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cell component ontology

Peter Karp pkarp at AI.SRI.COM
Wed Nov 2 12:50:29 PST 2005

Larry, You make some perfectly reasonable points.  Our final
response will have to be to amend the CCO web pages to give
more elaborate answers to the questions you raise, and that will likely
take 1-2 weeks.  In the meantime, here are some shorter answers.
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

Larry.Hunter at wrote:
> Dear Peifen & CCO folks,
> Thanks for making public your Cell Component Ontology.  It's great to
> have people contributing their ontological work to the public!  I've
> also cc'd this message to the best email address I could find at new
> NCBO (see, which, moving forward, I think will
> probably be the best place to have these discussions.
> I do have a couple of concerns about the CCO that I'd like hear your
> responses to. 
> First, I agree with Anand's concerns (below) about the use of
> instances in the CCO ontology.  

I'll respond to these issues taking your next message into account,
in my next message.
> Second, I think that anyone proposing an ontology that overlaps with
> the domain of an existing OBO ontology (in this case, the cellular
> component branch of the GO) has an obligation to at least explain the
> relationships between the new ontology and the existing one.  Even
> better would be to provide the information necessary for a merge of
> the two.  It seems to me that many of the concepts in the CCO appear
> in the GO. I think you need to tell us which concepts are new, where
> there are conflicts, and how this ontology improves on the existing
> one.  One possibility, given the difference in size between the GO and
> the CCO, is that the CCO might be useful as a sort of "GO Slim" for
> cell components.  

OK, we will document these issues more in our web pages, but the CCOdocument
page does already address these in some detail.  Again, I wonder if
you saw it.  Our
web pages do already acknowledge GO and the fact that we have built on
many terms from GO.  Of the 149 classes+instances in CCO, 99 already have
links to GO.  Thus, CCO already tells you which of its terms correspond
to GO, and which are new (those that lack GO links).  Our main motivations
for creating CCO were that GO lacked many terms we need, GO lacks the
proper Is-A taxonomy structure for embedding and properly reasoning
with these terms (which of course I have been complaining about for
years -- will the GO developers ever properly implement Is-A?),
and GO lacks relationships that we needed for our
application, namely Component-Of and Surrounded-By.

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, or of any new bioinformatics database that overlaps
with any existing bioinformatics database.


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