Question: Query UniProt database with Mnemonic identifier
1
gravatar for camachofrancine
16 months ago by
United States
camachofrancine110 wrote:

I have a list of UniProt Names, Mnemonic identifier of a UniProtKB entry. I am trying to query the UniProt database to retrieve the information of that entry that matches the mnemonic identifier and following filtering: Human taxa and Reviewed. Is there a way to do this in R? What I currently am doing is trying to use UniProt.ws package from Bioconductor. However I do not know what key type to use for querying with Uniprot Names. Is this possible with Bioconductor or do I need a different R package to proceed?

ids<-c("A4_HUMAN","ABCA1_HUMAN") #example of Mnemonic  ids 
test<-UniProt.ws(taxId=9606) # search only humans 
#lookup key types for Taxa 
keytypes(test) # check which key types I can use to query for Human

Any advice on how to proceed, would be much appreciated?

Thanks!

uniprot R • 463 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by camachofrancine110

Update: I was able to convert using http://www.uniprot.org/mapping/ from UniProtKB AC/ID to UniProtKB. This works, but would like to be able to implement some code. Thanks!

ADD REPLYlink written 16 months ago by camachofrancine110
1

You can access the UniProt Batch retrieval/IDmapping service (https://www.uniprot.org/uploadlists) programmatically, too, cf https://www.uniprot.org/help/api_batch_retrieval and https://www.uniprot.org/help/api_idmapping for code examples.

Please note however that the /mapping service will be deprecated soon: https://www.uniprot.org/help/uploadlists_change

ADD REPLYlink written 15 months ago by Elisabeth Gasteiger1.6k
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