Dear list,

I would like to retrieve for a list of uniprot_swissprot_accession IDs info such as Gene Symbol, Entrezgene ID, etc. I was thinking of using biomaRt for this, but I found out that biomaRt is not able to retrieve info for aprox. 50% of my input IDs. Of course I manually checked on-line whether these IDs still exist in SwissProt, and this is the case.

An example:
Input:
Name
O08523
O08524
O08526
O08528
O08529
O08530

biomaRt output:
uniprot_swissprot_accession	uniprot_swissprot	entrezgene	ensembl_transcript_id
O08523	TECTA_MOUSE	21683	ENSMUST00000042190
O08524	TECTB_MOUSE	21684	ENSMUST00000025936
O08528	HXK2_MOUSE	15277	ENSMUST00000000642
O08529	CAN2_MOUSE	12334	ENSMUST00000068505
O08530	EDG1_MOUSE	13609	ENSMUST00000055676

As can be observed, biomaRt is not able to retrieve info for the (missing) swissprot accession o08526. Manually checking swisprott gives (e.g.) gene name Vav-T (http://www.expasy.org/uniprot/O08526). In other words, o08526 is a valid accession entry.

Any advice on how to retrieve as much info as possible on swissprot accession entries is much appreciated.

Guido

 
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands

tel: (+)31 317 485788
fax: (+)31 317 483342

internet:   http://nutrigene.4t.com
email:      guido.hooiveld@wur.nl


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