remove slots that are only for `submission-schema`

[mslarae13]

These slots are in nmdc-schema

• rna_isolate_meth
• dna_lr_isolate_meth
• dna_isolate_meth
• emsl_store_temp
• project_id
• sample_shipped
• sample_type
• replicate_number
• technical_reps

This was so we could create the submission-schema. We now have the ability to create slots in submission-schema without them coming from nmdc-schema.

These slots were not moved out of nmdc-schema, but should be

• remove slots from nmdc-schema in favor of extraction class & provide via submission-schema

• rna_isolate_meth, dna_lr_isolate_meth, dna_isolate_meth

• in the submission portal, we need to collect the long read & short read extraction information. Upon ingest to mongoDB, this information should be on an Extraction record. The slot `` will never have a record in mongo. @turbomam has requested, to avoid confusion, we do not have this slot in nmdc-schema. We can create an alias on Extraction so it's clear that this information from the submission portal is capture here, but that that slot will not hold any information in mongodb.

• remove slots from nmdc-schema & provide via submission-schema

• NMDC doesn't care or need to track this information.

  • emsl_store_temp : NMDC doesn't need to store this
  • project_id : NMDC will store this via Study slot emsl_project_identifiers
  • sample_shipped: NMDC doesn't need to store this
  • sample_type : TBD, definitely remove from the portal.yaml file. But should be on Biosample?
  • replicate_number : TBD, definitely remove from the portal.yaml file. But should be on Biosample?
  • technical_reps: TBD, definitely remove from the portal.yaml file. But should be on Biosample?

[mslarae13]

1 task is settle on if NMDC should track
sample_type
replicate_number
technical_reps

Would appreciate thoughts from @aclum , @lamccue
Right now, these 3 slots don't exist in any records in NMDC. We could start tracking this information wen we pull records in from the submission portal. ATM, this is exclusively for EMSL samples.

• should NMDC store this information?
• Should this be for all Biosamples or only EMSL ones?

Note, sample_type could be auto populated using the environmental extension selected. We've wanted to do this in the submission portal but haven't.

[aclum]

It seems like this information would potentially be useful for users interpreting EMSL data in the context of NMDC, especially replicate_number and technical_reps so I'm inclined to say keep it.