Using Owlready2 for biological ontologies

Posted by quirinmanz on
URL: http://owlready.306.s1.nabble.com/Using-Owlready2-for-biological-ontologies-tp3296.html

Hi,
Thanks for your tool!

I am trying to use Owlready2 to parse the Cell Ontology (https://github.com/obophenotype/cell-ontology/releases).
Currently, getting ancestors, does not work.

>>> from owlready2 import *
>>> onto = get_ontology("cl-base.owl").load()
>>> target_class = onto.search(iri = "*0000163")[0]
>>> target_class.ancestors()
{owl.Thing, obo.CL_0000163}

I tried to use the reasoner which gives me a java heap space expection, but it seems like increasing owlready2.JAVA_MEMORY = 6000, for example does not change the subprocess command.

Do you have anywhere you could point me to?

Best,
Quirin