Ontologies and Graph-tool Python

Question

Is there a way to create a graph from an ontology file using Graph-tool library in Python?

I've done some research and what I've found is:

• Graph Tool doesn't support .owl and .rdf files.
• There is no obvious way to convert an ontology to a graph using this library, as far as I know (I hope I missed something that someone here knows about).

What I have tried:

I had the idea of converting OWL ontologies and OBO to a NetworkX Graph then to a Graph-tool graph (because all of my previous work was done with Graph-tool).

Method 1: Used onto2nx library.

Problems:

• Really slow at loading ontologies and it stops half way.
• Isn't documented at all so I couldn't even get an idea on how it works even after checking the source code (The person who created it was notified but didn't reply).

Method 2: Used RDFLib library.

I've based my solution no this answer but:

Problems:

• The method to store the networkx ontology graph in a GraphML file doesn't support the mixed graphs (directed and unidirected edges together) which is exactly what I need.

Answer 1

Have you tried this:

https://readthedocs.org/projects/the-data-driven-ontology-toolkit-ddot/downloads/pdf/latest/

It has a function tonetworkx, maybe that’ll help.