ICBO Summary

While the rest of Phenoscape was at ASIH running the ontology workshop and announcing the database and website release, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies in Buffalo, NY.
ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions.  There were
also software demos during the lunch breaks, and two panel discussions.
Although there were several sessions devoted to ontologies of disease and clinical practice, there
were a number of talks of interest to Phenoscapers.  Among these were several alignment talks, including
one from the BGEE group on Homonto and Chris Mungall’s on cross products and Uberon.  There were also sessions
on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation.
There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating
existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological
modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of
physiology, cognition, and NLP.
There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology
and a ‘behavior lunch’ on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.
There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list ().
There was also a lot of discussion generated by the proposed ontology of homology relations (the 1.0 version; 1.1 released recently(http://bgee.unil.ch/bgee/download/homology_ontology_v1.1.obo)), although the consensus from the numerous people I discussed
it with was that it needed more work (which is happening).
Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in
contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.
There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included
a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons suggested a discussion
on open publishing, the Elsevier representation was quiet restrained, and it was Larry Hunter who made the strongest argument that publishers currently
provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on an infectous disease.
The second panel was on the Future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion
were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologies
will be as common in biology and medical departements as statisticians are today.
The text from all the presentations and posters will be made available at Nature Proceedings (http://precedings.nature.com/collections/icbo-2009).  There was
also an ICBO group on FriendFeed (http://friendfeed.com/icbo) with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will
be posted a more detailed report on my personal blog (http://ontethology.blogspot.com).

While the rest of Phenoscape was at the ASIH meeting, involved with the ontology workshop and the release of the database and website, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies (ICBO) in Buffalo, NY.  ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions. There were also software demos during the lunch breaks, and two panel discussions.

Although many of the sessions were devoted to ontologies of disease and clinical practice, there were a number of talks of interest to Phenoscapers. Among these were several alignment talks, including one from the BGEE group on Homolonto and Chris Mungall’s on GO cross products and Uberon.  There were also sessions on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation. There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of physiology, cognition, and NLP.

There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology and a “behavior lunch” on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.  There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list.

There was also a lot of discussion generated by the proposed ontology of homology relations, although the consensus from the numerous people I discussed it with was that it needed more work.

Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.

There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons, suggested a discussion on open publishing, the Elsevier representation was quite restrained, and it was Larry Hunter who made the strongest argument that publishers currently provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on a tropical disease, and there seemed to be consensus that semantic markup ought to be either the author’s or the publisher’s responsibility, rather than the current post-publication markup by project curators.

The second panel was on the future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologists will be as common in biology and medical departments as statisticians are today.

The text from all the presentations and posters will be made available at Nature Proceedings.  There was also an ICBO group on FriendFeed with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will be posting a more detailed report on my personal blog.

2 Responses to ICBO Summary

  1. Julien Roux says:

    Thank you for your kind remarks. For your information, the latest version of our ontology of homology relations will always be downloadable at http://bgee.unil.ch/download/homology_ontology.obo
    Best,
    Julien

  2. pmidford says:

    Thanks Julien – I’ve updated the link in the post.

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