Teleost Taxonomy Ontology

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Summary

This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichtyes (sharks and rays), Sarcopterygia (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 we added nearly 15,000 common names provided by FishbaseAdditional names and synonyms are added as a result of our curation activities.

Details of changes are recorded in the TTO_Changes page, (though this is not frequently updated), and summarized in the cvs commit comments.

The current release may be found here.

License

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To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Teleost Taxonomy Ontology (TTO). This work is published from the United States.

Organization

                              Ictaluridae   -------------------->  TaxRank:Family
                                   ^               has_rank
                                   |
                              is_a |
                                   |
                               Ictalurus    -------------------->  TaxRank:Genus
                                   ^             has_rank
                                   |
                              is_a |
                                   |
Channel catfish <--------+Ictalurus punctatus ---------------->  TaxRank:Species
                         |                       has_rank
                         |
Silurus argentinus<------+


List of term and database identifier prefixes

  • TTO: Term defined in the TTO
  • NCBITaxon: ID from NCBI taxonomy database
  • CASSPC: ID from the Catalog of Fishes species table (CAS = California Academy of Sciences)
  • CASGEN: ID from the Catalog of Fishes genus table
  • TAXRANK: Term defined in the Taxonomic Rank Vocabulary
  • urn: URN from external resource, generally an lsid from GNI.

List of Relations and Synonym Types

Name Relation or Synonym Notes
COMMONNAME synonym type synonymous common name
MISSPELLING synonym type synonym resulting from identifiable misspelling
TAXONNAMEUSAGE synonym type synonym that includes an (author year) citation
property_value: has_rank metadata relation links taxa to ranks
property_value: is_extinct boolean metadata relation indicates taxa only known from fossils

Notes

  • The taxonomic rank specified by the has_rank relation is specified by its identifier. The most common are TAXRANK:0000004 (family), TAXRANK:0000005 (genus), TAXRANK:0000006 (species).
  • In general TTO does not assign intermediate ranks (e.g., subclass). There are a few exceptions that may be removed.
  • At present is_extinct does not include recently extinct taxa.

Detailed Term Counts

Item Count
Total Terms 38590
Total Synonyms 59557
Common Name Synonyms 14754
Synonyms resulting from misspelling 18
Extinct Taxa 228
Cross references to names in NCBI taxonomy 13318
Phyla 1
Classes 3
Orders 68
Families 566
Genera 5263
Species 32653