - - storage conditions - is_a: core field - string_serialization: '{text};{duration}' + from_schema: https://w3id.org/mixs + keywords: + - condition + - storage + string_serialization: '{text};{period}' slot_uri: MIXS:0000327 - multivalued: false range: TextValue substructure_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level title: substructure type examples: - value: basement - from_schema: http://w3id.org/mixs/terms - aliases: - - substructure type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type slot_uri: MIXS:0000767 + range: SUBSTRUCTURE_TYPE_ENUM multivalued: true - range: substructure_type_enum sulfate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of sulfate in the sample title: sulfate examples: - value: 5 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - sulfate - is_a: core field slot_uri: MIXS:0000423 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true sulfate_fw: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Original sulfate concentration in the hydrocarbon resource title: sulfate in formation water - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - sulfate in formation water - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - sulfate + - water slot_uri: MIXS:0000407 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true sulfide: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of sulfide in the sample title: sulfide examples: - value: 2 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - sulfide - is_a: core field slot_uri: MIXS:0000424 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true surf_air_cont: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: Contaminant identified on surface title: surface-air contaminant examples: - value: radon - from_schema: http://w3id.org/mixs/terms - aliases: - - surface-air contaminant - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000759 + range: SURF_AIR_CONT_ENUM + recommended: true multivalued: true - range: surf_air_cont_enum surf_humidity: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percentage - occurrence: - tag: occurrence - value: '1' description: 'Surfaces: water activity as a function of air and material moisture' title: surface humidity + comments: + - percent or float? examples: - - value: 10% - from_schema: http://w3id.org/mixs/terms - aliases: - - surface humidity - is_a: core field + - value: '0.1' + from_schema: https://w3id.org/mixs + keywords: + - humidity + - surface slot_uri: MIXS:0000123 - multivalued: false - range: QuantityValue + range: float + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true surf_material: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Surface materials at the point of sampling title: surface material examples: - value: wood - from_schema: http://w3id.org/mixs/terms - aliases: - - surface material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - material + - surface slot_uri: MIXS:0000758 - multivalued: false - range: surf_material_enum + range: SURF_MATERIAL_ENUM surf_moisture: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: parts per million, gram per cubic meter, gram per square meter - occurrence: - tag: occurrence - value: '1' description: Water held on a surface title: surface moisture examples: - value: 0.01 gram per square meter - from_schema: http://w3id.org/mixs/terms - aliases: - - surface moisture - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - moisture + - surface slot_uri: MIXS:0000128 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true surf_moisture_ph: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: ph measurement of surface title: surface moisture pH examples: - value: '7' - from_schema: http://w3id.org/mixs/terms - aliases: - - surface moisture pH - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - moisture + - ph + - surface slot_uri: MIXS:0000760 - multivalued: false - range: double + range: float + recommended: true surf_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: Temperature of the surface at the time of sampling title: surface temperature examples: - value: 15 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - surface temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - surface + - temperature slot_uri: MIXS:0000125 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true suspend_part_matter: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Concentration of suspended particulate matter title: suspended particulate matter examples: - value: 0.5 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - suspended particulate matter - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - particle + - particulate + - suspended slot_uri: MIXS:0000741 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true suspend_solids: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: suspended solid name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million - occurrence: - tag: occurrence - value: m description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances title: suspended solids - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - suspended solids - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - solids + - suspended string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 multivalued: true range: TextValue tan: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' - description: 'Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' + description: 'Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' title: total acid number - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total acid number - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - number + - total slot_uri: MIXS:0000120 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true target_gene: - annotations: - expected_value: - tag: expected_value - value: gene name description: Targeted gene or locus name for marker gene studies title: target gene examples: - value: 16S rRNA, 18S rRNA, nif, amoA, rpo - from_schema: http://w3id.org/mixs/terms - aliases: - - target gene - is_a: sequencing field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - target slot_uri: MIXS:0000044 - multivalued: false range: TextValue target_subfragment: - annotations: - expected_value: - tag: expected_value - value: gene fragment name description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA title: target subfragment examples: - value: V6, V9, ITS - from_schema: http://w3id.org/mixs/terms - aliases: - - target subfragment - is_a: sequencing field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - target slot_uri: MIXS:0000045 - multivalued: false range: TextValue temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - description: Temperature of the sample at the time of sampling. + description: Temperature of the sample at the time of sampling title: temperature examples: - value: 25 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: + from_schema: https://w3id.org/mixs + keywords: - temperature - is_a: environment field slot_uri: MIXS:0000113 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true temp_out: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: '1' description: The recorded temperature value at sampling time outside title: temperature outside house examples: - value: 5 degree Celsius - from_schema: http://w3id.org/mixs/terms - aliases: - - temperature outside house - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - house + - temperature slot_uri: MIXS:0000197 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tertiary_treatment: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: tertiary treatment type - occurrence: - tag: occurrence - value: '1' description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment title: tertiary treatment - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - tertiary treatment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - treatment string_serialization: '{text}' slot_uri: MIXS:0000352 - multivalued: false - range: TextValue tidal_stage: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Stage of tide title: tidal stage examples: - value: high tide - from_schema: http://w3id.org/mixs/terms - aliases: - - tidal stage - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000750 - multivalued: false - range: tidal_stage_enum + range: TIDAL_STAGE_ENUM tillage: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: m description: Note method(s) used for tilling title: history/tillage examples: - value: chisel - from_schema: http://w3id.org/mixs/terms - aliases: - - history/tillage - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - history slot_uri: MIXS:0001081 + range: TILLAGE_ENUM multivalued: true - range: tillage_enum tiss_cult_growth_med: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI,url or free text - occurrence: - tag: occurrence - value: '1' description: Description of plant tissue culture growth media used title: tissue culture growth media examples: - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf - from_schema: http://w3id.org/mixs/terms - aliases: - - tissue culture growth media - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}|{text}' + from_schema: https://w3id.org/mixs + keywords: + - culture + - growth slot_uri: MIXS:0001070 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true toluene: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of toluene in the sample title: toluene - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - toluene - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000154 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_carb: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: Total carbon content title: total carbon - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - total slot_uri: MIXS:0000525 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_depth_water_col: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' description: Measurement of total depth of water column title: total depth of water column examples: - value: 500 meter - from_schema: http://w3id.org/mixs/terms - aliases: - - total depth of water column - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - total + - water slot_uri: MIXS:0000634 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_diss_nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' title: total dissolved nitrogen examples: - value: 40 microgram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - total dissolved nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - dissolved + - nitrogen + - total slot_uri: MIXS:0000744 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_inorg_nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter - occurrence: - tag: occurrence - value: '1' description: Total inorganic nitrogen content title: total inorganic nitrogen examples: - value: 40 microgram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - total inorganic nitrogen - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - inorganic + - nitrogen + - total slot_uri: MIXS:0000745 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_iron: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, milligram per kilogram - occurrence: - tag: occurrence - value: '1' description: Concentration of total iron in the sample title: total iron - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total iron - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - total slot_uri: MIXS:0000105 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_nitro: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: 'Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen' title: total nitrogen concentration examples: - value: 50 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - total nitrogen concentration - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - concentration + - nitrogen + - total slot_uri: MIXS:0000102 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_nitro_cont_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining the total nitrogen title: total nitrogen content method examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total nitrogen content method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + from_schema: https://w3id.org/mixs + keywords: + - content + - method + - nitrogen + - total slot_uri: MIXS:0000338 - multivalued: false range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true tot_nitro_content: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: microgram per liter, micromole per liter, milligram per liter - occurrence: - tag: occurrence - value: '1' description: Total nitrogen content of the sample title: total nitrogen content examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total nitrogen content - is_a: core field + - value: 35 milligrams Nitrogen per kilogram of soil + from_schema: https://w3id.org/mixs + keywords: + - content + - nitrogen + - total slot_uri: MIXS:0000530 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_org_c_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining total organic carbon title: total organic carbon method examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total organic carbon method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + from_schema: https://w3id.org/mixs + keywords: + - carbon + - method + - organic + - total slot_uri: MIXS:0000337 - multivalued: false range: TextValue + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true tot_org_carb: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram Carbon per kilogram sample material - occurrence: - tag: occurrence - value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' + description: Total organic carbon content title: total organic carbon examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total organic carbon - is_a: core field + - value: '0.02' + from_schema: https://w3id.org/mixs + keywords: + - carbon + - organic + - total slot_uri: MIXS:0000533 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_part_carb: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' description: Total particulate carbon content title: total particulate carbon examples: - value: 35 micromole per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - total particulate carbon - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - carbon + - particle + - particulate + - total slot_uri: MIXS:0000747 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_phosp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: micromole per liter, milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' title: total phosphorus examples: - value: 0.03 milligram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - total phosphorus - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - phosphorus + - total slot_uri: MIXS:0000117 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_phosphate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per liter, micromole per liter - occurrence: - tag: occurrence - value: '1' description: Total amount or concentration of phosphate title: total phosphate - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total phosphate - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - phosphate + - total slot_uri: MIXS:0000689 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tot_sulfur: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of total sulfur in the sample title: total sulfur - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - total sulfur - is_a: core field - slot_uri: MIXS:0000419 - multivalued: false - range: QuantityValue + from_schema: https://w3id.org/mixs + keywords: + - sulfur + - total + slot_uri: MIXS:0000419 + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true train_line: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The subway line name title: train line examples: - value: red - from_schema: http://w3id.org/mixs/terms - aliases: - - train line - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - train slot_uri: MIXS:0000837 - multivalued: false - range: train_line_enum + range: TRAIN_LINE_ENUM train_stat_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The train station collection location title: train station collection location examples: - value: forest hills - from_schema: http://w3id.org/mixs/terms - aliases: - - train station collection location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - train slot_uri: MIXS:0000838 - multivalued: false - range: train_stat_loc_enum + range: TRAIN_STAT_LOC_ENUM train_stop_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The train stop collection location title: train stop collection location examples: - value: end - from_schema: http://w3id.org/mixs/terms - aliases: - - train stop collection location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - stop + - train slot_uri: MIXS:0000839 - multivalued: false - range: train_stop_loc_enum + range: TRAIN_STOP_LOC_ENUM turbidity: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: formazin turbidity unit, formazin nephelometric units - occurrence: - tag: occurrence - value: '1' description: Measure of the amount of cloudiness or haziness in water caused by individual particles title: turbidity examples: - value: 0.3 nephelometric turbidity units - from_schema: http://w3id.org/mixs/terms - aliases: - - turbidity - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000191 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tvdss_of_hcr_press: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m) title: depth (TVDSS) of hydrocarbon resource pressure - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - depth (TVDSS) of hydrocarbon resource pressure - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - hydrocarbon + - pressure + - resource slot_uri: MIXS:0000397 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true tvdss_of_hcr_temp: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: meter - occurrence: - tag: occurrence - value: '1' - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) title: depth (TVDSS) of hydrocarbon resource temperature - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - depth (TVDSS) of hydrocarbon resource temperature - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - depth + - hydrocarbon + - resource + - temperature slot_uri: MIXS:0000394 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true typ_occup_density: - annotations: - expected_value: - tag: expected_value - value: measurement value - occurrence: - tag: occurrence - value: '1' description: Customary or normal density of occupants title: typical occupant density examples: - value: '25' - from_schema: http://w3id.org/mixs/terms - aliases: - - typical occupant density - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - density slot_uri: MIXS:0000771 - multivalued: false - range: double + range: float ventilation_rate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cubic meter per minute, liters per second - occurrence: - tag: occurrence - value: '1' description: Ventilation rate of the system in the sampled premises title: ventilation rate examples: - value: 750 cubic meter per minute - from_schema: http://w3id.org/mixs/terms - aliases: - - ventilation rate - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - rate slot_uri: MIXS:0000114 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true ventilation_type: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: ventilation type name - occurrence: - tag: occurrence - value: '1' description: Ventilation system used in the sampled premises title: ventilation type examples: - value: Operable windows - from_schema: http://w3id.org/mixs/terms - aliases: - - ventilation type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type string_serialization: '{text}' slot_uri: MIXS:0000756 - multivalued: false - range: TextValue + multivalued: true vfa: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of Volatile Fatty Acids in the sample title: volatile fatty acids - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - volatile fatty acids - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000152 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true vfa_fw: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter - occurrence: - tag: occurrence - value: '1' description: Original volatile fatty acid concentration in the hydrocarbon resource title: vfa in formation water - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - vfa in formation water - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - water slot_uri: MIXS:0000408 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true vis_media: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: enumeration - occurrence: - tag: occurrence - value: '1' description: The building visual media title: visual media examples: - value: 3D scans - from_schema: http://w3id.org/mixs/terms - aliases: - - visual media - is_a: core field + from_schema: https://w3id.org/mixs + string_serialization: '[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]' slot_uri: MIXS:0000840 - multivalued: false - range: vis_media_enum viscosity: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cP at degree Celsius - occurrence: - tag: occurrence - value: '1' - description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) + description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 C) title: viscosity - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - viscosity - is_a: core field + from_schema: https://w3id.org/mixs string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 - multivalued: false range: TextValue volatile_org_comp: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: volatile organic compound name;measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: microgram per cubic meter, parts per million, nanogram per liter - occurrence: - tag: occurrence - value: m description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound title: volatile organic compounds examples: - value: formaldehyde;500 nanogram per liter - from_schema: http://w3id.org/mixs/terms - aliases: - - volatile organic compounds - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - organic string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000115 multivalued: true range: TextValue wall_area: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The total area of the sampled room's walls title: wall area - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - wall area - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - area + - wall slot_uri: MIXS:0000198 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true wall_const_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + description: The building class of the wall defined by the composition of the building elements and fire-resistance rating title: wall construction type examples: - value: fire resistive - from_schema: http://w3id.org/mixs/terms - aliases: - - wall construction type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type + - wall slot_uri: MIXS:0000841 - multivalued: false - range: wall_const_type_enum + range: WALL_CONST_TYPE_ENUM wall_finish_mat: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The material utilized to finish the outer most layer of the wall title: wall finish material examples: - value: wood - from_schema: http://w3id.org/mixs/terms - aliases: - - wall finish material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - material + - wall slot_uri: MIXS:0000842 - multivalued: false - range: wall_finish_mat_enum + range: WALL_FINISH_MAT_ENUM wall_height: annotations: - expected_value: - tag: expected_value - value: value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: centimeter - occurrence: - tag: occurrence - value: '1' description: The average height of the walls in the sampled room title: wall height - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - wall height - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - height + - wall slot_uri: MIXS:0000221 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true wall_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The relative location of the wall within the room title: wall location examples: - value: north - from_schema: http://w3id.org/mixs/terms - aliases: - - wall location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - wall slot_uri: MIXS:0000843 - multivalued: false - range: wall_loc_enum + range: SHARED_ENUM_0 wall_surf_treatment: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The surface treatment of interior wall title: wall surface treatment examples: - value: paneling - from_schema: http://w3id.org/mixs/terms - aliases: - - wall surface treatment - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - surface + - treatment + - wall slot_uri: MIXS:0000845 - multivalued: false - range: wall_surf_treatment_enum + range: WALL_SURF_TREATMENT_ENUM wall_texture: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The feel, appearance, or consistency of a wall surface title: wall texture examples: - value: popcorn - from_schema: http://w3id.org/mixs/terms - aliases: - - wall texture - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - texture + - wall slot_uri: MIXS:0000846 - multivalued: false - range: wall_texture_enum + range: SHARED_ENUM_4 wall_thermal_mass: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: joule per degree Celsius - occurrence: - tag: occurrence - value: '1' description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint title: wall thermal mass - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - wall thermal mass - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - mass + - wall slot_uri: MIXS:0000222 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true wall_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Signs of the presence of mold or mildew on a wall title: wall signs of water/mold examples: - value: no presence of mold visible - from_schema: http://w3id.org/mixs/terms - aliases: - - wall signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' + from_schema: https://w3id.org/mixs + keywords: + - wall slot_uri: MIXS:0000844 - multivalued: false - range: TextValue + range: SHARED_ENUM_1 wastewater_type: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: wastewater type name - occurrence: - tag: occurrence - value: '1' - description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + description: The origin of wastewater such as human waste, rainfall, storm drains, etc title: wastewater type - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - wastewater type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type string_serialization: '{text}' slot_uri: MIXS:0000353 - multivalued: false - range: TextValue water_cont_soil_meth: - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' description: Reference or method used in determining the water content of soil title: water content method - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - water content method - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' + from_schema: https://w3id.org/mixs + keywords: + - content + - method + - water slot_uri: MIXS:0000323 - multivalued: false + domain_of: + - Soil range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true water_content: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: gram per gram or cubic centimeter per cubic centimeter - occurrence: - tag: occurrence - value: '1' description: Water content measurement title: water content - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - water content - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - content + - water slot_uri: MIXS:0000185 - multivalued: false range: string water_current: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cubic meter per second, knots - occurrence: - tag: occurrence - value: '1' description: Measurement of magnitude and direction of flow within a fluid title: water current examples: - value: 10 cubic meter per second - from_schema: http://w3id.org/mixs/terms - aliases: - - water current - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - water slot_uri: MIXS:0000203 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true water_cut: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: percent - occurrence: - tag: occurrence - value: '1' description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams title: water cut + comments: + - percent or float? examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - water cut - is_a: core field + - value: 45% + from_schema: https://w3id.org/mixs + keywords: + - water slot_uri: MIXS:0000454 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true water_feat_size: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: square meter - occurrence: - tag: occurrence - value: '1' description: The size of the water feature title: water feature size - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - water feature size - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - feature + - size + - water slot_uri: MIXS:0000223 - multivalued: false - range: QuantityValue + range: TextValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true water_feat_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of water feature present within the building being sampled title: water feature type examples: - value: stream - from_schema: http://w3id.org/mixs/terms - aliases: - - water feature type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - feature + - type + - water slot_uri: MIXS:0000847 - multivalued: false - range: water_feat_type_enum + range: WATER_FEAT_TYPE_ENUM water_prod_rate: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: cubic meter per day - occurrence: - tag: occurrence - value: '1' description: Water production rates per well (e.g. 987 m3 / day) title: water production rate - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - water production rate - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - production + - rate + - water slot_uri: MIXS:0000453 - multivalued: false - range: QuantityValue + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true water_temp_regm: annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: degree Celsius - occurrence: - tag: occurrence - value: m description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: water temperature regimen examples: - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - water temperature regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen + - temperature + - water slot_uri: MIXS:0000590 - multivalued: true range: TextValue + multivalued: true watering_regm: annotations: - expected_value: - tag: expected_value - value: measurement value;treatment interval and duration - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milliliter, liter - occurrence: - tag: occurrence - value: m description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: watering regimen examples: - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: http://w3id.org/mixs/terms - aliases: - - watering regimen - is_a: core field - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + from_schema: https://w3id.org/mixs + keywords: + - regimen + - water slot_uri: MIXS:0000591 - multivalued: true range: TextValue + multivalued: true weekday: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The day of the week when sampling occurred title: weekday examples: - value: Sunday - from_schema: http://w3id.org/mixs/terms - aliases: - - weekday - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000848 - multivalued: false - range: weekday_enum + range: WEEKDAY_ENUM win: - annotations: - expected_value: - tag: expected_value - value: text - occurrence: - tag: occurrence - value: '1' description: 'A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' title: well identification number - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - well identification number - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - identifier + - number slot_uri: MIXS:0000297 - multivalued: false range: TextValue + recommended: true wind_direction: annotations: - expected_value: - tag: expected_value - value: wind direction name - occurrence: - tag: occurrence - value: '1' + Preferred_unit: + tag: Preferred_unit + value: degrees or cardinal direction description: Wind direction is the direction from which a wind originates title: wind direction - examples: - - value: Northwest - from_schema: http://w3id.org/mixs/terms - aliases: - - wind direction - is_a: core field - string_serialization: '{text}' + from_schema: https://w3id.org/mixs + keywords: + - direction + - wind slot_uri: MIXS:0000757 - multivalued: false range: TextValue wind_speed: - annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit - value: meter per second, kilometer per hour - occurrence: - tag: occurrence - value: '1' - description: Speed of wind measured at the time of sampling + description: speed of wind measured at the time of sampling title: wind speed - examples: - - value: 21 kilometer per hour - from_schema: http://w3id.org/mixs/terms - aliases: - - wind speed - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - speed + - wind slot_uri: MIXS:0000118 - multivalued: false range: QuantityValue + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true window_cond: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The physical condition of the window at the time of sampling title: window condition examples: - value: rupture - from_schema: http://w3id.org/mixs/terms - aliases: - - window condition - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - condition + - window slot_uri: MIXS:0000849 - multivalued: false - range: window_cond_enum + range: SHARED_ENUM_2 window_cover: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of window covering title: window covering examples: - value: curtains - from_schema: http://w3id.org/mixs/terms - aliases: - - window covering - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - window slot_uri: MIXS:0000850 - multivalued: false - range: window_cover_enum + range: WINDOW_COVER_ENUM window_horiz_pos: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The horizontal position of the window on the wall title: window horizontal position examples: - value: middle - from_schema: http://w3id.org/mixs/terms - aliases: - - window horizontal position - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - window slot_uri: MIXS:0000851 - multivalued: false - range: window_horiz_pos_enum + range: WINDOW_HORIZ_POS_ENUM window_loc: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The relative location of the window within the room title: window location examples: - value: west - from_schema: http://w3id.org/mixs/terms - aliases: - - window location - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - location + - window slot_uri: MIXS:0000852 - multivalued: false - range: window_loc_enum + range: SHARED_ENUM_0 window_mat: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of material used to finish a window title: window material examples: - value: wood - from_schema: http://w3id.org/mixs/terms - aliases: - - window material - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - material + - window slot_uri: MIXS:0000853 - multivalued: false - range: window_mat_enum + range: WINDOW_MAT_ENUM window_open_freq: - annotations: - expected_value: - tag: expected_value - value: value - occurrence: - tag: occurrence - value: '1' description: The number of times windows are opened per week title: window open frequency - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - window open frequency - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - frequency + - window slot_uri: MIXS:0000246 - multivalued: false range: TextValue window_size: annotations: - expected_value: - tag: expected_value + Expected_value: + tag: Expected_value value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: inch, meter - occurrence: - tag: occurrence - value: '1' description: The window's length and width title: window area/size - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - window area/size - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - window string_serialization: '{float} {unit} x {float} {unit}' slot_uri: MIXS:0000224 - multivalued: false range: TextValue window_status: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: Defines whether the windows were open or closed during environmental testing title: window status examples: - value: open - from_schema: http://w3id.org/mixs/terms - aliases: - - window status - is_a: core field - string_serialization: '[closed|open]' + from_schema: https://w3id.org/mixs + keywords: + - status + - window slot_uri: MIXS:0000855 - multivalued: false - range: TextValue + range: WINDOW_STATUS_ENUM window_type: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The type of windows title: window type examples: - value: fixed window - from_schema: http://w3id.org/mixs/terms - aliases: - - window type - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - type + - window slot_uri: MIXS:0000856 - multivalued: false - range: window_type_enum + range: WINDOW_TYPE_ENUM window_vert_pos: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' description: The vertical position of the window on the wall title: window vertical position examples: - value: middle - from_schema: http://w3id.org/mixs/terms - aliases: - - window vertical position - is_a: core field + from_schema: https://w3id.org/mixs + keywords: + - window slot_uri: MIXS:0000857 - multivalued: false - range: window_vert_pos_enum + range: WINDOW_VERT_POS_ENUM window_water_mold: - annotations: - expected_value: - tag: expected_value - value: enumeration - occurrence: - tag: occurrence - value: '1' - description: Signs of the presence of mold or mildew on the window. + description: Signs of the presence of mold or mildew on the window title: window signs of water/mold examples: - value: no presence of mold visible - from_schema: http://w3id.org/mixs/terms - aliases: - - window signs of water/mold - is_a: core field - string_serialization: '[presence of mold visible|no presence of mold visible]' + from_schema: https://w3id.org/mixs + keywords: + - window slot_uri: MIXS:0000854 - multivalued: false - range: TextValue + range: SHARED_ENUM_1 xylene: annotations: - expected_value: - tag: expected_value - value: measurement value - preferred_unit: - tag: preferred_unit + Preferred_unit: + tag: Preferred_unit value: milligram per liter, parts per million - occurrence: - tag: occurrence - value: '1' description: Concentration of xylene in the sample title: xylene - examples: - - value: '' - from_schema: http://w3id.org/mixs/terms - aliases: - - xylene - is_a: core field + from_schema: https://w3id.org/mixs slot_uri: MIXS:0000156 - multivalued: false - range: QuantityValue - core field: - description: basic fields - from_schema: http://w3id.org/mixs/terms - abstract: true - environment field: - description: field describing environmental aspect of a sample - from_schema: http://w3id.org/mixs/terms - abstract: true - investigation field: - description: field describing aspect of the investigation/study to which the sample belongs - from_schema: http://w3id.org/mixs/terms - abstract: true - nucleic acid sequence source field: - from_schema: http://w3id.org/mixs/terms - abstract: true - sequencing field: - from_schema: http://w3id.org/mixs/terms - abstract: true + range: TextValue + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_collec_method: + description: The method employed for collecting the sample + title: sample collection method + from_schema: https://w3id.org/mixs + keywords: + - method + - sample + slot_uri: MIXS:0001225 + range: string + notes: cloned from MIxS 6.2 samp_collect_method + samp_collec_device: + notes: cloned from MIxS 6.2 samp_collect_device + range: string source_file: assets/other_mixs_yaml_files/mixs_template.yaml diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 82bbb97fc4..df08d6222a 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -122,6 +122,31 @@ settings: id_version: "(\\.[0-9]{1,})" id_locus: "(_[A-Za-z0-9_\\.-]+)?$" + country: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) # from https://github.com/GenomicsStandardsConsortium/mixs/blob/main/src/mixs/schema/mixs.yaml + parameters: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + region: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + room_name: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + software: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + specific_location: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + storage_condition_type: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + termLabel: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + unit: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + version: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + DOI: ^doi:10.\d{2,9}/.*$ + NCBItaxon_id: NCBITaxon:\d+ + PMID: ^PMID:\d+$ + URL: ^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$ + adapter: '[ACGTRKSYMWBHDVN]+' + ambiguous_nucleotides: '[ACGTRKSYMWBHDVN]+' + duration: P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W) + float: '[-+]?[0-9]*\.?[0-9]+' + integer: '[1-9][0-9]*' + lat: (-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) + lon: -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2}) + room_number: '[1-9][0-9]*' + scientific_float: '[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?' + termID: '[a-zA-Z]{2,}:[a-zA-Z0-9]\d+' + subsets: sample subset: description: @@ -480,7 +505,8 @@ classes: Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon. slots: - - host_disease_stat + - samp_collec_method # see assets/yq-for-mixs_subset_modified.txt for foced alignment with MIxS 6.2 + - samp_collec_device # see assets/yq-for-mixs_subset_modified.txt for foced alignment with MIxS 6.2 - neon_biosample_identifiers - host_taxid - embargoed @@ -584,7 +610,6 @@ classes: - collection_date - conduc - cool_syst_id - - core field - crop_rotation - cult_root_med - cur_land_use @@ -633,7 +658,6 @@ classes: - env_local_scale - env_medium - env_package - - environment field - escalator - ethylbenzene - exp_duct @@ -700,7 +724,6 @@ classes: - host_common_name - host_diet - host_dry_mass - - host_family_relation - host_genotype - host_growth_cond - host_height @@ -725,7 +748,6 @@ classes: - inorg_particles - inside_lux - int_wall_cond - - investigation field - iw_bt_date_well - iwf - last_clean @@ -762,7 +784,6 @@ classes: - non_min_nutr_regm - nucl_acid_amp - nucl_acid_ext - - nucleic acid sequence source field - number_pets - number_plants - number_resident @@ -850,11 +871,8 @@ classes: - root_med_solid - root_med_suppl - salinity - - salinity_meth - salt_regm - samp_capt_status - - samp_collec_device - - samp_collec_method - samp_collect_point - samp_dis_stage - samp_floor @@ -888,7 +906,6 @@ classes: - sediment_type - seq_meth - seq_quality_check - - sequencing field - sewage_type - shad_dev_water_mold - shading_device_cond @@ -905,7 +922,6 @@ classes: - sludge_retent_time - sodium - soil_horizon - - soil_text_measure - soil_texture_meth - soil_type - soil_type_meth @@ -1044,7 +1060,6 @@ classes: - humidity_regm - light_regm - phosphate - - samp_collec_method - samp_size - source_mat_id - watering_regm @@ -1344,9 +1359,6 @@ classes: - value: 5 mg N/ L todos: - check description. How are they different? - salinity_meth: - examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 sieving: comments: - Describe how samples were composited or sieved. @@ -1829,7 +1841,7 @@ enums: sense orientation: description: Orientation that corresponds to the coding sequence of messenger RNA. - + InstrumentModelEnum: permissible_values: Orbitrap: @@ -2554,15 +2566,15 @@ slots: - OBI:0002475 is_stranded: - description: Is the (RNA) library stranded or non-stranded (unstranded). + description: Is the (RNA) library stranded or non-stranded (unstranded). range: boolean - comments: - - A value of true means the library is stranded, flase means non-stranded. + comments: + - A value of true means the library is stranded, flase means non-stranded. stranded_orientation: description: Lists the strand orientiation for a stranded RNA library preparation. range: StrandedOrientationEnum - + mass: title: mass @@ -2717,8 +2729,6 @@ slots: packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - in_subset: - - mixs extension range: TextValue # pattern: '[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon # resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc diff --git a/tests/test_getters.py b/tests/test_getters.py deleted file mode 100644 index f93c032f26..0000000000 --- a/tests/test_getters.py +++ /dev/null @@ -1,35 +0,0 @@ -import logging - -import unittest - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_nmdc_view import ViewGetter -from nmdc_schema.get_slots_from_class import ClassSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - - -class Getters(unittest.TestCase): - def test_view_getter(self): - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - self.assertEqual(nmdc_view.schema.name, "NMDC") - - def test_schema_slots_getter(self): - schema_slots_getter = SchemaSlotsGetter() - schema_slots = schema_slots_getter.get_schema_slots() - self.assertIsNotNone(schema_slots) - - def test_get_slots_from_class(self): - class_name = "Study" - class_slot_getter = ClassSlotsGetter() - class_slots = class_slot_getter.get_class_slots(class_name) - self.assertIsNotNone(class_slots) - - def test_get_mixs_slots(self): - mg = MIxSSlotsGetter() - mixs_slots = mg.get_unique_slot_names() - self.assertIsNotNone(mixs_slots) - - -if __name__ == "__main__": - unittest.main()