Library for working with OWL, with an emphasis on the subset of OWL required by users of GO and OBO ontologies, plus convenience methods.

Currently what is supported is:

• The "OBO Basic" subset of OWL
• Individuals and connections between them (LEGO/Noctua models)

It is not intended for performing advanced processing of all OWL axiom types. For that we recommend:

• jython + the OWLAPI. See LINK TO DAVID'S EXAMPLES HERE
• FuXi

To see the capabilities of this library, see the tests/ directory

Some typical use cases this library is intended to address:

• produce basic ontology reports (e.g. table of IDs plus labels)
• Translate ontology representation to a networkx graph using a subset of relations (ObjectProperties)
• Analyze LEGO models

What it won't do:

• parse GAFs
• complex OWL processing

PACKAGE NAMES, APIS ETC ALL SUBJECT TO CHANGE!!

Proposed Refactor:

Use the following set of packages:

• ontol
  • Ontology.py
  • OWLParser
  • NetworkExporter => rename
  • reasoner
    • BasicReasoner
• lego
  • Lego
• assoc