Obtaining a mapping of RefSeq ACs to Uniprot ACs

Question

I am trying to obtain a mapping for RefSeq Accession Numbers to Uniprot Accession Numbers.

I can write a script to do this for a list of RefSeq ACs like this:

#!/usr/bin/python

"""
Derived from:
  http://www.uniprot.org/help/programmatic_access#id_mapping_python_example
"""

import urllib
import urllib2

url = 'http://www.uniprot.org/mapping/'

params = {
    'from':'P_REFSEQ_AC',
    'to':'ACC',
    'format':'tab',
    'query':'NP_511114.2 NP_004295.2 NP_031465.2 XP_004934106.1',
}

data = urllib.urlencode(params)
request = urllib2.Request(url, data)

# Please set your email address here to help us debug in case of problems.
contact = "email@example.com"
request.add_header('User-Agent', 'Python %s' % contact)
response = urllib2.urlopen(request)
page = response.read(200000)
print page

I am curious if there is a way to request the entire mapping of human genes to proteins.

I have tried to configure a query from the Uniprot resources, but I can't see how to get RefSeq data from this tool.

http://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606#customize-columns

I am happy to use a resource other than Uniprot.

Answer 1

You have a bunch of options:

1. You can use Biomart. Biomart is a standalone tool, but also have a pyton and R libraries. So it gives you more options depending on your preferred programming language. This is a widely used tool and in general works well.

   • biomart http://www.biomart.org/
   • biomart python library
   • biomart R library (from bioconductor) Biomart is widely used and have extensive documentation.

2. Use a python library called pyEntrezID https://pypi.python.org/pypi/pyEntrezId/1.4.7 You can do all sort of conversions of ids, however I've never tried it.

3. You can try NCBI eutils or one of the Ensembl REST API endpoints