Teleost Anatomy Ontology (TAO) working again on the NCBO Bioportal

May 18, 2008

Searching as well as visualizing the Teleost Anatomy Ontology (TAO) on the NCBO Bioportal was broken for more than a week but has been fixed since Friday.

The other good update from the Bioportal development is that terms can now be found by their synonyms as well. For example, try searching TAO for the ‘dermosphenotic’, which at present isn’t the name of a term in the ontology. Instead, you get the ‘infraorbital 5‘, for which dermosphenotic is a synonym.

Fish morphologists will note that this is actually problematic, since in reality the dermosphenotic is the synonym for the last infraorbital bone. In zebrafish, with which we seeded the TAO, this is indeed the 5th in the series of infraorbitals, but in other clades of teleosts it is the 6th or yet another one. But that’s another story, which we’ll highlight in a forthcoming post on building the TAO.

The Teleost Taxonomy Ontology

May 14, 2008

One of the two main ontologies developed and used by the Phenoscape project is the Teleost Taxonomy Ontology (TTO). Although the Phenoscape project is focused on the Ostariophysi, the TTO covers not just teleosts, but all the species listed in Bill Eschmeyer’s Catalog of Fish. This post will discuss how the current TTO was constructed and the work flow we use to update it. A later posting will discuss the effort to update the ontology to better represent current thinking about metaphysical status of species and other taxonomic terms.

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Teleost Anatomy and Taxonomy Ontologies on-line at the NCBO BioPortal

January 31, 2008

The Teleost Anatomy Ontology (TAO) and the Teleost Taxonomy Ontology (TTO) are finally on-line and searchable on the NCBO BioPortal.

The ontologies were deposited into the OBO versioning system already in November, but a database loading problem prevented their functioning in the BioPortal browser earlier.