Dataset Open Access

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

Poelen, Jorrit


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    <subfield code="a">20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements</subfield>
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    <subfield code="a">&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;https://www.wikidata.org/wiki/Q140)&amp;nbsp;to NCBI&amp;#39;s lion (&lt;em&gt;Panthera leo&lt;/em&gt;, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;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. http://doi.org/10.5281/zenodo.1211767 . The columns contain the following:&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;wikidata taxon item id (e.g., Q140 or https://www.wikidata.org/wiki/Q140)&lt;/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 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.,&amp;nbsp;&lt;a href="https://github.com/globalbioticinteractions/nomer/blob/c3a1f5a2ebfb87ffc67e3bace19b82d96c0d25e8/nomer/src/main/java/org/globalbioticinteractions/nomer/util/WikidataTaxonRankLoader.java"&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;https://www.wikidata.org/wiki/Q774014).&lt;/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;/ol&gt;

&lt;p&gt;The datasets can be recreated by scripts in&amp;nbsp;https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata or &lt;a href="https://doi.org/10.5281/zenodo.1428949"&gt;https://doi.org/10.5281/zenodo.1428949&lt;/a&gt;&amp;nbsp;.&lt;/p&gt;</subfield>
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