[BioPython] Bio.EUtils

[Michiel de Hoon]

Dear Eric,

Thank you for your reply.
For esearch and efetch, can you use Bio.WWW.NCBI instead?
Something like:
>>> from Bio.WWW import NCBI
>>> handle = NCBI.esearch(db="taxonomy", term="your_search_term")
>>> result = handle.read() # Gets the search results in XML format.
and similar for NCBI.efetch.
Or does Bio.EUtils parse the XML results?

One caveat: Bio.WWW.NCBI will be updated and renamed Bio.Entrez in Biopython 1.45.

Thanks,

--Michiel.

Eric Gibert <ericgibert at yahoo.fr> wrote: 
Dear Michel,


I use DBIdsClient from Bio.EUtils to fetch data from the taxonomy database
of NCBI to update the table "taxon" and "taxon_name" in my BioSQL database
with the NCBI data.

I added one line definition in /Bio/EUtils/Config.py to declare that db:
Databases.TAXONOMY = _add_db(DatabaseInfo("taxonomy", 1))

Then I can use  client.search and result.efetch without problem.

Eric


-----Original Message-----
From: biopython-bounces at lists.open-bio.org
[mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Michiel de Hoon
Sent: Friday, January 25, 2008 9:05 PM
To: biopython at biopython.org
Subject: [BioPython] Bio.EUtils

Hello everybody,

I am looking at the various ways Biopython interacts with NCBI's Entrez
search engine, and if possible to organize and document this a bit more.
Currently there are several modules that interact with Entrez. The most
extensive one is Bio.EUtils, but there are also simpler modules such as
Bio.WWW.NCBI. I was wondering:
1) Is anybody using Bio.EUtils?
2) If so, could you give an example script that uses Bio.EUtils?
So we can get an idea of the amount of overlap between Bio.EUtils and
Bio.WWW.NCBI and others.

Thanks!

--Michiel.


       
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