Dataset Open Access

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

Poelen, Jorrit

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<oai_dc:dc xmlns:dc="" xmlns:oai_dc="" xmlns:xsi="" xsi:schemaLocation="">
  <dc:creator>Poelen, Jorrit</dc:creator>
  <dc:description>This supplementary data publication contains:

links-globi-wd-ott.tsv.gz: 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 (e.g., NCBI:9606) that map into OTT, GloBI and Wikidata. For instance, the line "NCBI:9689{tab}WD:Q140" indicates that wikidata links their lion (Panthera leo, to NCBI's lion (Panthera leo,;id=9689).

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

	wikidata taxon item id (e.g., Q140 or
	scientific name of taxon item id (e.g., Panthera leo, Mammalia)
	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., Nomer's WikidataTaxonRankLoader ). 
	parent ids if taxon item id using pipes "|" as separators if there's multiple parents.  Please note that some taxon items have multiple parents (e.g.,
	external taxonomic identifiers that taxon item link to (e.g. "ITIS:162532|EOL:8266|GBIF:2960|WORMS:125440") . If muliple are present, pipes "|" 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.

The datasets can be recreated by scripts in or .</dc:description>
  <dc:title>20 GB in 10 minutes: Data linking across major biodiversity databases: Data supplements</dc:title>
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