Dataset Open Access

20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements

Poelen, Jorrit

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  <identifier identifierType="DOI">10.5281/zenodo.1213477</identifier>
      <creatorName>Poelen, Jorrit</creatorName>
    <title>20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements</title>
    <date dateType="Issued">2018-04-06</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1213476</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;This supplementary data publication contains:&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;links-globi-wd-ott.tsv.gz:&lt;/strong&gt;&amp;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&amp;nbsp;(e.g., NCBI:9606) that map into OTT, GloBI and Wikidata. For instance, the line &amp;quot;NCBI:9689{tab}WD:Q140&amp;quot; indicates that wikidata links their lion (&lt;em&gt;Panthera leo&lt;/em&gt;,&amp;nbsp;;nbsp;to NCBI&amp;#39;s lion (&lt;em&gt;Panthera leo&lt;/em&gt;,;amp;id=9689).&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;wikidata-taxon-info20171227.tsv.gz:&amp;nbsp;&lt;/strong&gt;a terse 5 column file in tab-separated format of taxon objects extracted from&amp;nbsp;WikiData. (2018). Wikidata dump 2017-12-27 [Data set]. Zenodo. . The columns contain the following:&lt;/p&gt;

	&lt;li&gt;wikidata taxon item id (e.g., Q140 or;/li&gt;
	&lt;li&gt;scientific name of taxon item id (e.g., Panthera leo, Mammalia)&lt;/li&gt;
	&lt;li&gt;rank id of the taxon item id (e.g., Q7432 species or To retrieve a full list of wikidata taxon rank ids and their common names, you can use sparql to query wikidata (e.g.,&amp;nbsp;&lt;a href=""&gt;Nomer&amp;#39;s WikidataTaxonRankLoader&lt;/a&gt;&amp;nbsp;).&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;parent ids if taxon item id using pipes &amp;quot;|&amp;quot; as separators if there&amp;#39;s multiple parents.&amp;nbsp;&amp;nbsp;Please note that some taxon items have multiple parents (e.g.,&amp;nbsp;;/li&gt;
	&lt;li&gt;external taxonomic identifiers that taxon item link to (e.g. &amp;quot;ITIS:162532|EOL:8266|GBIF:2960|WORMS:125440&amp;quot;) . If muliple are present, pipes &amp;quot;|&amp;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.&lt;/li&gt;

&lt;p&gt;The datasets can be recreated by scripts in&amp;nbsp; or &lt;a href=""&gt;;/a&gt;&amp;nbsp;.&lt;/p&gt;</description>
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