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[Go-database] terms to which a gene is not annotated

Chris Mungall cjm at fruitfly.org
Mon Sep 27 11:05:06 PDT 2004



On Mon, 27 Sep 2004, Steve Carroll wrote:

> Hello,
>
> I am a graduate student doing a project that involves the GO, and I have
> what may be a naive question:  for a given gene, there is a list of terms
> to which that gene is annotated, so with some confidence we can say that
> gene belongs to those classes (and their ancestors in the GO).  But can we
> also say that the gene in question does NOT belong to the classes defined
> by the terms to which it is not annotated?  Or is it better to treat
> membership in those classes as unknowns?  Does the answer to this question
> depend on the gene or the actual terms to which it is annotated?  For
> example, does annotation to some term preclude the possibility of
> annotation to some other term?

Hi Steve

In general, the possibility of annotation to another class is never
precluded by annotation to a different class

Even when we consider two classes that are disjoint - for example, the
nucleus does not border or overlap the extracellular space - it is still
possible for a gene product to be active in the nucleus in one context and
for the same gene product to be active in the extracellular space in some
other context. Gene products frequently have multiple roles.

The only time we can say with confidence that a gene product is not
associated with a class (or the *descendants* of that class) is when a
curator specifically makes a negative association, based on experimental
evidence and expert judgement. See the association format docs, or the go
database docs if you wish to query based on these.

Cheers
Chris

> In case it is of any relevance, I am using the SGD database for my
> application.
> I am not subscribed to these lists, so please respond directly to me.
> Thankyou in advance for any help.
>
> Sincerely,
>
> Steve Carroll
> M.S. Student
> Computer Science
> Rutgers University
>
> _______________________________________________
> Go-database mailing list
> Go-database at mail.fruitfly.org
> http://mail.fruitfly.org/mailman/listinfo/go-database
>

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