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Planteome / plant-stress-ontology

An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies. Formerly called the Ontology of Plant Stress
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Cannot import test_aps_diseases.owl AND upper_level.owl at the same time?? #7

Closed austinmeier closed 7 years ago

austinmeier commented 8 years ago

@marieALaporte why can I not have oops-edit.owl import both of these ontologies at the same time? I manually added the import to the ontology imports section in Protege, but when I save and reload, it always defaults back to only importing test_aps_diseases.owl, and leaves upper_level.owl out. Do I need to modify something to allow multiple direct imports?

marieALaporte commented 8 years ago

I think that your problem is caused by the fact that the 2 ontologies test_aps_diseases.owl and upper_level.owl are sharing the same namespace (http://purl.obolibrary.org/obo/auto). They are defined as being the same ontology: the URI of the 2 ontologies is the same. Some interesting reading about that: https://www.w3.org/TR/2004/REC-owl-guide-20040210/#StructureOfOntologies

How to fix that: test_aps_diseases.owl : The URI of this ontology should be something like http://purl.obolibrary.org/obo/oops/patternapply/test_aps_diseases.owl upper_level.owl : The URI of this ontology should be something like http://purl.obolibrary.org/obo/oops/patternapply/upper_level.owl

Then you will have I think to remove the old import (http://purl.obolibrary.org/obo/auto) and import the 2 files (in Protégé) and that should work.

austinmeier commented 8 years ago

Ohhhh, I was wondering why the namespace for those ontologies was "auto". Is that a byproduct of using the same python script to generate them? (apply-pattern.py) Thanks for the lesson, and quick reply. I'll do some tinkering today.

marieALaporte commented 8 years ago

I think you can customize the ontology URI by playing with the lines 26/27 of the apply-pattern.py script

austinmeier commented 8 years ago

Yeah, I assumed there was a line or two in there that caused them both to be the same. Luckily, it's in python, and I can actually read python!

edit: yup, it's a simple command line argument that allows you to just change the name at the time of running! That Chris, he thinks of everything.