[Annotation] filtering IEA translations?

[Harold Drabkin]

We get our IEAs based on ip2go from domains contained in SwissProt 
records. However, we make sure we only use the curated records and not 
Trembl records. These appear to often contain domains that are kind of 
weird. For example, there is an S6 kinase domain that often appears, and 
then this results in getting ip2GO for ribosome, etc. for proteins that 
aren't ribosomal.
How are you getting the domain assignments?

Harold

Doug wrote:
> 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 When we originally made 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
>
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