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InterPro Ids in GOA association file? Is it needed?

Suzanna Lewis suzi at fruitfly.org
Mon Nov 28 17:19:00 PST 2005


Sorry Harold, I don't understand what you are saying.

Are you saying that all of the dbxrefs in column 8 (the with column) 
must _all_ be of the same kind in any given associations file? That 
cant' be right.

Column 8 effectively does use dbxrefs now, as does the reference 
column, and it's fine if both columns are dbxrefs, but they do mean 
different things. Column 8 is an xref to the thing from which the 
inference was drawn. The other column is the xref to the citation for 
who/what drew this inference.

I don't see where the problem is.

-S

On Nov 28, 2005, at 1:49 PM, Harold Drabkin wrote:

> Yes, we did do this when th Fantom data was ISS; however, now they are 
> RC/IEA, and in our "WITH-FIELD" study group, there seems to be 
> conrtention abut what can go in the with field if IEA;
> Midori, correct me if I got this wrong, but basically, IF you use a 
> specific kind of DBX ref in the with field (say, an interpro ID), then 
> you must only use an interpro ID and not anything else (for example, a 
> UniProt ID or EC number; both are valid dbxrefs also). However, I 
> think this is like using either EMBL:, UniProt:, or protein_id: in the 
> column for ISS, etc. (yes all are seqids, but some are nucleic acids 
> and some are proteins).
>
> I would like to dbxrefs in the with column for IEA myself.
>
> Harold
>
> Suzanna Lewis wrote:
>
>> Exactly. I also think these belong in column 8.
>>
>> On Nov 28, 2005, at 11:46 AM, David Hill wrote:
>>
>>> 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
>>>>>
>>>>>
>>>>> -- 
>>>>> This message is from the GOFriends moderated mailing list.  A list 
>>>>> of public
>>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>>> Problems with the list?           E-mail: 
>>>>> owner-gofriends at geneontology.org
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>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> This message is from the GOFriends moderated mailing list.  A list 
>>>> of public
>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>> Problems with the list?           E-mail: 
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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
>>>
>>
>>
>> -- 
>> This message is from the GOFriends moderated mailing list.  A list of 
>> public
>> announcements and discussion of the Gene Ontology (GO) project.
>> Problems with the list?           E-mail: 
>> owner-gofriends at geneontology.org
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>> gofriends-request at geneontology.org
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>
>


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