[ensembl-dev] Uniprot IDs

[Magali]

Hi Peter,

There is a pipeline used to link external references, like Uniprot and
Refseq, to the ensembl objects (gene, transcript, translation).
For this link to be generated, the identity between the source and the
ensembl object should be close enough to 100%.
For the example you are looking at, the Trembl protein is a fragment of
only 99 amino acids, which would therefore not match closely enough the
full length protein in ensembl.

In a more general perspective, we do distinguish Trembl entries from
Uniprot/Swissprot entries, as the former are not reviewed. It is
therefore less likely to find a matching mapping for Trembl entries.


Hope that helps,
Magali

On 01/09/12 09:29, Robinson, Peter wrote:
> 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
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/