Question: Extracting domain list for proteins Using UniProt.ws in R
0
gravatar for Farhad
3.8 years ago by
Farhad10
Turkey
Farhad10 wrote:

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.

 

 

 

 

ADD COMMENTlink modified 23 months ago by brennanpincardiff200 • written 3.8 years ago by Farhad10
1

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.

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche21k

Thanks for your reply,

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

ADD REPLYlink written 3.8 years ago by Farhad10
1
gravatar for Elisabeth Gasteiger
3.8 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

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

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Elisabeth Gasteiger1.6k
0
gravatar for brennanpincardiff
23 months ago by
United Kingdom
brennanpincardiff200 wrote:

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

ADD COMMENTlink modified 23 months ago • written 23 months ago by brennanpincardiff200
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