Too many InvalidReferenceViolation messages

[jamesaoverton]

When reasoning over most of the ontologies that I build, I see a lot of these "ERROR" messages that are not genuine errors. Here's an example @zhengj2007 sent me:

ERROR org.obolibrary.robot.ReasonOperation - Reference violations found: 169 - reasoning may be incomplete
2018-10-04 11:20:28,093 ERROR org.obolibrary.robot.ReasonOperation - Reference InvalidReferenceViolation [axiom=SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000001> owl:Thing), referencedObject=owl:Thing, category=DANGLING]

I'd like to suppress these. Maybe a whitelist of terms to ignore would be enough. Maybe there's a more general solution. @cmungall ?

See also #1 and #259.

[mcourtot]

Seeing the same - shall I just ignore those?

C02XG3Q1JHD3:ontology courtot$ make test robot reason -i duo-edit.owl -r ELK relax reduce -r ELK annotate -V http://purl.obolibrary.org/obo/duo/releases/date +%Y-%m-%d/duo.owl -o duo.owl 2018-12-18 11:21:35,447 ERROR org.obolibrary.robot.ReasonOperation - Reference violations found: 63 - reasoning may be incomplete 2018-12-18 11:21:35,448 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000001> owl:Thing), referencedObject=owl:Thing, category=DANGLING] 2018-12-18 11:21:35,448 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=Declaration(ObjectProperty(<http://usefulinc.com/ns/doap#file-release>)), referencedObject=<http://usefulinc.com/ns/doap#file-release>, category=DANGLING]

[jamesaoverton]

I think this message is just saying that owl:Thing is not defined, so when BFO:0000001 refers to owl:Thing the reference is "dangling". That's safe to ignore. So I don't want to see these messages. @cmungall ?

[cmungall]

Yes, owl:Thing does not conform to OBO principles! I think including all owl builtins (top/bottom x class/property) should be ignored

[jamesaoverton]

Mitigated by #568, released in 1.4.3.