Reorganize graph data files

[bentsherman]

Currently a graph is represented as three files:

1. edge list
2. node/module list
3. ontology info

We should condense these files into two files:

1. node list (id, module id, ontology terms)
2. edge list

This representation would significantly decrease load time because the ontology info file has a lot of information that is not used by the graph.

[bentsherman]

With the new binary format for the correlation matrix produced by ACE-KINC, we should probably refactor BioDepVis to use this format once it becomes more widely-used. This could be part of a v3.0.0 release.