[Biopython-dev] Python GO database interface development
bartek at rezolwenta.eu.org
Tue Sep 2 07:51:16 EDT 2003
Some time ago (in July, I believe), I've posted similar question on this list.
It appeared that Bertrand Frottier have written some code for his own use, and
we started to develop it to the stage that it would be general enough to be
incorporated to the biopython. (Also Arnaud von Cortenbosch was involved in that
The project sort of died, mostly because of lack of time, but I still would like
to work on it. As for now, there's some of the old code contributed by Bertrand
(mostly for xml and www interface to GO) and some newer stuff that can do very
basic things with mysql GO database.
If anyone is interested in helping with development, that would be just great
(however I have to admit, that I'll probably not be able to work on it this week).
You can find the sources at http://rezolwenta.eu.org/cgi-bin/cvsweb/pygo/
Quoting Jay Hesselberth <jhessel at u.washington.edu>:
> I was wondering if there is any ongoing development of a Python based
> interface to the GO (Gene Ontology) database. I'm in need of one, and
> don't particularly want to reinvent the wheel for this.
> If not, I was thinking of basing my code off of the Perl API with only
> some of the core functionality, e.g. an interface to a local database and
> perhaps an interface to AMIGO, though I'm not sure I'll be needing that.
> Does anyone have experience with the Perl API? Are there features that
> are lacking / could be improved in a newer, Python based interface?
> Jay Hesselberth jhessel at u.washington.edu
> University of Washington
> Department of Genome Sciences
> Health Sciences Building K-222 / Box 357730
> Seattle, WA 98195
> Biopython-dev mailing list
> Biopython-dev at biopython.org
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