Why not just use the ID mapping service on the front page of http://www.uniprot.org/ ?
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written
by
David Westergaard
Because I have a file containing 27k queries, but the mapping system can only detect matches to 17k of them. My original file contains Ensembl identifiers for genes. For example, ENSG00000203815 appears in the unmapped list, even though a match is found in Ensembl: http://www.ensembl.org/Multi/Search/Results?q=ENSG00000203815;site=ensembl
I have two files to compare to uniprot in order to download the txt related page.
Thank you for your time.
ENSG00000203815 cannot be mapped to UniProt by the IDmapping service because this identifier is not in the current EnsEMBL database - it has been deprecated:
http://www.ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000203815
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written
by
Elisabeth Gasteiger
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It seems from your comment below that by "gene names" you mean "Ensembl gene symbols". And by "uniprot entry names" you mean - what? IDs, such as
P09874, or names such asPARP1_HUMAN?Once your terms are defined correctly, we can craft an answer (which, by the way, is "BioMart").
Awesome thank you!
I'm trying the BioMart conversion from Ensembl Gene ID to UniProt/SwissProt ID.