Data File Which Maps Between Gene Names and Uniprot Protein IDs

Question

[pwg46]

Hello,

I am looking for a data file, which provides mappings between Gene Names and Uniprot Protein IDs. For example, entering ERN2 refers to Q76MJ5 when entered into Uniprot's website.

Thanks

Answer 1

[Jean-Karim Heriche]

Have a look at Ensembl's Biomart. In attributes, select associated gene name and UniProt/SwissProt ID.

Answer 2

[me]

Why don't you use the www.uniprot.org search functionality and using the columns button and download in format tab-delimited to get a list of UniProt Acc\tGene Name? e.g. http://www.uniprot.org/uniprot/?limit=10&force=no&format=tab&columns=id,genes

This you can then use in any tool of your own design.

Answer 3

[pld]

If you have access to the UniProt blast database you can grab them using blastdbcmd.

A word of caution: UniProt does a good job of standardizing symbols (what you're referring to) as well as short and full names, within UniProt. It can be difficult getting complete mapping if you're using non-standard symbols or naming.

Answer 4

[Elisabeth Gasteiger]

If the use of the UniProt website as proposed above doesn't suit you, you might also consider proceeding as described here.