Saturday, December 12, 2009

Another ontology project receives funding

The National Center for Research Resources has awarded (warning: PDF) $998,509 over two years to Northwestern University and the University of Maryland to develop the Disease Ontology. This funding is part of the American Recovery and Reinvestment Act. The principal investigators are Warren Kibbe, PhD of Northwestern University and Lynn Schriml, PhD, from the University of Maryland.

For more information on the Disease Ontology, see:

    Disease Ontology wiki
    Disease Ontology SourceForge site

The advisors to the project include key members and creators of the Open Biomedical Ontologies Foundry.

Saturday, July 25, 2009

ICBO Update

This week has been a busy one, with lots of events. I finished out the tutorials with a second day of events, powers, and dispositions, referent tracking, a WebProtege tutorial, and a discussion of outstanding issues with respect to Basic Formal Ontology, the Information Artifact Ontology, and the Infectious Disease Ontology.

The conference proper began yesterday. Highlights included a presentation by Stefan Schulz entitled "SNOMED CT's Ontological Commitment". It turns out that SNOMED CT is very unclear about its ontological commitment, which will hamper interoperability. Do so-called 'concepts' in SNOMED CT refer to entries in medical records, situations, or entities in reality?? One can find aspects of all three in SNOMED CT, and they're not clearly delineated and often mixed in the same hierarchy.

Another highlight yesterday was Werner Ceusters' presentation about the eyeGene research database. Again, the information model confuses entities in reality (the L1 Level of Reality), beliefs and hypotheses about L1 entities (the L2 Level of Reality), and information about L1 and L2 entities (the L3 Level of Reality). He recommends that the eyeGene database reform to make careful distinctions among them. And he believes it to be feasible.

A third highlight yesterday was Albert Goldfain's paper on the ontology of resistance, with special attention to methicillin-resistant Staphylococcus aureus (MRSa). He gave a detailed, precise, and high-fidelity representation of resistance.

Today's highlights included a presentation by Harold Solbrig, who gave an account of how he is trying to eliminate use of the word 'concept' in Biomedical Informatics and health care information technology. He nicely demonstrated how the word 'concept' leads otherwise reasonable people to cause all sorts of pathology in their representations (e.g., information models, data models, terminologies, etc). Although he has yet to convince people or the International Standards Organization (ISO) to eliminate the word altogether, by getting them to use 'ConceptDescription' in place of 'Concept', he has been able to limit the carnage.

Chris Mungall led off the day with an excellent paper "Cross-Product Extensions of the Gene Ontology". Because of combinatorial explosion, it is unwise to pre-coordinate every term that one might use from an ontology. However, by exploring the combinatorial space and isolating it from the core ontology, Mungall et al. were able to improve the quality of the core ontology as well as facilitate annotations with post-coordinated terms.

Melanie Courtot gave an excellent presentation (and got the biggest laugh of the day) on "MIREOT: The Minimum Information to Reference an External Ontology Term". Rather than duplicating terms from other ontologies, one wants to use terms from them when defining terms in one's own ontology. However, importing the entire ontology is impractical as they often are quite large. The MIREOT then, is the source ontology URI plus the source term URI plus the source term direct superclass URI. More software support is needed for this approach, but overall it is absolutely the right direction to go.

Later this evening, there is a poster session, dinner, and the plenary keynote. Tomorrow, more paper sessions and concluding remarks.

Monday, July 20, 2009

From the International Conference on Biomedical Ontology

I am attending the first International Conference on Biomedical Ontology (ICBO) at the University at Buffalo. Today was the first of four days of tutorials before the ICBO officially opens on Friday.

I am taking the "Ontology of Events, Dispositions, and Powers" tutorial, co-taught by Randall Dipert and Neil Williams. Dipert led off in the morning session with a discussion of events. Williams followed in the afternoon with dispositions.

It turns out that defining 'event' without the aid of the modal notions of necessity and possibility is difficult.

And that a proper analysis of dispositions that goes beyond subjunctive conditionals (which alone are insufficient to define dispositions) is nearly impossible without resorting to circularity.

Overall, two excellent sessions.

Sunday, July 5, 2009

Funding received for development of chemistry ontology (ChEBI)

The Biotechnology and Biological Sciences Research Council (BBSRC) of the United Kingdom has awarded a 3 year grant to develop the Chemical Entities of Biological Interest (ChEBI) ontology, and to reform its structure to use Basic Formal Ontology as its upper-level ontology, according to the blog of one of the researchers on the grant.

Christoph Steinbeck, at the European Bioinformatics Institute, on May 19th, wrote:

We received our official award letter from BBSRC Tools and Resources Fund today for the ChEBI ontology development grant. Needless to say, we are thrilled. We are now going to work together with Michael Ashburner’s group at the University of Cambridge to align ChEBI with other OBO Foundry ontologies by adoption of the Basic Formal Ontology and the Relationship Types Ontology.

Friday, February 6, 2009

European "SemanticHEALTH Report" calls for SNOMED CT reform

In a report (warning: pdf) for the European Commission's ICT for Health organization, the SemanticHEALTH project recommends:
Demonstration of a semantically sound and well quality assured reformulation of one or more suitable subsets of SNOMED CT, in order to provide evidence for long term decisions on the role of SNOMED CT in Europe.

The report criticizes SNOMED CT, saying:
For the time being we must therefore state that SNOMED CT is only fit for purpose as a controlled vocabulary and system of managed identifiers, but it can not yet safely be used as a source of semantics...

Per the International Health Terminology Standards Development Organization (IHTSDO), which owns and maintains SNOMED CT:
The focus is on enabling the implementation of semantically accurate health records that are interoperable.

If the report's criticism is true (and we believe it is), then SNOMED CT is not fit for its primary purpose.

Monday, January 26, 2009

Duke and SUNY at Buffalo get grant to build ontology

The National Institute for Allergy and Infectious Diseases (NIAID) has awarded Duke University a $1.25 million grant to develop the Infectious Disease Ontology (IDO). SUNY at Buffalo receives a $250,000 subcontract under the award.

The goal of the grant is to create an ontology of the bacterium Staphylococcus aureus, and its related genes, proteins, capsule, pathophysiology, and diseases. If researchers from multiple institutions all encode their data using IDO, then they can combine their data sets more easily to generate new scientific knowledge.

The grant represents something of a novelty for the National Institutes of Health (one of which is NIAID), because it issues few grants or requests for proposals with a focus of ontology development. Congratulations to the researchers involved, and we wish them success, as their success could determine whether the NIH funds similar work.