[ensembl-dev] Uniprot IDs

[Robinson, Peter]

Hi,

I am new to Ensembl API and might be missing something obvious, but I would like to get a list of Uniprot IDs for all proteins in the mouse with the corresponding Ensembl IDs (gene, protein, transcript). I have had a look at biomart on the main Ensembl website but there does not seem to exist complete mapping information. For instance


 Iglv3 ENSMUSG00000076939

does not have a links to uniprot in Biomart but

 Iglv2 ENSMUSG00000076940

does have a link to P01728 (LV2A_MOUSE)

However, there is a Uniprot (Trembl) entry for Iglv1 => A2NVW3 (A2NVW3_MOUSE).


Does this mean that the mapping simply has not been done (I realize how much work this all is!), or is there some way to actually get the corresponding mapping using some tool of Ensembl API (or elsewhere)? Roughly speaking less than half of the entries seem to have mappings, but at least most of the proteins are represented in Uniprot.

thanks, Peter


PD Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
peter.robinson at charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651