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cell component ontology

Larry.Hunter at Larry.Hunter at
Wed Nov 2 08:55:15 PST 2005

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 believe the standard practice for
shared ontologies is to model all objects as types (classes), and
reserve instances for users who want to represent specific tokens
(e.g. the nucleus of this particular cell).  In fact, I'm not quite
sure I understand your explanation below -- how would I express
something like "The nuclei of hepatocytes can vary in size" if nuclei
are instances in the ontology itself?

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.  


Peifen Zhang writes:

 > In CCO, we treat ER as a class since it refers to the generalization
 > of the two subtypes of ER, smooth and rough. Nucleus and 
 > similarly other organelles are consistently described as
 > instances throughout our ontology, because they refer to the actual
 > organelles of the organism being modeled in a given database.

 > Anand Kumar wrote:
 > > I am not sure which mailing list this should go to. However, you have the
 > > following relation in the new ontology.
 > >
 > > Superclasses: organelle
 > > Subclasses: vacuole, microbody, endoplasmic reticulum, endosome, vesicle,
 > > plastid
 > >
 > > Instances: thylakoid (sensu Cyanobacteria), nucleus, mitochondrion, 
 > > lysosome,
 > > Golgi apparatus
 > >
 > > GO does not have instances but atleast it does not do the mistake of 
 > > putting
 > > together "nucleus", which is a class, as an instance, which is "this 
 > > nucleus",
 > > "nuclues of that bacterium in that petri dish".
 > >
 > > Why would you treat nucleus as instance and endoplasmic reticulum as a 
 > > class? GO
 > > has problems but atleast not of those sorts.

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