[Go] advice changing IDs/the solution

Fri Aug 29 08:11:43 PDT 2008

If anybody needs to map UniProt identifiers which include obsoletes to 
current accession numbers in future, this is the solution:
Val

What you can do is use the batch retrieval on www.uniprot.org, which 
supports obsolete entry names:
Go to the "Retrieve" tab (http://www.uniprot.org/batch/) and enter or 
upload your list of identifiers, then click on "Retrieve".
You will get to a page offering several download formats, including full 
entries or list of primary accession numbers.
What this approach is not guaranteed to provide is a 1-to-1 
correspondence, in the case where your original list contains entry 
names that correspond to deleted, merged or demerged entries.

Valerie Wood wrote:
>
>
> 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.
>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>> <mailto:Go at geneontology.org>
>> http://fafner.stanford.edu/mailman/listinfo/go
>>> =====================================
>>>
>>> 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. 