Summer Curation Drive

August 24, 2009

On March 29, 2009, we initiated an ambitious goal (informally dubbed the ‘5K Karacters Kuration Goal’) to curate over 5,000 characters for 3,500 species from 50 papers by June 15. The reason for this annotation push was the planned beta release of the Phenoscape Knowledgebase at the Joint Meeting of Ichthyologists and Herpetologists (22-27 July 2009) in Portland, Oregon. We formed a curator team including Jeff Engeman, Terry Grande, Eric Hilton, John Lundberg, and Paula Mabee, and we each took on a significant chunk (either 500 or 1000 characters) of the ichthyological literature.   Read the rest of this entry »


Relations Ontology Workshop

June 10, 2008

Peter Midford and I recently attend the two-day Relations Ontology workshop in Denver, Colorado. The goal of the meeting was to further develop the Relations Ontology (RO) by moving relations from RO proposed (ontology for relations yet to be officially added to RO) to RO, and adding any new relations proposed by attendees. Impressively, almost all of the items on the original agenda were covered, and an ‘action list’ was produced to focus efforts subsequent to the meeting.

Phenoscape had several relations on the agenda, and Peter and I have summarized the discussion, definitions, and examples used.

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The Teleost Anatomy Ontology

May 22, 2008

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.

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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.


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.