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cell component ontology

Larry.Hunter at Larry.Hunter at
Wed Nov 2 16:40:38 PST 2005

 > I wonder though if you saw the web page under the "[more]" link
 > toward the top of the CCO page -- the page I am referring to is


You're right, I had overlooked that.  Thanks for pointing it out.  In
your revisions to the site, you might consider a more perspicuous name
for that link... :-)

 > creating CCO were that GO lacked many terms we need, GO lacks the
 > proper Is-A taxonomy structure ...  GO lacks relationships that we
 > needed for our application, namely Component-Of and Surrounded-By.

I understand these differences in general, and the web page that I
missed provides more of the necessary information.  Anything you (as
an author of an ontology that overlaps an existing one) can do to
facilitate ontology merging is, of course, extremely important. 

 > Please though, let's not treat OBO as if it had some special
 > status.  Your same point is true of any new ontology that overlaps
 > with any existing ontology

Although my point holds for any new ontology in a domain where there
is an existing one, I do think OBO does have a special status.  OBO
ontologies (well, some of them, particularly the GO) have been used by
many investigators for diverse purposes, and have been subject to
extensive public comment.  That makes them worthy of particularly
careful comparison relative to a proposed overlapping ontology.

By the way, I feel I ought to mention that I particularly value the
"surrounded-by" relationship that CCO adds to link existing GO terms.
Mike Bada in my lab is similarly working on enriching GO terms; see
also a related paper by Johnson, et al, in the upcoming PSB.

I also hope that a dialog around the proper use of is-a and
component-of / part-of relationships leads us to a better
representation than the current GO, although I don't think it's an
easy thing to define the "right thing" (pace Barry Smith, e.g. in
Genome Biol. 2005;6(5):R46.)


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