Question: Query UniProt database with Mnemonic identifier
1
gravatar for frcamacho
2.2 years ago by
frcamacho190
United States
frcamacho190 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 • 788 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by frcamacho190

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 2.2 years ago by frcamacho190
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 2.2 years ago by Elisabeth Gasteiger1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1258 users visited in the last hour