Extend obsoletion action to allow replaced_by and support OBO merge semantics

[cmungall]

From @cmungall on May 19, 2015 15:22

The obsolete action current adds the owl:deprecated axiom and removes logical axioms, as well as label prefixing to get around the protege rendering bug, all good.

We would also like a way to easily add consider or replaced_by annotations. This is not too painful in the annotation editor, but OE users are used to doing this with a drag. No idea how easy this...

Another useful feature would be support OBO merge semantics. This means adding an annotation

obo:IAO_0000231=obo:IAO_0000227

i.e. 'has obsolescence reason' = 'terms merged'

to the class. In combination with a replaced_by, this will generate an alt_id in OBOF, as specced here:
owlcs/owlapi#317 (comment)

This may be best served by a different action, "Obsolete term for merge" that adds the merge annotation, but leaves it to the user to specify replaced_by?

@balhoff sorry to invade your github repo, we're not presupposing you will do this, I just wanted a place to track this, and your plugin seems the best start

Copied from original issue: balhoff/obo-actions#1

[cmungall]

From @balhoff on May 19, 2015 20:16

No problem, would be great to expand this tool.