Extracting domain list for proteins Using UniProt.ws in R

Question

[Farhad]

I encountered a problem using uniprot.ws package from R.

I want to get interpro domains for list of uniprot IDs using following command:

up <- UniProt.ws(taxId=9606)
select(up, keys=c("O76064"), columns=c("INTERPRO"), keytype="UNIPROTKB")

if I want to get these information for different organisms, is there any way to use this function without explicitly setting taxid to a specific one?

Generally I want to get domain list for list of uniprot IDs from different organisms, It would be really worthwhile for me to know other tools or a variation for above function for this purpose.

[Jean-Karim Heriche]

Try setting the taxID to an empty string. In principle, the UniProt REST API doesn't need it when you have accession numbers. Another option is to query the API yourself. See the (well hidden) UniProt REST API documentation.

[Farhad]

Thanks for your reply,

I tried empty string but it doesn't work. I try to write my own query.

Answer 1

[Elisabeth Gasteiger]

You could try URLs like the following, for each of your UniProtKB identifiers (see also http://www.uniprot.org/help/programmatic_access ):

http://www.uniprot.org/uniprot/?query=id:P12345&format=tab&columns=id,database%28InterPro%29

Answer 2

[brennanpincardiff]

Hello, I was wondering if anybody had an answer to this question. I know it's 22 months old but... I think the answer is really that UniProt.ws doesn't allow the extracting domain list for proteins but I would welcome anybody telling me this was untrue. The reason that I'm interested in this is that I have created an R package, called drawProteins, currently in Github and in submission to Bioconductor. I have written some functions that uses the UniProt API and downloads protein domain lists to create a dataframe with a domain list of a protein or proteins. Demo on my blog site if you want to test or have a look. It has been suggested that I have reinvented functionality that's in UniProt.ws but having looked at it, I'm not sure that this is the case as the list of features that UniProt.ws supplies does not seem appropriate to draw a schematic of the protein. Any other help or comment would be great. Thanks, Paul