Using Owlready2 for biological ontologies

[quirinmanz]

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

[Jiba]

Hello,

After running the reasoner, I get two additional ancestors:

>>> sync_reasoner()
>>> print(target_class.ancestors())
{obo.UBERON_0000061, obo.CL_0000163, owl.Thing, obo.CL_0000000}

Is that the result you expect?

I have no particular problem for running the reasoner ; I am using the following version of Java under Linux:

jiba dans src :  java -version
openjdk version "1.8.0_392"
OpenJDK Runtime Environment (build 1.8.0_392-b08)
OpenJDK 64-Bit Server VM (build 25.392-b08, mixed mode)

Which version are you using? Do you have also other ontologies loaded at the same time that may increase the volume of data for the reasoner?

Jiba