Add option to annotate extracted entities with source

[beckyjackson]

See #390

--annotate-with-source true will add rdfs:isDefinedBy to the term. Does not include annotations on the axiom, but that can be added as well. I'm not sure if this should be a different option though?

--sources <arg> allows you to define a term-to-source map file (as CSV or TSV) to redirect adopted entities, e.g.:

term,source
BFO:0000050,RO

If the term to extract isn't in that mapping file, the source is created from the term's IRI.

You can also do full IRIs for the sources (or terms) in the map.

term,source
http://purl.obolibrary.org/obo/BFO_0000050,http://purl.obolibrary.org/obo/ro.owl

[cmungall]

Code looks good.

Re: the ability to map via CSV. Potentially useful but I'd like some time to think this through. Don't want to unnecessarily complicate either ROBOT or the overall complexity of OBO ontology organization. I think if an ontology does adopt a URI then they should take responsibility for the isDefinedBys and they shouldn't be injected by an extract method. But overall we lack OBO docs on PURL adoption.

[beckyjackson]

@cmungall - I forgot to add in a check for if the rdfs:isDefinedBy annotation already exists. I just updated the code with that.

I know there has been some talk surrounding term "adoption" recently, especially with the OBO Core work. As this is something that impacts the OBO Foundry on a wider scale, this definitely requires more thought & input, but I wanted to have some sort of mock-up to demonstrate how it would work within ROBOT. Eventually, ROBOT could potentially have a default term-to-source map, like the prefix map, which would work behind the scenes. Again, these are just some first thoughts.

[jamesaoverton]

@cmungall I'd like to get this PR merged. The core functionality to add isDefinedBy is something we should have had from the beginning. The override feature is nice-to-have, regardless of what we settle on as an adoption stretegy, since we already have a few OBO terms that have moved from BFO to RO.

[cmungall]

agreed, merge away, conflict looks simple to fix

[beckyjackson]

Alright, this should be good to go!