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cell component ontology

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Wed Nov 2 16:24:14 PST 2005


Peter and friends,

I just want at this stage to comment on one statement from Peter:
"Our main motivations
for creating CCO were that GO lacked many terms we need .."

Many databases use GO and they often come across terms that are absent from the GO
but needed. We have a rigorous mechanism for allowing anyone to request new terms,
via our Sourceforge site, and that is used very extensively. I would not like the
absence of a term ... or of a number of terms ... to be used as a reason for not
using the GO ! We have always been very responsive to requests for terms or large
subtrees within the GO (witness our collaboration with the PAMGO folks).

In principle GO also always has an is_a path to the root. I would admit that I am not
sure that this has been completely fitted yet, but it is certainly what we want to have.

The new relationships in CCO are interesting, and I see no reason in principle why
they could not be incorporated in the GO.

My concern, shared by Larry, is that one of the strengths of the use of GO by databases
is that we achieve - in this domain - a de facto integration of these databases. Users
can now query well over 20 very different databases for gene products annotated with GO
terms. if the ontologies fork that will no longer be true. Had the MetaCyc databases
used the GO then they could have submitted a MetaCyc gene_association table to the GO
database and be included within this integrated set (within the domains of knowledge
covered by the GO).

Michael

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