Dataset Open Access
Poelen, Jorrit
<?xml version='1.0' encoding='utf-8'?> <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd"> <identifier identifierType="DOI">10.5281/zenodo.1213477</identifier> <creators> <creator> <creatorName>Poelen, Jorrit</creatorName> <givenName>Jorrit</givenName> <familyName>Poelen</familyName> </creator> </creators> <titles> <title>20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements</title> </titles> <publisher>Zenodo</publisher> <publicationYear>2018</publicationYear> <dates> <date dateType="Issued">2018-04-06</date> </dates> <resourceType resourceTypeGeneral="Dataset"/> <alternateIdentifiers> <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1213477</alternateIdentifier> </alternateIdentifiers> <relatedIdentifiers> <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1213476</relatedIdentifier> </relatedIdentifiers> <version>0.1</version> <rightsList> <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights> <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights> </rightsList> <descriptions> <description descriptionType="Abstract"><p>This supplementary data publication contains:</p> <p><strong>links-globi-wd-ott.tsv.gz:</strong>&nbsp;aggregate list of taxon graphs from Open Tree of Life Taxonomy (OTT), GloBI and Wikidata. This tab separated two column table, describe the taxonomic identifiers&nbsp;(e.g., NCBI:9606) that map into OTT, GloBI and Wikidata. For instance, the line &quot;NCBI:9689{tab}WD:Q140&quot; indicates that wikidata links their lion (<em>Panthera leo</em>,&nbsp;https://www.wikidata.org/wiki/Q140)&nbsp;to NCBI&#39;s lion (<em>Panthera leo</em>, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9689).</p> <p><strong>wikidata-taxon-info20171227.tsv.gz:&nbsp;</strong>a terse 5 column file in tab-separated format of taxon objects extracted from&nbsp;WikiData. (2018). Wikidata dump 2017-12-27 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1211767 . The columns contain the following:</p> <ol> <li>wikidata taxon item id (e.g., Q140 or https://www.wikidata.org/wiki/Q140)</li> <li>scientific name of taxon item id (e.g., Panthera leo, Mammalia)</li> <li>rank id of the taxon item id (e.g., Q7432 species or https://www.wikidata.org/wiki/Q7432). To retrieve a full list of wikidata taxon rank ids and their common names, you can use sparql to query wikidata (e.g.,&nbsp;<a href="https://github.com/globalbioticinteractions/nomer/blob/c3a1f5a2ebfb87ffc67e3bace19b82d96c0d25e8/nomer/src/main/java/org/globalbioticinteractions/nomer/util/WikidataTaxonRankLoader.java">Nomer&#39;s WikidataTaxonRankLoader</a>&nbsp;).&nbsp;</li> <li>parent ids if taxon item id using pipes &quot;|&quot; as separators if there&#39;s multiple parents.&nbsp;&nbsp;Please note that some taxon items have multiple parents (e.g.,&nbsp;https://www.wikidata.org/wiki/Q774014).</li> <li>external taxonomic identifiers that taxon item link to (e.g. &quot;ITIS:162532|EOL:8266|GBIF:2960|WORMS:125440&quot;) . If muliple are present, pipes &quot;|&quot; are used to separate the links. Only a selection of taxonomic schemes was used, namely: NCBI, GBIF, ITIS, WORMS, FISHBASE, IF (index fungorum) and EOL.</li> </ol> <p>The datasets can be recreated by scripts in&nbsp;https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata or <a href="https://doi.org/10.5281/zenodo.1428949">https://doi.org/10.5281/zenodo.1428949</a>&nbsp;.</p></description> </descriptions> </resource>
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