Fast Ensembl gene ID - UniProtID mapping

[Melanie Schneider]

Hi,

With the genome coordinates endpoint I’m getting the mapping between Ensembl gene ID and UniProt ID. Unfortunately, streaming an entire organism is a bit slow, so I was wondering whether it is possible to reduce the amount of data by specifying the required fields (e.g. only ‘accession’ and 'gnCoordinate’)? (I couldn’t find anything about it in the documentation.) Or, do you know another way to speed up the streaming?

Thanks a lot!

Melanie

_________________________

Melanie Schneider

Protein Computational Scientist

European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton

Cambridge, UK

[Manas Joshi]

Hi,

You mean mapping ensembl gene id to uniprot id? Have you tried biomart? I use the R package for biomart (biomaRt) and it gets my job done just fine.

Manas