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

[Benjamin Hitz]

> 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.

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.

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu



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