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Only remove relation if same input instance for #276
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@dustine32
dustine32 committed Oct 26, 2023
1 parent cb1497f commit 35f360c
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Showing 3 changed files with 35 additions and 40 deletions.
53 changes: 17 additions & 36 deletions exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@
import org.geneontology.gocam.exchange.QRunner.BindingInput;
import org.geneontology.gocam.exchange.QRunner.ComplexInput;
import org.geneontology.gocam.exchange.QRunner.InferredEnabler;
import org.geneontology.gocam.exchange.QRunner.InferredInputRegulator;
import org.geneontology.gocam.exchange.QRunner.InferredOccursIn;
import org.geneontology.gocam.exchange.QRunner.InferredRegulator;
import org.geneontology.gocam.exchange.QRunner.InferredTransport;
Expand Down Expand Up @@ -977,8 +978,8 @@ RuleResults applySparqlRules(String model_id, QRunner tbox_qrunner) {
r = inferRegulatesViaOutputRegulates(model_id, r); //must be run before convertEntityRegulatorsToBindingFunctions
logger.debug("inferring regulates from output enables");
r = inferRegulatesViaOutputEnables(model_id, r);
logger.debug("inferring provides input for then removing causal relation");
r = inferProvidesInputRemoveCausalRelation(model_id, r);
logger.debug("inferring provides input for");
r = inferProvidesInput(model_id, r);
logger.debug("inferring small molecule regulators");
r = inferSmallMoleculeRegulators(model_id, r, tbox_qrunner);
logger.debug("deleting complexes with active units");
Expand Down Expand Up @@ -1374,45 +1375,25 @@ private RuleResults inferProvidesInput(String model_id, RuleResults r) {
Integer provides_input_count = r.checkInitCount(provides_input_rule, r);
Set<String> provides_input_pathways = r.checkInitPathways(provides_input_rule, r);

Set<InferredRegulator> provides_input = qrunner.getInferredInputProviders();
Set<InferredInputRegulator> provides_input = qrunner.getInferredInputProviders();
provides_input_count+=provides_input.size();
for(InferredRegulator ir : provides_input) {
provides_input_pathways.add(ir.pathway_uri);
//create ?reaction2 obo:RO_0002333 ?input
OWLNamedIndividual r1 = this.makeAnnotatedIndividual(ir.reaction1_uri);
OWLNamedIndividual r2 = this.makeAnnotatedIndividual(ir.reaction2_uri);
OWLObjectProperty o = df.getOWLObjectProperty(IRI.create(ir.prop_uri));
String r1_label = "'"+this.getaLabel(r1)+"'";
String r2_label = "'"+this.getaLabel(r2)+"'";
String o_label = "'"+this.getaLabel(o)+"'";
Set<OWLAnnotation> annos = getDefaultAnnotations();
String explain = "Provides Input For Rule. The relation "+r1_label+" "+o_label+" "+r2_label+" was inferred because:\n "+
"reaction1 has an output that is an input of reaction 2. ";
annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
this.addRefBackedObjectPropertyAssertion(r1, o, r2, Collections.singleton(model_id), GoCAM.eco_inferred_auto, default_namespace_prefix, annos, model_id);
applyAnnotatedTripleRemover(r1.getIRI(), causally_upstream_of.getIRI(), r2.getIRI());
}
r.rule_hitcount.put(provides_input_rule, provides_input_count);
r.rule_pathways.put(provides_input_rule, provides_input_pathways);
qrunner = new QRunner(go_cam_ont);
return r;
}

private RuleResults inferProvidesInputRemoveCausalRelation(String model_id, RuleResults r) {
/*
* Searches for inferred input reaction pairs to delete causally_upstream_of relation added earlier
*/
String provides_input_rule = "Provides Input For Rule";
Integer provides_input_count = r.checkInitCount(provides_input_rule, r);
Set<String> provides_input_pathways = r.checkInitPathways(provides_input_rule, r);

Set<InferredRegulator> provides_input = qrunner.getInferredInputProviders();
provides_input_count+=provides_input.size();
for(InferredRegulator ir : provides_input) {
for(InferredInputRegulator ir : provides_input) {
provides_input_pathways.add(ir.pathway_uri);
//create ?reaction2 obo:RO_0002333 ?input
OWLNamedIndividual r1 = this.makeAnnotatedIndividual(ir.reaction1_uri);
OWLNamedIndividual r2 = this.makeAnnotatedIndividual(ir.reaction2_uri);
//Check if rxns are already connected via common input/output instance
if (!ir.input_instance_uri.equals(ir.output_instance_uri)) {
OWLObjectProperty o = df.getOWLObjectProperty(IRI.create(ir.prop_uri));
String r1_label = "'"+this.getaLabel(r1)+"'";
String r2_label = "'"+this.getaLabel(r2)+"'";
String o_label = "'"+this.getaLabel(o)+"'";
Set<OWLAnnotation> annos = getDefaultAnnotations();
String explain = "Provides Input For Rule. The relation "+r1_label+" "+o_label+" "+r2_label+" was inferred because:\n "+
"reaction1 has an output that is an input of reaction 2. ";
annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(explain)));
this.addRefBackedObjectPropertyAssertion(r1, o, r2, Collections.singleton(model_id), GoCAM.eco_inferred_auto, default_namespace_prefix, annos, model_id);
}
applyAnnotatedTripleRemover(r1.getIRI(), causally_upstream_of.getIRI(), r2.getIRI());
}
r.rule_hitcount.put(provides_input_rule, provides_input_count);
Expand Down
20 changes: 17 additions & 3 deletions exchange/src/main/java/org/geneontology/gocam/exchange/QRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -440,6 +440,18 @@ class InferredRegulator {
}
}

class InferredInputRegulator extends InferredRegulator {
String output_instance_uri;
String input_instance_uri;
InferredInputRegulator(String r1_uri, String p_uri, String r2_uri, String pathway, String entity,
String entity_type, String output_uri, String input_uri) {
super(r1_uri, p_uri, r2_uri, pathway, entity, entity_type);
output_instance_uri = output_uri;
input_instance_uri = input_uri;
}

}

Set<InferredRegulator> getInferredRegulatorsQ1() {
Set<InferredRegulator> ir = new HashSet<InferredRegulator>();
String query = null;
Expand Down Expand Up @@ -587,8 +599,8 @@ Set<InferredRegulator> getInferredAnonymousRegulators() {
return irs;
}

Set<InferredRegulator> getInferredInputProviders() {
Set<InferredRegulator> ir = new HashSet<InferredRegulator>();
Set<InferredInputRegulator> getInferredInputProviders() {
Set<InferredInputRegulator> ir = new HashSet<InferredInputRegulator>();
String query = null;
try {
query = IOUtils.toString(QRunner.class.getResourceAsStream("query2update_provides_input_for.rq"), StandardCharsets.UTF_8);
Expand All @@ -602,12 +614,14 @@ Set<InferredRegulator> getInferredInputProviders() {
Resource reaction1 = qs.getResource("reaction1");
Resource reaction2 = qs.getResource("reaction2");
Resource pathway = qs.getResource("pathway");
Resource r1output = qs.getResource("r1output");
Resource r2input = qs.getResource("reaction2input");
//reaction1 provides_input_for reaction 2
String pathway_uri = "";
if(pathway!=null) {
pathway_uri = pathway.getURI();
}
ir.add(new InferredRegulator(reaction1.getURI(), GoCAM.provides_direct_input_for.getIRI().toString(), reaction2.getURI(), pathway_uri, "", ""));
ir.add(new InferredInputRegulator(reaction1.getURI(), GoCAM.provides_direct_input_for.getIRI().toString(), reaction2.getURI(), pathway_uri, "", "", r1output.getURI(), r2input.getURI()));
}
qe.close();
return ir;
Expand Down
2 changes: 1 addition & 1 deletion ...nge/src/main/resources/org/geneontology/gocam/exchange/query2update_provides_input_for.rq
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ prefix skos: <http://www.w3.org/2004/02/skos/core#>
#and reaction1 causally_upstream_of reaction2
#then reaction1 directly_positively_regulates reaction2

select distinct ?reaction2 ?reaction1 ?reaction2inputLabel ?reaction2Label ?reaction1Label ?pathway
select distinct ?reaction2 ?reaction1 ?reaction2inputLabel ?reaction2Label ?reaction1Label ?pathway ?r1output ?reaction2input
where {
# limit to relationships in the same Pathway
# promiscuous molecules make this important to avoid explosions
Expand Down

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