Huseyin Kir

@jamesaoverton I simplified the example files. I can happily implement further improvements if required.

@beckyjackson Updated CHANGELOG to point PR instead of the issue to be compatible with old ones.

> I finally got around to trying this—generally looks great!. My main interest is in annotating axioms with `wasDerivedFrom` in `merge`. I ran this test: > > ``` > ./bin/robot...

I think this exception throwing should be part of the reasoning operation here: https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/ReasonOperation.java#L517 not in the Ontology Helper. This will also help me to use [OntologyHelper#addAxiomAnnotations](https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java#L109) in the scope...

Yes, this will solve our issue and term level is OK for us. Also, if you don't have the resources for this development, I would gladly do the implementation.

Using the `rdfs:isDefinedBy` annotation for both relationships may cause some complications. In the 'annotate-with-source' [documentation](http://robot.obolibrary.org/extract.html#adding-source-annotations), it is said that: > If the term already has an annotation using this property...

We can use date string as versionInfo. But some common terms are redefined in multiple ontologies. For example, `http://purl.obolibrary.org/obo/BFO_0000002` defined in both cl, pato and uberon. If I have an...

Since we want to cherry-pick the annotation property to remove, having a new parameter `--drop_axioms_annotation` made more sense. Created the related PR #1023

Sure, I can take this

completed: https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md