[Annotation] filtering IEA translations?

[David Hill]

I think if the problem is with the mis-assignment of the domain, then 
the translation should be kept and the interpro domain assignment should 
be corrected.



Doug wrote:
> So in my example, I would speculate wildly that the zebrafish gene 
> does in fact have a domain that looks very much like something that 
> would cause beta-catenin binding, but is perhaps different enough as 
> to not promote such binding...so the translation should be stricken 
> from the translation file until the domain model itself can be 
> improved so it can distinguish between domains that do and don't bind 
> beta-catenin?
>
>
> Doug Howe, Ph.D.
> Scientific Curator
> Zebrafish Nomenclature Coordinator
> Zebrafish Information Network
> 541-346-0120
> dhowe at cs.uoregon.edu
>
>
>
> On Mar 12, 2009, at 12:41 PM, David Hill wrote:
>
>> I think we should remove the translation. When we originally made 
>> these translation table, we used the very conservative rule that if 
>> we could find an exception to the translation being correct, we would 
>> remove it. Otherwise, erroneous data may be generated for organisms 
>> that don't have experimental support.
>>
>> David
>>
>> Doug wrote:
>>> For groups that apply interpro2go, spkw2go, or ec2go translation files:
>>>
>>> If a translation from interpro2go for example takes you to a GO term 
>>> which is directly contradictory to an experimentally supported 
>>> annotation in your database, do you apply the IEA annotation or do 
>>> you filter it out?
>>>
>>> Example:
>>>    We have an IPI annotation to NOT beta-catenin binding and an IEA 
>>> annotation (translation of InterPro:IPR009428) to 'beta-catenin 
>>> binding' on our lzic gene.  Should such an IEA annotation be made 
>>> when it conflicts with experimental annotations?
>>>
>>> I see no problem as long as the evidence code is taken into 
>>> account...what do others think?
>>>
>>> -Doug
>>>
>>> Doug Howe, Ph.D.
>>> Scientific Curator
>>> Zebrafish Nomenclature Coordinator
>>> Zebrafish Information Network
>>> 541-346-0120
>>> dhowe at cs.uoregon.edu
>>>
>>>
>>>
>>> _______________________________________________
>>> Annotation mailing list
>>> Annotation at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>> -- 
>> David P. Hill, Ph.D.
>> Bioinformatics Scientist: Ontology Development
>> Gene Ontology Consortium
>> The Jackson Laboratory
>> www.geneontology.org
>> www.informatics.jax.org
>> tel:207-288-6430
>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430