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Prepare EML for GBIF upload #83

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9f422eb
Create prepare_eml_for_GBIF.Rmd
sannegovaert Sep 12, 2024
9d7d5c0
upload data
sannegovaert Sep 12, 2024
7f6453b
fix typo's
sannegovaert Sep 12, 2024
3f3be26
remove dx. in link
sannegovaert Sep 13, 2024
0c87a1d
reorder
sannegovaert Sep 13, 2024
e4ea86e
Clean Resource citation identifier
sannegovaert Sep 13, 2024
991d34d
fix typo
sannegovaert Sep 13, 2024
f7fbcdd
remove taxonomicCoverage id
sannegovaert Sep 13, 2024
8a3bef9
account for more than 1 species in taxonomic coverage
sannegovaert Sep 13, 2024
e627b42
update description
sannegovaert Sep 17, 2024
f70b492
update description
sannegovaert Sep 17, 2024
0f762d5
Rename file
peterdesmet Sep 18, 2024
73eb6a2
Minor textual updates (not to code)
peterdesmet Sep 18, 2024
98f0d96
Correct link in description
peterdesmet Sep 18, 2024
c2c95c3
Use shorter url
peterdesmet Sep 18, 2024
1962e41
Merge branch 'main' into prepare_eml_for_gbif
sannegovaert Jan 22, 2025
14fd09a
change folder structure
sannegovaert Jan 22, 2025
66d5638
read eml directly from IMIS url
sannegovaert Jan 22, 2025
9793eea
set all mailAdresses to NULL, because of off emails
sannegovaert Jan 22, 2025
3e21b9a
update processed eml
sannegovaert Jan 22, 2025
e136080
Update etn-occurrences.Rproj
sannegovaert Mar 31, 2025
293ee07
wrap more paragraphs in <![CDATA[
sannegovaert Mar 31, 2025
66ef500
apply to all datasets
sannegovaert Mar 31, 2025
bb52392
reorder CDATA wrap code
sannegovaert Apr 1, 2025
c0a2b40
update to EML 2.2.0
sannegovaert Apr 2, 2025
0c085c1
split in paragraphs and add <p></p> tags
sannegovaert Apr 2, 2025
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typo
sannegovaert Apr 2, 2025
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242 changes: 242 additions & 0 deletions data/2011_RIVIERPRIK/processed/eml.xml
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<?xml version="1.0" encoding="UTF-8"?>
<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" xmlns:dc="https://www.dublincore.org/specifications/dublin-core/dcmi-terms" xml:lang="en" packageId="eml.1.1" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 https://rs.gbif.org/schema/eml-gbif-profile/1.1/eml.xsd" system="https://www.vliz.be/imis">
<additionalMetadata>
<describes>
<para>Extra metadata added by VLIZ to add parameter, platform info, as well as GBIF fields</para>
</describes>
<metadata>
<gbif>
<citation>Buysse, D.; Mouton, A.; Baeyens, R.; De Maerteleire, N.; Desmet, P.; Gelaude, E.; Jacobs, Y.; Pauwels, I.; Reyserhove, L.; Coeck, J.; (2020): 2011_RIVIERPRIK - Acoustic telemetry data for river lamprey (Lampetra fluviatilis) in the upper Scheldt river (Belgium). Marine Data Archive. https://dx.doi.org/10.14284/429<identifier>https://doi.org/10.14284/429</identifier></citation>
<dateStamp>2024-07-09T01:33:06+00:00</dateStamp>
<hierarchyLevel>dataset</hierarchyLevel>
<physical>
<objectName>Online dataset</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://rshiny.lifewatch.be/etn-data/</url>
</online>
</distribution>
</physical>
<physical>
<objectName>Metadata</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://www.vliz.be//en/imis?dasid=5867</url>
</online>
</distribution>
</physical>
</gbif>
<parameter>Fish detections</parameter>
<parameter>Fish sex</parameter>
<parameter>Fish total length</parameter>
<parameter>Wet weight of fish</parameter>
</metadata>
</additionalMetadata>
<dataset>
<title xml:lang="en">2011_RIVIERPRIK - Acoustic telemetry data for river lamprey (Lampetra fluviatilis) in the upper Scheldt river (Belgium)</title>
<creator>
<individualName>
<givenName>David</givenName>
<surName>Buysse</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-4437-5678</userId>
</creator>
<creator>
<individualName>
<givenName>Ans</givenName>
<surName>Mouton</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
</creator>
<creator>
<individualName>
<givenName>Raf</givenName>
<surName>Baeyens</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-0651-3056</userId>
</creator>
<creator>
<individualName>
<givenName>Nico</givenName>
<surName>De Maerteleire</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<electronicMailAddress>nico.demaerteleire@inbo.be</electronicMailAddress>
</creator>
<creator>
<individualName>
<givenName>Peter</givenName>
<surName>Desmet</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-8442-8025</userId>
</creator>
<creator>
<individualName>
<givenName>Emilie</givenName>
<surName>Gelaude</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
</creator>
<creator>
<individualName>
<givenName>Yves</givenName>
<surName>Jacobs</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
</creator>
<creator>
<individualName>
<givenName>Ine</givenName>
<surName>Pauwels</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<electronicMailAddress>ine.pauwels@inbo.be</electronicMailAddress>
<userId directory="https://orcid.org/">0000-0002-2856-8787</userId>
</creator>
<creator>
<individualName>
<givenName>Lien</givenName>
<surName>Reyserhove</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<electronicMailAddress>lien.reyserhove@inbo.be</electronicMailAddress>
<userId directory="https://orcid.org/">0000-0001-7484-9267</userId>
</creator>
<creator>
<individualName>
<givenName>Johan</givenName>
<surName>Coeck</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0003-2732-7428</userId>
</creator>
<metadataProvider>
<individualName>
<givenName>Peter</givenName>
<surName>Desmet</surName>
</individualName>
<electronicMailAddress>peter.desmet@inbo.be</electronicMailAddress>
<userId directory="https://orcid.org/">0000-0002-8442-8025</userId>
</metadataProvider>
<pubDate>2020-11-19</pubDate>
<language>en</language>
<abstract>
<para><![CDATA[This is an acoustic telemetry dataset published by the Research Institute for Nature and Forest (INBO). It contains animal (fish) tracking data collected by what later became the Permanent Belgian Acoustic Receiver Network <a href="https://lifewatch.be/en/fish-acoustic-receiver-network"> (https://lifewatch.be/en/fish-acoustic-receiver-network)</a> for the project/study 2011_rivierprik, using VEMCO tags (V7, V8) and receivers (VR2, VR2W). In total 39 adult individuals of river lamprey (<i>Lampetra fluviatilis</i>) were captured, tagged and released in 2011 and 2012, to study the effect of weirs and shipping locks on their upstream spawning migration in the tidal and/or non-tidal part of the Scheldt river and its tributaries.]]></para>
<para>The disruption of longitudinal and lateral connectivity of rivers has led to ecological catastrophes such as the extinction of several diadromous fish species. River lamprey is an important indicator species for the integrity of ecosystems and connectivity within and between catchment areas. In the highly fragmented Scheldt river basin first restoration actions are undertaken, such as the building of nature-like bypasses. The migration patterns in the river catchment and their behaviour at a tidal barrier, lock-weir complexes and fish bypasses (passage timing and delay) in the upper Scheldt river show that the disrupted water management of the river and in consequence of its barriers and bypasses are one keys to (un)successful spawning migration in the catchment, beside spawning habitat deterioration.</para>
<para>The study was commissioned by the Vlaamse Waterweg NV.</para>
<para>Data were exported from the European Tracking Network data portal &lt;a href="http://www.lifewatch.be/etn"&gt; (http://www.lifewatch.be/etn) &lt;/a&gt; developed by VLIZ using the ETN R package &lt;a href="https://inbo.github.io/etn/"&gt; (https://inbo.github.io/etn/) &lt;/a&gt; developed by INBO. Field definitions can be found at &lt;a href="https://inbo.github.io/etn/articles/etn_fields.html"&gt;https://inbo.github.io/etn/articles/etn_fields.html&lt;/a&gt;.</para>
</abstract>
<keywordSet>
<keyword>Acoustic telemetry</keyword>
<keyword>Spawning migrations</keyword>
<keywordThesaurus>ASFA Thesaurus List</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Acoustic Telemetry</keyword>
<keywordThesaurus>ETN Context</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Animal movement</keyword>
<keyword>Animal tracking</keyword>
<keyword>Biologging</keyword>
<keyword>Impact assessment</keyword>
<keyword>Migration barriers</keyword>
<keyword>River lamprey</keyword>
<keyword>VEMCO</keyword>
<keywordThesaurus>N/A</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Migration</keyword>
<keywordThesaurus>CSA Technology Research Database Master Thesaurus</keywordThesaurus>
</keywordSet>
<intellectualRights>
<para>To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the <ulink url="http://creativecommons.org/publicdomain/zero/1.0/legalcode"><citetitle>Public Domain (CC0 1.0)</citetitle></ulink>. Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.</para>
</intellectualRights>
<coverage>
<geographicCoverage id="http://marineregions.org/mrgid/2469">
<geographicDescription>Belgium, Flanders</geographicDescription>
</geographicCoverage>
<geographicCoverage id="http://marineregions.org/mrgid/2542">
<geographicDescription>Belgium, Scheldt</geographicDescription>
</geographicCoverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>2011-12-13</calendarDate>
</beginDate>
<endDate>
<calendarDate>2012-07-03</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
<taxonomicCoverage>
<taxonomicClassification>
<taxonRankName>species</taxonRankName>
<taxonRankValue>Lampetra fluviatilis (Linnaeus, 1758)</taxonRankValue>
</taxonomicClassification>
</taxonomicCoverage>
</coverage>
<maintenance>
<description>
<para/>
</description>
<maintenanceUpdateFrequency>Not planned</maintenanceUpdateFrequency>
</maintenance>
<contact>
<individualName>
<givenName>David</givenName>
<surName>Buysse</surName>
</individualName>
<organizationName>Research Institute for Nature and Forest (INBO)</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-4437-5678</userId>
</contact>
</dataset>
</eml:eml>
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