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cell component ontology

Peifen Zhang peifenz at acoma.Stanford.EDU
Tue Nov 1 11:34:16 PST 2005


Dear Anand,

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.


Best Regards,

Peifen


On Mon, 31 Oct 2005, Anand Kumar wrote:

> Dear Peifen,
>
> 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.
>
> Kind Regards,
> Anand.
>
>

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