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Re: [ontolog-forum] Next steps in using ontologies as standards

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "John F. Sowa" <sowa@xxxxxxxxxxx>
Date: Tue, 13 Jan 2009 00:25:59 -0500
Message-id: <496C25E7.8010502@xxxxxxxxxxx>
Elisa,    (01)

Thanks for the info:    (02)

 > The closest thing I'm aware of is Stanford's BioPortal --
 > see http://bmir.stanford.edu/projects/view.php/ncbo .    (03)

That site leads to the Open Biomedical Ontologies (OBO) Foundry:    (04)

    http://obofoundry.org/    (05)

Following is an excerpt:    (06)

    The OBO Foundry is a collaborative experiment involving developers
    of science-based ontologies who are establishing a set of principles
    for ontology development with the goal of creating a suite of
    orthogonal interoperable reference ontologies in the biomedical
    domain. The groups developing ontologies who have expressed an
    interest in this goal are listed below, followed by other relevant
    efforts in this domain.    (07)

    In addition to a listing of OBO ontologies, this site also provides
    a statement of the OBO Foundry principles, discussion fora,
    technical infrastructure, and other services to facilitate ontology
    development.  We welcome feedback and encourage participation.    (08)

This site appears to be a good start.  But note that their ontologies
are all very specialized.  For example:    (09)

    Amphibian gross anatomy, Chemical entities of biological interest,
    Medaka fish anatomy and development, Mosquito insecticide resistance    (010)

This confirms the point that Doug Lenat has mentioned for years:
the most useful ontologies for applications are the low-level ones,
not the upper levels.    (011)

OBO also lacks an organization that relates the ontologies by
specialization and generalization.  For a Foundation Ontology,
it would be important to support a hierarchy of modules at all
levels.   The upper levels are valuable for stating common
generalizations among many lower-level theories.    (012)

So I would say that the OBO is a good beginning, which should be
considered and evaluated.  But more organization is needed to
relate the theories in a hierarchy.    (013)

John    (014)

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