I've used BiomaRt to map Ensemble to Entrez Id's and Uniprot Accession Id's . Recently, biomart made some changes and it seems that Unimart is no longer available? If i try this code (that was working before), i get:
mart = useMart(biomart = 'unimart',dataset='uniprot',verbose = T) Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and ending tag mismatch: body line 4 and html Premature end of data in tag html line 2 Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 7 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2
I tried changing the host option as I did with the Ensemble :
listMarts(host="www.ensembl.org") <-- works listMarts(host="www.uniprot.org") <--- does NOT work
I read somewhere in the past that unimart support was later updated to work again and I wonder if that is the same now? Is there a fix for this? Am I missing something?
One thing I forgot to mention is that I could also get the protein and gene names and symbols from Unimart, which is something I'm also looking for.