Remove role GCIs from biochebi output

[balhoff]

See https://github.com/geneontology/go-ontology/issues/17911#issuecomment-544609253

[balhoff]

How this works:

• the command runner loads an OWL ontology embedded as a resource inside owltools, and passes it to BioChebiGenerator: https://github.com/owlcollab/owltools/blob/5518cabeffb8abedd5efd869238b2975cc481ee5/OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java#L5823-L5875
• the embedded ontology imports both ChEBI and also an ontology http://purl.obolibrary.org/obo/go/extensions/substance_by_role.owl, which is actually served from the GO release imports folder and magically found by a line in the GO build catalog file: https://github.com/geneontology/go-ontology/blob/2fe891866790048684448260baca4fbe2d53e057/src/ontology/catalog-v001.xml#L9
• substance_by_role.owl defines GOCHE terms which have logical definitions making a chemical entity for each role
• BioChebiGenerator does the rest of the work creating GCIs for conjugate acid/base

Not sure how substance_by_role.owl was originally created.

[balhoff]

@cmungall is the solution for the immediate problem to simply completely remove the import of substance_by_role.owl?

[balhoff]

This will leave all these substance terms without labels. Perhaps instead we need a version of this file with logical definitions removed?

[vanaukenk]

From 2019-10-28 ontology editors call:

@balhoff will create a branch with the substance_by_role.owl removed to see what effects this might have on inferences.

[balhoff]

Not sure how substance_by_role.owl was originally created.

Update: substance_by_role.owl is made by the GO ontology makefile:

https://github.com/geneontology/go-ontology/blob/7cabd1f10d2599d5ad8ae2833bc3fad0837e07c6/src/ontology/Makefile#L471-L487