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InterPro Ids in GOA association file? Is it needed?

David Hill dph at informatics.jax.org
Mon Nov 28 11:46:32 PST 2005


Suzi and Evelyn,

I also don't see why this can't just go in column 8 since the interpro 
ID would be a valid dbxref. This is what we did with the original fantom 
data.

David

Suzanna Lewis wrote:

>
> On Nov 28, 2005, at 6:26 AM, Evelyn Camon wrote:
>
>> Dear GO friends,
>>
>> We have been discussing here at EBI whether we should include the 
>> InterProID in our association files so that users of this file could 
>> quickly deduce the exact InterProID source of the annotation.
>>
>> At the moment we use GOA:interPro in the 6th column of the 
>> association file called DB:Reference. We also add to this column for 
>> manual annotation PUBMED:9058808, for other IEA annotations 
>> GOA:hamap, GOA:spkw, GOA:spec.
>
>
> If you are now doing this already what is the new thing you are 
> proposing?
>
> Since Interpro matches are how you are determining the GO assignment I 
> wonder why you aren't using the with column (column 8) for the 
> interpro ID?
>
>>
>> I understand that adding this information would expand the size of 
>> the association file we produce and slow down our release procedure. 
>> We are wondering whether this would be a hinderance and if indeed it 
>> is widely useful or not. Do most people prefer to apply the 
>> InterPro2go mapping to there datasets or are they using other 
>> computing means to link
>> UniProt AC->InterProID->GO:ID. If they were having difficulty with 
>> the latter we could produce UniProt AC->InterProID->GO:ID as an extra 
>> file perhaps.
>
>
> please do not create an extra file.
>
>>
>> We would very much like to know how this would affect GO Tools and GO
>> Consortium members that download our data and if it would be useful 
>> or not. Please feedback to us anything that you would consider an 
>> approvement to our services.
>>
>> kind regards
>> Evelyn Camon
>> GOA-Coordinator
>>
>>
>> -- 
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>
>
>
> -- 
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> public
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-- 
David P. Hill, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
Gene Ontology Consortium
Gene Expression Database
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
tel:207-288-6430
htpp://www.informatics.jax.org


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