Evolutionary Biology & Ontologies Workshop report

July 11, 2008

Our first educational and outreach event “Evolutionary Biology & Ontologies Workshop” was held at the Evolution meetings in Minneapolis, Minnesota (June 20, 2008), and we felt it was a big success.  We had lots of enthusiasm and over 50 attendees for this all day workshop, which was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). 

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine). 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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Taxonomy as ontology: opening up the debate

May 15, 2008

We 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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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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Poster at the Evolution Meetings

April 30, 2008

Aside from the Evolutionary Biology and Ontologies Workshop that we organize together with the NCBO at the Evolution Meeting 2008 in Minneapolis, we will also be presenting a poster. For your advance pleasure, here is the abstract that we wrote, only to realize that registration for a poster presentation actually did not require or even offer any abstract submission.

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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.