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Taxonomic Backbones
Taxon Names Resolver: http://resolver.globalnames.org/
An overview by Christian for the MDB project, transfered and updated by Peter
| GBIF | Open Tree of Life | WikiData | Catalogue of Life | ITIS | NCBI | |
|---|---|---|---|---|---|---|
| no. of species | 2.5 million | 2.3 million | 2.1 million | 1.6 million | 374.000 | |
| no. of taxa | 5.3 million | 724,000 | 506.000 | |||
| sources | 60% Catalogue of Life 40% 50 other sources | Mainly NCBI, GBIF and IRMNG, other smaller data bases | All items in wikidata describing a taxon. Numerous bots. | 158 data bases | ||
| API | rest api | rest api | SPARQL | web service | Web service (wsdl) | Web site |
| Download | Darwin Core Archive | Collection of csv files | - | - | MySQL, Postgres and others | bcp-like dump files (Microsoft) |
| Last update | 8/2016 | 9/2016continuously | continously | 10/2016 | 9/2016 | 2016 |
| example | http://api.gbif.org/v1/species/5231190 | https://tree.opentreeoflife.org/opentree/argus/opentree7.0@ott93302 | http://tinyurl.com/jnoqoep | http://www.catalogueoflife.org/col/webservice?name=Platalea+leucorodia | https://www.itis.gov/ | https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=drosophila+miranda |
GBIF
- Currently 2,525,274 species, total of 5,307,978 names (inkl. higher taxa)
- The Catalogue of Life as the largest single primary source contributes 59,8% of all names (previously 60,9%). See http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
- Current GBIF taxonomic back bone: http://gbif.blogspot.de/
- GBIF backbone taxonomy wish list: https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/GBIF-backbone-taxonomy-wish-list
- Access: rest api or download as DC: http://rs.gbif.org/datasets/backbone/backbone-current.zip
- Updated 8/2016
Open Tree of Life reference
- (visible) taxon counts: 2.338.745 (https://tree.opentreeoflife.org/about/taxonomy-version/ott2.10)
- Mainly based on NCBI Taxonomy, GBIF and IRMNG
- Access: rest api and download (csv/tsv)
- Updated 9/2016
WikiData
- 2,100,000 correct scientific name of a taxon (12/2015)
- Access: sparql endpoint and via numerous tools (e.g. https://www.npmjs.com/package/wikidata-cli)
- Updated: continously
- A large portion comes from bots like Succu
- These bots harvest sources like Europeaner, Catalog of live and others.
- Wiki Data taxonomy properties: https://www.wikidata.org/wiki/Wikidata
- Useful collection or SPARQL queries of taxon bot: https://www.wikidata.org/wiki/User:Succu/SPARQL
- Info on the awesome LanguageService: https://www.mediawiki.org/wiki/Wikidata_query_service/User_Manual
- Example: http://tinyurl.com/glmxcxk
- See http://git.morphdbase.de/christian/MDB_SPARQL_Queries for examples.
Proposal
The GBIF Taxonomic Backbone provides the best coverage of taxa, ensures high data quality and frequent updates. However wiki data has a superior language management and valuable additional data. For the benefit of the MDB users these data should be combined.
This can be easily achieved with two queries to the public apis of both providers, linked by the GBIF id.
Example “Wattwurm”:
Both entries are linked by the GIBIF ID 5197443.