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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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Replaced single-element property chain with subproperty axiom #19

Closed gaurav closed 6 years ago

gaurav commented 6 years ago

This closes #4, and allows JFact 5 to reason over this ontology when resolving phyloreferences. I used Protege 4.3 to create this file, so the OWL API version has increased from 3.3.1957 to 3.4.2.

Note that this change explicitly asserts that obo:CDAO_0000174 (has_Descendant) and obo:CDAO_0000149 (has_Child) are object properties. I'm not sure if this is necessary, but I don't think it does any harm.

balhoff commented 6 years ago

@gaurav just a tangential suggestion—for storage in version control I much prefer OWL Functional syntax over RDF/XML. OWL API outputs it one axiom per line.

gaurav commented 6 years ago

@balhoff Thanks for the suggestion! I've been using Functional Syntax for some debugging recently and I can see why you'd prefer it to RDF/XML!

gaurav commented 6 years ago

@hlapp I got Protege 4.3 installed on my computer and made the change there, which resulted in a much more readable diff since it keeps us in OWLAPI 3.x! Let me know what you think.

Protege 4.3 has odd issues with reading the CDAO ontology, so I'd like to move this phylogeny to Protege 5 (and OWLAPI 4.x). I've created a PR for that at #20.

hlapp commented 6 years ago

Note that this change explicitly asserts that obo:CDAO_0000174 (has_Descendant) and obo:CDAO_0000149 (has_Child) are object properties. I'm not sure if this is necessary, but I don't think it does any harm.

Not sure where the potential problem is here that you saw. Both properties are already asserted as object properties in CDAO, so this isn't redefining anything or even only adding an axiom that hadn't been there.