The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for teleost fishes. In this first post about the TAO, I’ll introduce the structure of the ontology and its development, and discuss some of the challenges we’ve come across in building a multi-species ontology. You can browse the TAO by using the NCBO BioPortal.
The Teleost Anatomy Ontology
May 22, 2008
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Anatomy Ontology, Morphology, Ontology, Relations | Tagged: Anatomy Ontology, Ontology | 
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Posted by wdahdul
Teleost Anatomy Ontology (TAO) working again on the NCBO Bioportal
May 18, 2008Searching 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.
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Anatomy Ontology, Teleosts | Tagged: NCBO | 
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Posted by Hilmar
Taxonomy as ontology: opening up the debate
May 15, 2008We have created a new mailing list, obo-taxonomy, under the OBO (Open Biomedical Ontologies) umbrella. Our motivation for this new forum is to really open up the discussion surrounding the issues of what should be a proper ontological representation of taxonomy and phylogeny, for example proper semantics of the relationship between taxonomic groups, and between specimens and species. If you care about or have thoughts or opinions on these and related questions, we encourage you to subscribe to this new list.
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Development, Ontology, Taxonomy Ontology | Tagged: community, mailing list | 
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Posted by Hilmar
The Teleost Taxonomy Ontology
May 14, 2008One 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.
2 Comments | Ontology, Taxonomy Ontology, Teleosts | Tagged: NCBO, taxonomy | Permalink
Posted by pmidford
