Add robot export to standard output products

[cmungall]

Once this is merged: ontodev/robot#481

We can add standard TSV products. I would propose that a TSV is made for every product - e.g. subsets, base file, basic, merged

Note that this presents a mild challenge as BFO/RO labels will not be present in base products, necessitating the use of a CURIE rather than label in the command and output. But perhaps this is fine.

The main challenge here is the usual standardization vs customizability. It will likely be too hard to agree on one standard report (much as users would like this), as ontologies are still massively different in their usage of annotation properties, and whether users require a relational graph (as is always the case for go/cl/uberon/mondo/envo/etc). So it probably makes sense to have the options set in ODK, and to allow the user to select an "ontology profile" and then customize if needed.

This is my proposed list of columns, annotated with profile. A=all/union. For better or worse I chose ontologies that exemplify a style of APs. Here go subsumes mondo:

• CURIE, Label A
• SubClassOf, Label A
• Definition A
• {exact,related,broad,narrow}Synonym go
• Xref go
• SKOS exactMatch mondo
• SKOS closeMatch mondo
• SKOS broadMatch mondo
• SKOS narrowMatch mondo
• equivalentClass (named class only) A
• logical definitions??? just use dosdp-query for this?
• curator note obi
• alternative term obi
• various other IAO metadata terms obi
• part of, label go
• develops from, label go

[cmungall]

This is now in robot master, and will be in next release

[cmungall]

It may be useful to have a 'core relations' in the project config that would determine both creation of basic ontology as well as which relations are exported here

[jamesaoverton]

Does robot export (on master) now have everything you need for this use case?

[matentzn]

@cmungall Can you give a bit more detail here? I want to prepare a new ODK release, and this is the last ticket I wanted to make a stab at before I do.