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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
737a7fc
typo
sannegovaert Apr 2, 2025
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304 changes: 304 additions & 0 deletions data/processed/2010_PHD_REUBENS/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>Reubens, J.; Degraer, S.; Desmet, P.; Moens, T.; Reyserhove, L.; Vincx, M.; (2020): 2010_PHD_REUBENS - Acoustic telemetry data for Atlantic cod (Gadus morhua) in the C-Power wind farm in the southern North Sea (Belgium). Marine Data Archive. https://dx.doi.org/10.14284/437<identifier>https://doi.org/10.14284/437</identifier></citation>
<dateStamp>2025-01-08T10:51:47+01:00</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://emodnet.ec.europa.eu/geonetwork/srv/eng/catalog.search#/metadata/6d617269-6e65-696e-666f-000000005846</url>
</online>
</distribution>
</physical>
<physical>
<objectName>Online dataset</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://www.eurobis.org/toolbox/en/download/occurrence/dataset/5846</url>
</online>
</distribution>
</physical>
<physical>
<objectName>GBIF dataset</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://www.gbif.org/dataset/06d9eb55-ab67-45da-a697-18cc42e7cd3c</url>
</online>
</distribution>
</physical>
<physical>
<objectName>IPT</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://ipt.inbo.be/archive?r=2010_phd_reubens</url>
</online>
</distribution>
</physical>
<physical>
<objectName>IPT</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">http://ipt.inbo.be/resource?r=2010_phd_reubens</url>
</online>
</distribution>
</physical>
<physical>
<objectName>IPT</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://ipt.vliz.be/eurobis/resource?r=2010_phd_reubens</url>
</online>
</distribution>
</physical>
<physical>
<objectName>Online dataset</objectName>
<characterEncoding>UTF-8</characterEncoding>
<dataFormat>
<externallyDefinedFormat>
<formatName>HTML</formatName>
</externallyDefinedFormat>
</dataFormat>
<distribution>
<online>
<url function="download">https://obis.org/dataset/63061840-e725-4c74-bdbc-65f31a8e28c8</url>
</online>
</distribution>
</physical>
<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=5846</url>
</online>
</distribution>
</physical>
</gbif>
<parameter>Fish detections</parameter>
<parameter>Fish total length</parameter>
</metadata>
</additionalMetadata>
<dataset>
<title xml:lang="en">Acoustic telemetry data for Atlantic cod (Gadus morhua) in the C-Power wind farm in the southern North Sea (Belgium)</title>
<creator>
<individualName>
<givenName>Jan</givenName>
<surName>Reubens</surName>
</individualName>
<organizationName>Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-9823-5670</userId>
</creator>
<creator>
<individualName>
<givenName>Steven</givenName>
<surName>Degraer</surName>
</individualName>
<organizationName>Koninklijk Belgisch Instituut voor Natuurwetenschappen; Operationele Directie Natuurlijk Milieu</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-3159-5751</userId>
</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>Tom</givenName>
<surName>Moens</surName>
</individualName>
<organizationName>Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0001-6544-9210</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>
<userId directory="https://orcid.org/">0000-0001-7484-9267</userId>
</creator>
<creator>
<individualName>
<givenName>Magda</givenName>
<surName>Vincx</surName>
</individualName>
<organizationName>Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie</organizationName>
<address>
<country>BE</country>
</address>
</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>2024-08-30</pubDate>
<language>en</language>
<abstract>
<para><![CDATA[This is an acoustic telemetry dataset published by Ghent University. 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 2010_phd_Reubens, using VEMCO tags (V9) and receivers (VR2W). In total 41 individuals of Atlantic cod (<i>Gadus morhua</i>) were captured, tagged and released in 2010 and 2011 in the C-Power wind farm in the Belgian part of the North Sea, to study their movement behaviour and assess the impacts of offshore wind farms on their movement ecology. This dataset also includes the data of the synchronisation tags present in the study. To calculate exact 2D positions using acoustic telemetry, the time difference of arrival of signals at different receivers is used. Therefore sync tags are needed to account for clock drift in the receivers.]]></para>
<para><![CDATA[Intensive exploitation of the marine environment by mankind can alter the natural habitat of marine organisms drastically. The addition of artificial hard substrates (e.g. offshore wind turbines) to soft-sediment sandy bottoms is a pervasive example of an anthropogenic habitat change. In this study, we assess the influence of offshore wind farms on the spatio-temporal movement ecology of Atlantic cod (<i>Gadus morhua</i>). The results of this study will be useful for management measures for the conservation and restoration of the cod population.]]></para>
<para>This study was funded by Research Foundation - Flanders (FWO).</para>
<para>Data have been standardized to Darwin Core using the &lt;a href="https://inbo.github.io/etn/"&gt;etn&lt;/a&gt; package and are downsampled to the first detection per hour. The original data are managed in the European Tracking Network data platform (&lt;a href="https://lifewatch.be/etn/"&gt;https://lifewatch.be/etn/&lt;/a&gt;) and are available in Reubens et al. (2020, &lt;a href="https://doi.org/10.14284/437"&gt;https://doi.org/10.14284/437&lt;/a&gt;).</para>
</abstract>
<keywordSet>
<keyword>Acoustic telemetry</keyword>
<keyword>Home range</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>VEMCO</keyword>
<keywordThesaurus>N/A</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Data</keyword>
<keywordThesaurus>Assemble KO Types</keywordThesaurus>
</keywordSet>
<intellectualRights>
<para>This work is licensed under a <ulink url="http://creativecommons.org/licenses/by/4.0/legalcode"><citetitle>Creative Commons Attribution (CC-BY) 4.0 License</citetitle></ulink>.</para>
</intellectualRights>
<coverage>
<geographicCoverage id="http://marineregions.org/mrgid/2550">
<geographicDescription>ANE, Belgium, Belgian Coast</geographicDescription>
</geographicCoverage>
<geographicCoverage id="http://marineregions.org/mrgid/2438">
<geographicDescription>ANE, Belgium, Zeeland Banks, Thornton Bank</geographicDescription>
</geographicCoverage>
<geographicCoverage id="http://marineregions.org/mrgid/2350">
<geographicDescription>ANE, North Sea</geographicDescription>
</geographicCoverage>
<geographicCoverage>
<geographicDescription>EurOBIS calculated BBOX &gt; station Bounding Box</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>2.92157</westBoundingCoordinate>
<eastBoundingCoordinate>2.953</eastBoundingCoordinate>
<northBoundingCoordinate>51.552</northBoundingCoordinate>
<southBoundingCoordinate>51.53766667</southBoundingCoordinate>
</boundingCoordinates>
</geographicCoverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>2010-08-06</calendarDate>
</beginDate>
<endDate>
<calendarDate>2015-08-31</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
<taxonomicCoverage>
<taxonomicClassification>
<taxonRankName>species</taxonRankName>
<taxonRankValue>Gadus morhua Linnaeus, 1758</taxonRankValue>
</taxonomicClassification>
</taxonomicCoverage>
</coverage>
<maintenance>
<description>
<para/>
</description>
<maintenanceUpdateFrequency>Not planned</maintenanceUpdateFrequency>
</maintenance>
<contact>
<individualName>
<givenName>Jan</givenName>
<surName>Reubens</surName>
</individualName>
<organizationName>Vlaams Instituut voor de Zee</organizationName>
<address>
<country>BE</country>
</address>
<userId directory="https://orcid.org/">0000-0002-9823-5670</userId>
</contact>
</dataset>
</eml:eml>
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