Merge pull request #262 from geneontology/issue-237-delete-non-small-…

…mol-regs Delete non small mol regulator individuals
geneontology · May 24, 2023 · ef090f7 · ef090f7
2 parents 8f533df + 0f9291d
commit ef090f7
Showing 1 changed file with 31 additions and 23 deletions.
diff --git a/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java b/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java
@@ -1519,7 +1519,7 @@ private RuleResults convertEntityRegulatorsToBindingFunctions(String model_id, R
 BP has_part R
 	 * @return 
 	 */
-	private RuleResults inferSmallMoleculeRegulators(String model_id, RuleResults r, QRunner tbox_qrunner) {		
+	private RuleResults inferSmallMoleculeRegulators(String model_id, RuleResults r, QRunner tbox_qrunner) {
 		String entity_regulator_rule = "Entity Regulator Rule";
 		Integer entity_regulator_count = r.checkInitCount(entity_regulator_rule, r);
 		Set<String> entity_regulator_pathways = r.checkInitPathways(entity_regulator_rule, r);
@@ -1552,38 +1552,46 @@ private RuleResults inferSmallMoleculeRegulators(String model_id, RuleResults r,
 				}
 				//now get the actual regulating entities
 				Set<String> regulating_entities = new HashSet<String>();
-				for(InferredRegulator er : reaction_regulators.get(reaction_uri)) {
+				for(InferredRegulator er : regs) {
 					OWLClass entity_type_class = this.df.getOWLClass(IRI.create(er.entity_type_uri));
 					Set<OWLClass> entity_types = tbox_qrunner.getSuperClasses(entity_type_class, false);
-					//Only do this for chemical entities but not if nucleic acid or descendant
-					if(!entity_types.contains(chebi_chemical) || entity_types.contains(chebi_nucleic_acid)) {
-						continue;
-					}
+					entity_types.add(entity_type_class);  // Some of these are directly chebi_chemical
 					//catch cases where there may be more than one of the same entity
 					//avoid making multiple redundant binding functions for the same entity
 					if(!regulating_entities.add(er.entity_uri)) {
 						continue;
 					}
 					Set<OWLAnnotation> annos = getDefaultAnnotations();
 					OWLNamedIndividual regulator = makeUnannotatedIndividual(er.entity_uri);
-
-					OWLObjectProperty prop_for_deletion = GoCAM.involved_in_negative_regulation_of;
-					OWLObjectProperty regulator_prop = GoCAM.has_small_molecule_inhibitor;
-					String explain = "Entity Regulator Rule.  The relation was added to account for an assertion about an entity regulating the target reaction.";
-					if(er.prop_uri.equals("http://purl.obolibrary.org/obo/RO_0002429")) {
-						//String reg = " is involved in positive regulation of ";
-						annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
-						prop_for_deletion = GoCAM.involved_in_positive_regulation_of;
-						regulator_prop = GoCAM.has_small_molecule_activator;
-					}else {
-						//String reg = " is involved in negative regulation of ";
-						annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
-					}
-					//Connect the regulator to reaction via has_small_molecule_... relation
-					addRefBackedObjectPropertyAssertion(reaction, regulator_prop, regulator, Collections.singleton(model_id), GoCAM.eco_inferred_auto, default_namespace_prefix, annos, model_id);
 
-					//delete the original entity regulates process relation 
-					applyAnnotatedTripleRemover(regulator.getIRI(), prop_for_deletion.getIRI(), reaction.getIRI());
+					//Only do this for chemical entities but not if nucleic acid or descendant
+					if(entity_types.contains(chebi_chemical) && !entity_types.contains(chebi_nucleic_acid)) {
+						OWLObjectProperty prop_for_deletion = GoCAM.involved_in_negative_regulation_of;
+						OWLObjectProperty regulator_prop = GoCAM.has_small_molecule_inhibitor;
+						String explain = "Entity Regulator Rule.  The relation was added to account for an assertion about an entity regulating the target reaction.";
+						if(er.prop_uri.equals("http://purl.obolibrary.org/obo/RO_0002429")) {
+							//String reg = " is involved in positive regulation of ";
+							annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
+							prop_for_deletion = GoCAM.involved_in_positive_regulation_of;
+							regulator_prop = GoCAM.has_small_molecule_activator;
+						}else {
+							//String reg = " is involved in negative regulation of ";
+							annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
+						}
+						//Connect the regulator to reaction via has_small_molecule_... relation
+						addRefBackedObjectPropertyAssertion(reaction, regulator_prop, regulator, Collections.singleton(model_id), GoCAM.eco_inferred_auto, default_namespace_prefix, annos, model_id);
+
+						//delete the original entity regulates process relation 
+						applyAnnotatedTripleRemover(regulator.getIRI(), prop_for_deletion.getIRI(), reaction.getIRI());
+					} else {
+						// Delete individuals and log these out
+						String deleted_regulator_line = entity_type_class.getIRI().toString();
+						deleted_regulator_line += "\t"+this.getaLabel(entity_type_class);
+						deleted_regulator_line += "\t"+reaction_uri.toString();
+						deleted_regulator_line += "\t"+model_id;
+						System.out.println("DELETING_NON_SMALL_MOL_REGULATOR\t"+deleted_regulator_line);
+						deleteOwlEntityAndAllReferencesToIt(regulator);
+					}
 				}
 			}
 		}