[Annotation] filtering IEA translations?

[Doug]

I vaguely recall that interpro can mark domains as false positive  
hits.  The problem with that system is that I believe the domain hit  
remains but only interpro knows it is marked as a false positive...ie  
we don't get that false positive information when we sync our data  
with UniProt (our source for protein domains).  Perhaps I am mistaken  
there though?

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 2:32 PM, David Hill wrote:

> 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 When we originally made  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