Dataset Open Access

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

Poelen, Jorrit


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1213477", 
  "title": "20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements", 
  "issued": {
    "date-parts": [
      [
        2018, 
        4, 
        6
      ]
    ]
  }, 
  "abstract": "<p>This supplementary data publication contains:</p>\n\n<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>\n\n<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>\n\n<ol>\n\t<li>wikidata taxon item id (e.g., Q140 or https://www.wikidata.org/wiki/Q140)</li>\n\t<li>scientific name of taxon item id (e.g., Panthera leo, Mammalia)</li>\n\t<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>\n\t<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>\n\t<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>\n</ol>\n\n<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>", 
  "author": [
    {
      "family": "Poelen, Jorrit"
    }
  ], 
  "version": "0.1", 
  "type": "dataset", 
  "id": "1213477"
}
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