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

[Jim Hu]

On Feb 8, 2008, at 4:21 PM, Benjamin Hitz wrote:

>> Or in a real case that I think we'll be annotating at some point.   
>> Publication A claims that Protein X is a nuclease and this IDA  
>> annotation is used to transfer the GO association via ISS to other  
>> genomes.  A later publication, B, shows that X is not a nuclease;  
>> the authors of B have purified X more than the authors of A, and  
>> show that the nuclease activity is a contaminant.  In this kind of  
>> instance, I think it is not enough to drop annotations from A from  
>> the list of annotations made, because the annotation creep is  
>> likely to continue.  I think that the MOD wants to make a proactive  
>> assertion of NOT as a cry of "Please correct those ISS  
>> annotations".  In the absence of a NOT, the absence of a nuclease  
>> annotation might be misinterpreted as the MOD hasn't got to that  
>> paper yet.
>
> In this case - what you really want is for Publication A to be  
> retracted and the original annotation deleted.    There is no way,  
> under the current system,  to tell a priori which NOTs are  
> "retractions" and which are simply altered experimental conditions.

The data were correct for the original samples in Publication A as  
measured at the time. I don't think that's the kind of thing that ever  
gets retracted.

>
> I do agree that NOT annotations or something like them can be useful  
> - particularly at the curation level - but they are so RARELY useful  
> and so OFTEN misinterpreted that think they should be hidden away in  
> a dark and dingy corner of a database.

Since they are used so rarely, I'm not seeing where this dreaded  
misinterpretation is a problem.  Especially if NOT usage is restricted  
as much as possible to the cases where it would be useful.  I think  
that the hiding it away argument is worse than either discarding it  
altogether or showing it when it's there. YMMV, clearly.

Jim

>
> 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


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