Epistemic formalism (was Re: [Phenoscape] Re: [go] evidence code ontology)

[Jim Hu]

Ben,

Did you read my real world example?  There _are_ situations where an  
assertion of NOT is useful.

Jim

On Feb 8, 2008, at 1:58 PM, Ben Hitz wrote:

>> I think Tanya really hits the nail on the head here. I don't think  
>> any of us exhaustively annotate NOT.
>
> That is what I was trying to get at in my earlier email.
>
>> If my memory serves me correctly the original discussion of NOT was  
>> for something like a peptidase that had great sequence similarity  
>> to other known peptidases, but was shown to lack a key residue and  
>> was therefore catalytically inactive.
>
> But even this case is wrong!  There are kinases (and probably  
> proteases as well) which are missing key catalytic residues that  
> _are_ active (they use a slightly different catalytic mechanism, or  
> have a slightly different fold)  And assertion of "inactivity" for  
> an enzyme is flawed becase you never test all possible conditions  
> and substrates.
>
> The converse isn't true of positive annotations - someone says in  
> their paper "I did Z and found that X did Y".   If X didn't do Y  
> then it's true that "I did Z and found that X didn't do Y" is a  
> valid piece of information... if the GO tracked Zs - but it doesn't.
>
> Scientists use the GO as a set of assertions:  The GO asserts that  
> (under some undefined conditions) that gene_product X does Y.  The  
> assertion that X doesn't do Y is much less useful when you don't  
> know what conditions it's under.
>
> Ben
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://fafner.stanford.edu/pipermail/go/attachments/20080208/d209737e/attachment.html