[Go] advice changing IDs
Valerie Wood
val at sanger.ac.uk
Fri Aug 29 02:55:11 PDT 2008
So far I have tried all of the suggestions:
http://www.uniprot.org/?tab=mapping
http://pir.georgetown.edu/pirwww/search/idmapping.shtml
http://www.ebi.ac.uk/Tools/picr/
and
http://david.abcc.ncifcrf.gov/conversion.jsp
all of these tools will only map a variable proportion of the IDs (max
75%), because the 'obsoleted' IDs are not mapped.
I have mailed the EBI helpdesk to see if they can help. Authors
frequently use Uniprot IDs instead of accession numbers in papers so it
would be useful to know how to access the 'dead' ones. If I find a
webserver which does this I will let you know.
Thanks for all your responses
Val
Varsha Khodiyar wrote:
> Hi Val,
>
> Have you tried the ID conversion tool at DAVID?
>
> http://david.abcc.ncifcrf.gov/conversion.jsp
>
> Regards,
> Varsha
>
> -----Original Message-----
> From: go-bounces at genome.stanford.edu
> [mailto:go-bounces at genome.stanford.edu] On Behalf
> Of Valerie Wood
> Sent: Thursday, August 28, 2008 10:01 AM
> To: Anand Venkatraman
> Cc: GO mailing list
> Subject: Re: [Go] advice changing IDs
>
>
>
> I tried this,and it is almost what I want.
>
> However, out of the 1137 Uniprot identifiers it
> only maps 711 of them to SGD:S0 IDs. This is
> possibly because this is a dataset from a paper
> which is a few years old, and some of the IDs may
> have been obsoleted.
> If this is the case I have no idea how I can get
> these.
>
> Also, ideally I want to get to the S. cerevisiae
> systematic ids (i.e YOR123C etc). But I can get to
> these fairly easily if I can get all of the SGD:S0
> IDs.
>
> Does anyone have any suggestions for this (sorry
> for this abuse of the mailing list to take
> advantage of you collective expertise). If nobody
> has any other suggestions I guess I can ask on go
> friends.
>
> Thanks
>
> Val
>
>
>
>
>
>
>
> Anand Venkatraman wrote:
>
>> Hi Jim and Val,
>>
>> For 2AAA_YEAST, I presume you want it mapped to
>>
> something like
>
>> S000000014
>> Have a look at
>>
> http://www.uniprot.org/uniprot/P31383.txt and
> search
>
>> for SGD.
>>
>> As far as I know, as long as it is in the
>>
> UniProt record, a bioperl
>
>> script can do it either querying UniProt one at
>>
> a time or if there are
>
>> far too many records, then downloading the
>>
> yeast UniProt flatfile and
>
>> writing a script to query that would be the
>>
> better option.
>
>> If a web interface querying is preferred, then
>>
> UniProt has this
>
>> mapping tool (limited to 1000 queries at one
>>
> time)
>
>> http://www.uniprot.org/?tab=mapping
>>
>> Hope it helps. Let me know if you have any
>>
> questions.
>
>> Thanks,
>>
>> Anand
>>
>> ----- Original Message -----
>> From: "Jim Hu" <jimhu at tamu.edu>
>> To: "Anand Venkatraman" <anandv at neo.tamu.edu>
>> Sent: Wednesday, August 27, 2008 10:25:20 AM GMT
>>
> -06:00 US/Canada
>
>> Central
>> Subject: Fwd: [Go] advice changing IDs
>>
>> Can we help with this?
>>
>> Jim
>>
>> Begin forwarded message:
>>
>> *From: *Valerie Wood <val at sanger.ac.uk
>>
> <mailto:val at sanger.ac.uk>>
>
>> *Date: *August 27, 2008 9:56:53 AM CDT
>> *To: *GO mailing list
>>
> <go at genome.stanford.edu
>
>> <mailto:go at genome.stanford.edu>>
>> *Subject: **[Go] advice changing IDs*
>>
>>
>>
>> I wondered if anyone can remind me of one
>>
> the tools which will
>
>> convert between identifiers.
>>
>> Specifically I have a gene list of
>>
> cerevisiae genes which is in
>
>> Uniprot identifier format
>> i.e 2AAA_YEAST NOT accession number, and I
>>
> want to convert to SGD
>
>> systematic identifier.
>>
>> Thanks if you can help, I haven't used one
>>
> before and I have no
>
>> idea what to search for.
>>
>> Val
>>
>> --
>>
>>
> --------------------------------------------------
> -------------------------
>
>> Valerie Wood Tel: 01223 496909
>> S. pombe Genome Project Fax: 01223 494919
>>
> Wellcome Trust
>
>> Sanger Institute email: val at sanger.ac.uk
>>
> <mailto:val at sanger.ac.uk>
>
>> Wellcome Trust Genome Campus
>>
> http://www.genedb.org/genedb/pombe
>
>> Hinxton, Cambridge, CB10 1HH
>> http://www.sanger.ac.uk/Projects/S_pombe
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is
>>
> operated by Genome Research
>
>> Limited, a charity registered in England
>>
> with number 1021457 and a
>
>> company registered in England with number
>>
> 2742969, whose
>
>> registered office is 215 Euston Road,
>>
> London, NW1 2BE.
>
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>
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>>
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>
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>> =====================================
>>
>> Jim Hu
>>
>> Associate Professor
>>
>> Dept. of Biochemistry and Biophysics
>>
>> 2128 TAMU
>>
>> Texas A&M Univ.
>>
>> College Station, TX 77843-2128
>>
>> 979-862-4054
>>
>>
>>
>>
>
>
> --
> --------------------------------------------------
> -------------------------
> Valerie Wood Tel: 01223 496909
> S. pombe Genome Project Fax: 01223 494919
>
> Wellcome Trust Sanger Institute email:
> val at sanger.ac.uk
> Wellcome Trust Genome Campus
> http://www.genedb.org/genedb/pombe
> Hinxton, Cambridge, CB10 1HH
> http://www.sanger.ac.uk/Projects/S_pombe
>
>
>
>
--
---------------------------------------------------------------------------
Valerie Wood Tel: 01223 496909
S. pombe Genome Project Fax: 01223 494919
Wellcome Trust Sanger Institute email: val at sanger.ac.uk
Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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