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InterPro Ids in GOA association file? Is it needed?

Evelyn Camon camon at ebi.ac.uk
Tue Nov 29 03:09:12 PST 2005


 >> 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.

The possibility to do ...

PUBMED:9058808, for other IEA annotations InterPro:IPR000003
HAMAP:MF_00001, SPKW:KW-0016, EC:1.1.1.1 ??????

Evelyn




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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