[MOBY-l] An Ontology question

[Frank Gibbons]

Hi Ben,

I've been thinking about ways to extend the object (and service) ontology. 
In fact, as part of the BioGraphNet project for exchanging protein/genetic 
interaction networks (http://biographnet.sourceforge.net), Gabriel Berriz 
and I have added an 'interaction_partner' object, and then extended it with 
terms from the Proteomics Standards Initiative - Molecular Interaction 
(PSI-MI) controlled vocabulary for interaction_detection, at least to the 
first two levels.  Since this is development work so far, most of these 
changes have been made in the test Registry that Mark put up a few weeks 
ago, not in the 'real' registry.

So far, we've done this by hand, but clearly it would make much more sense 
to either automate it, or better yet, find a way to link from MOBY's object 
registry to a URI of PSI-MI's. Unfortunately, being an RDF newbie, I'm not 
really sure of the best way to do this, or even if it's possible. I know 
that Mark W. is meeting with the myGRID folks this summer, to discuss ways 
to re-use their massive ontology, so that may obviate any other plans.

It strikes me that it might not be desirable to include any ontology in all 
of its gory detail, at least in the absence of appropriate tools to 
navigate and visualise MOBY's ontologies. Martin Senger has written some 
really useful tools for that, but they generate static images rather than 
interactive ones, so once below the spatial resolution of your 
printer/screen, it's not possible to read it, and it's close to that right now.

Just a brain dump. What are you thinking?

-Frank

At 04:46 PM 7/22/2004, Benjamin Good wrote:
>Hello Moby,
>
>It seems that the moby system would benefit from a semantically richer 
>object ontology.  Has anyone thought about ways to leverage existing 
>ontologies (such as GO) for this purpose?
>
>curious to hear your thoughts
>-Ben
>
>
>
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PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
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