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[go-friends] question regarding gene_association files

Rachael Huntley huntley at ebi.ac.uk
Tue May 21 04:39:36 PDT 2013


The species-specific files (including human) use accessions from the 
UniProt complete proteomes sets 
(http://www.uniprot.org/keywords/KW-0181); this includes both reviewed 
(Swiss-Prot) and unreviewed (TrEMBL) accessions, so there will be a 
certain amount of overlap between the TrEMBL accessions and Swiss-Prot 
entries or spliceforms of the Swiss-Prot entries.

We are planning to release a new set of species-specific files that are 
based on one protein per gene, which should hopefully relieve some of 
the confusion.

Rachael.

On 20/05/2013 19:57, Judith Blake wrote:
> I think that is the plan.  Otherwise leads to redundancies in many 
> ways that are unwelcome in many ways.
>
> judy
>
> From: Rama Balakrishnan <ramab at stanford.edu <mailto:ramab at stanford.edu>>
> Date: Monday, May 20, 2013 2:49 PM
> To: Rachael Huntley <huntley at ebi.ac.uk <mailto:huntley at ebi.ac.uk>>
> Cc: "go-friends at mailman.stanford.edu 
> <mailto:go-friends at mailman.stanford.edu>" 
> <go-friends at mailman.stanford.edu <mailto:go-friends at mailman.stanford.edu>>
> Subject: Re: [go-friends] question regarding gene_association files
>
> The IDs listed here seem like the UnReviewed Tremble IDs. Are all 
> annotations to unreviewed IDs filtered out in the goa-human file?
>
> Rama
>
> On May 20, 2013, at 1:08 AM, Rachael Huntley wrote:
>
>> Hi Iddo,
>>
>> The UniProt file contains annotations for all proteins that have GO 
>> annotations in UniProtKB.
>> The human file is a subset of these annotations based on the UniProt 
>> complete proteome for human and so has annotations to a reduced set 
>> of accessions. It is also filtered for redundant annotations.
>>
>> Let me know if you have further questions.
>>
>> Rachael.
>>
>>
>> On 17/05/2013 20:33, Iddo Friedberg wrote:
>>>
>>> I am looking at two files: Hi,
>>>
>>> I am looking at two files: gene_association.goa_uniprot and 
>>> gene_assocaition.goa_human
>>>
>>> Apparently, there are some proteins in gene_association.goa_uniprot 
>>> that are designated as human by the Taxon_ID field, yet do not 
>>> appear in the goa_human file.
>>>
>>> Can someone tell me why that is? Here are some examples:
>>>
>>> A0A2G2
>>> A0A2G3
>>>  A0A2G4
>>>  A0A2G5
>>>  A0A2G6
>>>  A0A2G8
>>>  A0A2G9
>>>  A0A4R5
>>>  A0A4Z1
>>>  A0A502
>>> A0A2G2
>>>
>>> Thanks,
>>>
>>> Iddo
>>>
>>> -- 
>>> Iddo Friedberg
>>> http://iddo-friedberg.net/contact.html
>>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>> >>----.<--.>++++++.<<<<------------------------------------.
>>>
>>>
>>> _______________________________________________
>>> go-friends mailing list
>>> go-friends at lists.stanford.eduhttps://mailman.stanford.edu/mailman/listinfo/go-friends
>>
>>
>> -- 
>> Project Leader
>> UniProt - Gene Ontology Annotation Project
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge, CB10 1SD
>> UK
>>
>> Email:huntley at ebi.ac.uk
>> UniProt Gene Ontology Annotation Project:http://www.ebi.ac.uk/GOAhttp://twitter.com/emblebi
>> _______________________________________________
>> go-friends mailing list
>> go-friends at lists.stanford.edu <mailto:go-friends at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/go-friends
>
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-- 
Project Leader
UniProt - Gene Ontology Annotation Project
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK

Email: huntley at ebi.ac.uk
UniProt Gene Ontology Annotation Project: http://www.ebi.ac.uk/GOA
http://twitter.com/emblebi

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