From cmung...@gmail.com on July 10, 2013 19:05:51

Add an option or command to remove any classes that have no (inferred) instances.

This can be done in owltools at the moment, but requires a few steps. E.g. you can make a GAF from the annotations and use --extract-ontology-subset-by-gaf, but this is not convenient.

This would be particularly useful for pre-calculations of the allxall attribute matrix

Original issue: http://code.google.com/p/owltools/issues/detail?id=72