Search Mailing List Archives
[go-friends] question regarding gene_association files
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
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.
> 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?
> 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.
>> 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
>>> 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:
>>> Iddo Friedberg
>>> 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
>> Cambridge, CB10 1SD
>> 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>
> The information in this email, including attachments, may be
> confidential and is intended solely for the addressee(s). If you
> believe you received this email by mistake, please notify the sender
> by return email as soon as possible.
UniProt - Gene Ontology Annotation Project
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge, CB10 1SD
Email: huntley at ebi.ac.uk
UniProt Gene Ontology Annotation Project: http://www.ebi.ac.uk/GOA
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the go-friends