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/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .

Files
  
  README 
      this file

  taxonCache.tsv.gz 
     Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. 
 
  taxonCache.tsv.sha256
     sha256 hash of taxonCache.tsv

  taxonCacheFirst10.tsv
      Header and 10 following lines from taxonCache.tsv.gz.

  taxonCacheFirst10.tsv.sha256
      sha256 hash of taxonCacheFirst10.tsv
       
  taxonMap.tsv.gz 
      Links between taxon name and ids across various taxon providers. 

  taxonMap.tsv.sha256 
      sha256 hash of taxonMap.tsv.gz.md5 

  taxonMapFirst10.tsv
      Header and 10 following lines from taxonMap.tsv.gz.
 
  taxonMapFirst10.tsv.sha256
      sha256 hash of taxonMapFirst10.tsv

  prefixes.tsv
      Term prefixes and their associated uri schemes. 

  names.tsv.gz
      Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .

  names.tsv.gz.md5
      md5 hash of names.tsv.gz.md5

  namesUnresolved.tsv.gz
      Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .

  namesUnresolved.tsv.gz.md5
      md5 hash of namesUnresolved.tsv.gz 

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

  names.tsv.gz

    1 | providedTaxonId
    2 | providedTaxonName

   namesUnresolved.tsv.gz

    1 | providedTaxonId
    2 | providedTaxonName

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. https://doi.org/10.1016/j.ecoinf.2014.08.005.

Updates

org.globalbioticinteractions.taxon v0.3, 2018-03-02

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.

org.globalbioticinteractions.taxon v0.3.1, 2018-04-05

This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .

org.globalbioticinteractions.taxon v0.3.2, 2018-05-21

This taxon archive version includes the following:

1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).

2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 

3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.

4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.

5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. 

6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.

org.globalbioticinteractions.taxon v0.3.3, 2018-06-12

This taxon archive version includes the following:

1. normalizing taxonomic ranks using nomer's taxon rank matcher

2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.

3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . 

4. remove mapping to NCBI taxa with name "Small" (and associated OTT).


org.globalbioticinteractions.taxon v0.3.4, 2018-06-27

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023

Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. 

org.globalbioticinteractions.taxon v0.3.5, 2018-06-28

1. remove dubious provided name from taxon map. Names include "no name", "unidentified".
2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.
3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"
4. removed dubious mappings to "Boiga dendrophila"
5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651
6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"

Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.

org.globalbioticinteractions.taxon v0.3.6, 2018-09-10

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023

org.globalbioticinteractions.taxon v0.3.7, 2018-10-18

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023
2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .
3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 

org.globalbioticinteractions.taxon v0.3.8, 2018-11-15

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023

org.globalbioticinteractions.taxon v0.3.9, 2018-11-23

1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .
2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .
3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. 


org.globalbioticinteractions.taxon v0.3.10, 2018-11-26

1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 

org.globalbioticinteractions.taxon v0.3.11, 2018-12-21

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023
2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura$" | grep -v -P "Gamarus" |  grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer$" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```

org.globalbioticinteractions.taxon v0.3.12, 2019-06-05

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558

org.globalbioticinteractions.taxon v0.3.13, 2019-06-12

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558

org.globalbioticinteractions.taxon v0.3.14, 2019-08-19

1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .

org.globalbioticinteractions.taxon v0.3.15, 2019-08-26

1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558

org.globalbioticinteractions.taxon v0.3.16, 2019-09-22

1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .

