Package org.obolibrary.robot

Class ExplainOperation

java.lang.Object

org.obolibrary.robot.ExplainOperation

public class ExplainOperation
extends Object

Compute an explanation for an entailed axiom.

Author:

Jim Balhoff

Constructor Summary

Constructors

Constructor	Description
ExplainOperation()

Method Summary

Modifier and Type	Method	Description
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explain(org.semanticweb.owlapi.model.OWLAxiom axiom, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int maxExplanations)	Compute explanations for an entailed axiom.
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explainInconsistent(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int max)	Compute explanations for inconsistent ontology
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explainMostGeneralUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int max)	Compute explanations for all most general unsatisfiable classes Note that this is a very naive implementation which assumes and acyclic class hierarchy.
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explainRootUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int max)	Compute explanations for all root unsatisfiable classes See https://github.com/matthewhorridge/owlexplanation/blob/439c5ca67835f5e421adde725e4e8a3bcd760ac8/src/main/java/org/semanticweb/owl/explanation/impl/rootderived/StructuralRootDerivedReasoner.java#L122
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explainUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int max)	Compute explanations for all unsatisfiable classes
static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>>	explainUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, int max, int maxUnsat)	Compute explanations for all unsatisfiable classes
static String	renderAxiomImpactSummary(Map<org.semanticweb.owlapi.model.OWLAxiom,Integer> axiomMap, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLOntologyManager manager)
static String	renderExplanationAsMarkdown(org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom> explanation, org.semanticweb.owlapi.model.OWLOntologyManager manager)	Render an Explanation object as Markdown text, linking text labels to term IRIs and indenting axioms.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExplainOperation

public ExplainOperation()

Method Detail

explain

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explain(org.semanticweb.owlapi.model.OWLAxiom axiom,
                                                                                                                  org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                  org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                  int maxExplanations)

Compute explanations for an entailed axiom.

Parameters:

axiom - entailed axiom to explain

ontology - ontology to search for explanation

reasonerFactory - reasoner factory used to create reasoners to test entailments

maxExplanations - maximum number of explanations to compute

Returns:

explanations

explainInconsistent

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explainInconsistent(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                              org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                              int max)

Compute explanations for inconsistent ontology

Parameters:

ontology - the ontology to be tested

reasonerFactory - the reasoner factory to be used for determining the explanation

max - maximum number of explanations to be computed

Returns:

a set of explanations for inconsistent ontology

explainUnsatisfiableClasses

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explainUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                                      org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                                                                                                      org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                                      int max)

Compute explanations for all unsatisfiable classes

Parameters:

ontology - the ontology to be tested

reasoner - the reasoner to be used to determine the unsatisfiable classes

reasonerFactory - the reasoner factory to be used to compute the explanations

max - maximum number of explanations to be computed

Returns:

a set of explanations

explainUnsatisfiableClasses

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explainUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                                      org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                                                                                                      org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                                      int max,
                                                                                                                                      int maxUnsat)

Compute explanations for all unsatisfiable classes

Parameters:

ontology - the ontology to be tested

reasoner - the reasoner to be used to determine the unsatisfiable classes

reasonerFactory - the reasoner factory to be used to compute the explanations

max - maximum number of explanations to be computed

maxUnsat - cutoff - limit number of tested unsatisfiable classes to maxUnsat classes

Returns:

a set of explanations

explainRootUnsatisfiableClasses

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explainRootUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                                          org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                                                                                                          org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                                          int max)

Compute explanations for all root unsatisfiable classes See https://github.com/matthewhorridge/owlexplanation/blob/439c5ca67835f5e421adde725e4e8a3bcd760ac8/src/main/java/org/semanticweb/owl/explanation/impl/rootderived/StructuralRootDerivedReasoner.java#L122

Parameters:

ontology - the ontology to be tested

reasoner - the reasoner to be used to determine the unsatisfiable classes

reasonerFactory - the reasoner factory to be used to compute the explanations

max - maximum number of explanations to be computed

Returns:

a set of explanations

explainMostGeneralUnsatisfiableClasses

public static Set<org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom>> explainMostGeneralUnsatisfiableClasses(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                                                                 org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                                                                                                                 org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                                                                                                                                                 int max)

Compute explanations for all most general unsatisfiable classes Note that this is a very naive implementation which assumes and acyclic class hierarchy.

Parameters:

ontology - the ontology to be tested

reasoner - the reasoner to be used to determine the unsatisfiable classes

reasonerFactory - the reasoner factory to be used to compute the explanations

max - maximum number of explanations to be computed

Returns:

a set of explanations

renderExplanationAsMarkdown

public static String renderExplanationAsMarkdown(org.semanticweb.owl.explanation.api.Explanation<org.semanticweb.owlapi.model.OWLAxiom> explanation,
                                                 org.semanticweb.owlapi.model.OWLOntologyManager manager)

Render an Explanation object as Markdown text, linking text labels to term IRIs and indenting axioms.

Parameters:

explanation - explanation to render

manager - OWLOntologyManager containing source ontologies for explanation axioms

Returns:

Markdown-formatted explanation text

renderAxiomImpactSummary

public static String renderAxiomImpactSummary(Map<org.semanticweb.owlapi.model.OWLAxiom,Integer> axiomMap,
                                              org.semanticweb.owlapi.model.OWLOntology ontology,
                                              org.semanticweb.owlapi.model.OWLOntologyManager manager)