Global Biotic Interactions: Taxon Graph

Global Biotic Interactions: Taxon Cache and Taxon Map

Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. 

The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. 

While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.

For related discussion threads, see https://github.com/jhpoelen/eol-globi-data/issues/145 , https://github.com/jhpoelen/eol-globi-data/issues/274 , https://github.com/jhpoelen/eol-globi-data/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/jhpoelen/eol-globi-data/issues/274 .

Files
  
  README 
      this file
  
  taxonCache.tsv.gz 
      Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. Accessed at https://depot.globalbioticinteractions.org/datasets/org/globalbioticinteractions/taxon/0.4.2/taxon-0.4.2.zip on 5 March 2018.
 
  taxonCacheFirst10.tsv
      Header and 10 following lines from taxonCache.tsv.gz.
 
  taxonMap.tsv.gz 
      Links between taxon name and ids across various taxon providers. Accessed at https://depot.globalbioticinteractions.org/datasets/org/globalbioticinteractions/taxon/0.4.2/taxon-0.4.2.zip on 5 March 2018. 

  taxonMapFirst10.tsv
      Header and 10 following lines from taxonMap.tsv.gz.
 
  prefixes.tsv
      Term prefixes and their associated uri schemes. 

Column Descriptions

  taxonCache.tsv.gz 

    1 | id
    2 | name
    3 | rank
    4 | commonNames
    5 | path
    6 | pathIds 
    7 | pathNames
    8 | externalUrl
    9 | thumbnailUrl
 
  taxonMap.tsv.gz

    1 | providedTaxonId
    2 | providedTaxonName
    3 | resolvedTaxonId
    4 | resolvedTaxonName

References

Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. http://dx.doi.org/10.1016/j.ecoinf.2014.08.005.

Updates

2018-03-02
version: 0.3.0

This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.

2018-03-05
version: 0.4.1

Taxon Cache/Map created by merging WikiData map/cache with globalbioticinteractions.org:taxon:0.1 .

Same as v0.4 with corrected taxonCache header that includes commonNames. 

2018-03-05
version: 0.4.2

was created by:

taking globi taxon 0.4.1 
extracting all interaction names using elton
matching all taxon 0.4.1 using nomer
matching all unresolved taxa using nomer with "globi-globalnames" matcher

Then, to create taxonMap and taxonCache,
resulting SAME_AS and SYNONYM_OF external ids were mapped to wikidata ids using taxon-wikidata 0.4.1
split columns to produce taxonMap and taxonCache
These taxonMap and taxonCache files were then appended to the 0.4.1 cache.