Description : A Gene Ontology Programming Library

GOGrapher is a python library that uses the Gene Ontology to create a network relating terms to each other and proteins to terms. Given a species name or the name of one of the origin databases for the GODB (and an aspect), a directed unweighted graph is constructed (a GODiGraph - using networkx). Then, the following utilities can be used:

  • given a weighting class (that extends GOWeighter) all edges can be come weighted (creating a GOXDiGraph)
  • a utility to convert from/to protein symbols to protein ids found in other listings
  • permanent storage for a GO(X)DiGraph

Prerequisites

Getting Started

Check out repository: 

svn co https://projects.dbbe.musc.edu/public/GOGrapher/trunk GOGrapher
cd GOGrapher
su -
python setup.py install

Once this is finished, you're ready to use the library. Look in the examples directory for some example usages (the README file in that folder contains more information). You can look at the documentation page for viewing the resulting XGMML files in Cytoscape.

API

The API is available online at http://projects.dbbe.musc.edu/~mullerb/GOGrapherDocs.

Windows

GOGrapher will work on windows using the file based storage. Since pygraphviz does not currently work on Windows (see https://networkx.lanl.gov/wiki/pygraphviz/FAQ), graph images cannot be made on Windows. You can, however, still create XGMML files for viewing in Cytoscape.