Teleost Taxonomy Ontology

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

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).
• 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