[Go] advice changing IDs

[Varsha Khodiyar]

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
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with number 1021457 and a
>     company registered in England with number
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>     registered office is 215 Euston Road,
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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



-- 
 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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