Translation services for genes and proteins based on Ensembl

Genes and proteins may be referenced using a variety of identifier formats: Ensembl, Entrez, UniProt, RefSeq, Affy probes, etc. Translating between these names can be time consuming and error prone.

This workflow uses identifier translation files downloaded from Ensembl BioMart to translate gene and protein identifiers between formats. The files are downloaded separatedly for each organism and build, to account for changes overtime that could introduce inconsistencies.


The organism input parameter defines the organism and build to use. For instance Homo sapiens is written Hsa, and for the hg18 build you can specify it as Hsa/may2009.

The format is specified using the same text as appears in BioMart. The most important are:

The main tasks are: translate, and translate_tsv