duplicate_definition should take into account axiom annotations

[matentzn]

When we combine ontologies, we copy definitions and add provenance. For example, we re-use the definition of HP:0032154 in MONDO:0005318:

[Term]
id: HP:0032154
name: Aphthous ulcer
def: "Oral aphthous ulcers typically present as painful, sharply circumscribed fibrin-covered mucosal defects with a hyperemic border." [PMID:25346356]
synonym: "Canker sore" EXACT layperson []

[Term]
id: MONDO:0005318
name: canker sore
def: "Oral aphthous ulcers typically present as painful, sharply circumscribed fibrin-covered mucosal defects with a hyperemic border." [HP:0032154, PMID:25346356]

I believe the duplicate_definition check should be relaxed to include axiom annotations as well. What do you think @cmungall @jamesaoverton @balhoff?

[jamesaoverton]

I think this makes sense. Other annotation checks should probably ignore the axiom annotations as well.

I'd like to see a PR with the updated SPARQL.

[jamesaoverton]

@matentzn I'm assigning this to you, to show us how the SPARQL would be different.

[matentzn]

Are all robot report checks pure python? This is going to be impossible with pure SPARQL. The alternative would be to exclude definitions from the check with a particular axiom annotation like rdfs:isDefinedBy (or something new) assuming what follows is a reference saying: “this definition comes from elsewhere”.

[jamesaoverton]

ROBOT does not include any Python. All the ROBOT reports are in SPARQL: https://github.com/ontodev/robot/tree/master/robot-core/src/main/resources/report_queries

[matentzn]

Sorry @jamesaoverton I meant to say: owl api.. Brain scrambled. Pure SPARQL, no OWL API; from your answer I assume the answer stays: pure SPARQL. If so.. tough one.

[matentzn]

Implementing this is seriously too complicated. I think we should do something else: implement ROBOT normalise (https://github.com/ontodev/robot/issues/901), this way axioms like the ones causing this issue here would be merged first. As soon as the idea of ROBOT normalise is approved, we can close this issue here.