VTO Taxonomy Resources
Contents
Resources for Constructing a Vertebrate Taxonomy Ontology
There are two types of resources useful for building taxonomic ontologies: taxonomic resources which provide hierarchy and nomenclature resources which provide information about names. Both types of resources are used in taxonomic ontologies and listed here.
Fish
The TTO is derived from the catalog of fishes, which provides some taxonomy information and a great deal of nomenclature in the form of synonyms. It is updated several times a year and TTO should be rebuilt by requesting the appropriate files from Stan Blum.
The TTO also incorporates some common names from Fishbase and cross references (xrefs) from the Global Names Index.
Information for extinct taxa has been added as needed by curation, and the taxonomy is, as a rule, from the curated publication.
Amphibians
The ATO is derived from the AmphibiaWeb list, which provides both taxonomy and some synonyms from ITIS and ???.
Birds
IOU checklist provides a current taxonomy and some common names, but no taxonomic synonyms.
Mammals
Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered. NCBI and/or ITIS may be the best starting point.
Tools
VTO Construction Tool
Generated Taxonomic Ontology
This taxonomy covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), ATO, and the IOC taxonomy of living birds. Synonyms from ITIS and Catalog of Life were attached if the primary name matched a name in the existing taxonomy. Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the OBO format used for TTO and ATO, which includes the use of the Taxonomic Rank Vocabulary to tag taxa with specified rank. The version generated for the NESCent-sponsored Visual Systems Working Group is at ??.
