[BioPython] Querying Entrez Gene

[Christof Winter]

Dear Luca,

you probably need this:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/

The code below is Python, not Biopython, but should work. You further need to parse the 
resulting XML. There is also an EUtils package as part of Biopython, but I never tried it: 
http://biopython.org/DIST/docs/api/public/Bio.EUtils-module.html

Cheers,
Christof


# Python eutils example

import urllib2

eutilsURL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

def esummary(db, ids):
     idlist = ",".join(ids)
     url = eutilsURL + "esummary.fcgi?db=%(db)s&id=%(idlist)s&retmode=xml"
     req = urllib2.Request(url % vars())
     handle = urllib2.urlopen(req)
     return handle.read()

print esummary("gene", ["3487"])


Luca Beltrame wrote:
> Hello.
> I'm currently in need of querying the Entrez Gene database using a list of IDs 
> I have. After searching in the Biopython documentation, I have found no 
> indication of whether that is possible or not. 
> Is there a way to query NCBI's Entrez Gene database? 
> Thanks in advance.
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