Remove role GCIs from biochebi output

[balhoff]

See geneontology/go-ontology#17911 (comment)

[balhoff]

How this works:

• the command runner loads an OWL ontology embedded as a resource inside owltools, and passes it to BioChebiGenerator:

  owltools/OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java

  Lines 5823 to 5875 in 5518cab

  	@CLIMethod("--create-biochebi")
  	public void createBioChebi(Opts opts) throws Exception {
  	final String chebiPURL = "http://purl.obolibrary.org/obo/chebi.owl";
  	String chebiFile = null;
  	String output = null;
  	String ignoredSubset = "no_conj_equiv";
  	while (opts.hasOpts()) {
  	if (opts.nextEq("-o|--output")) {
  	output = opts.nextOpt();
  	}
  	else if (opts.nextEq("-c|--chebi-file")) {
  	chebiFile = opts.nextOpt();
  	}
  	else if (opts.nextEq("-i|--ignored-subset")) {
  	ignoredSubset = opts.nextOpt();
  	}
  	else {
  	break;
  	}
  	}
  	if (chebiFile != null) {
  	File inputFile = new File(chebiFile);
  	OWLOntology chebiOWL = pw.parse(IRI.create(inputFile).toString());
  	// sanity check:
  	// check that the purl is the expected one
  	boolean hasOntologyId = false;
  	OWLOntologyID ontologyID = chebiOWL.getOntologyID();
  	if (ontologyID != null) {
  	Optional<IRI> ontologyIRI = ontologyID.getOntologyIRI();
  	if (ontologyIRI.isPresent()) {
  	hasOntologyId = chebiPURL.equals(ontologyIRI.get().toString());
  	}
  	}
  	if (hasOntologyId == false) {
  	throw new RuntimeException("The loaded ontology file ("+chebiFile+") does not have the expected ChEBI purl: "+chebiPURL);
  	}
  	}
  	if (g == null) {
  	// load default template
  	InputStream stream = loadResource("bio-chebi-input.owl");
  	if (stream == null) {
  	throw new RuntimeException("Could not load default bio chebi input file: 'bio-chebi-input.owl'");
  	}
  	g = new OWLGraphWrapper(pw.getManager().loadOntologyFromOntologyDocument(stream));
  	}
  	BioChebiGenerator.createBioChebi(g, ignoredSubset);
  	if (output != null) {
  	OWLOntology ontology = g.getSourceOntology();
  	File outFile = new File(output);
  	ontology.getOWLOntologyManager().saveOntology(ontology, IRI.create(outFile));
  	}
  	}

• 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