org.obolibrary.robot

Class ReasonOperation

java.lang.Object

org.obolibrary.robot.ReasonOperation

public class ReasonOperation
extends Object

Reason over an ontology and add axioms.

Author:

James A. Overton

Constructor Summary

Constructors

Constructor and Description
ReasonOperation()

Method Summary

Modifier and Type	Method and Description
static Map<String,String>	getDefaultOptions() Return a map from option name to default option value, for all the available reasoner options.
static org.semanticweb.owlapi.reasoner.OWLReasoner	getTautologyChecker(boolean structural) Create a tautology checker.
static boolean	isTautological(org.semanticweb.owlapi.model.OWLAxiom axiom, org.semanticweb.owlapi.reasoner.OWLReasoner tautologyChecker, boolean structural) Given an OWLAxiom, a tautology checker reasoner, and a boolean, determine if the axiom is a tautology.
static void	reason(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory) Given an ontology and a reasoner factory, return the ontology with inferred axioms added after reasoning.
static void	reason(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, Map<String,String> options) Given an ontology, a reasoner factory, and a map of options, return the ontology with inferred axioms added after reasoning.
static void	removeRedundantSubClassAxioms(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner) Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.
static void	removeRedundantSubClassAxioms(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, Map<String,String> options) Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReasonOperation

public ReasonOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return a map from option name to default option value, for all the available reasoner options.

Returns:

a map with default values for all available options

reason

public static void reason(org.semanticweb.owlapi.model.OWLOntology ontology,
                          org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory)
                   throws OntologyLogicException,
                          org.semanticweb.owlapi.model.OWLOntologyCreationException,
                          InvalidReferenceException

Given an ontology and a reasoner factory, return the ontology with inferred axioms added after reasoning. Use default options.

Parameters:

ontology - the ontology to reason over

reasonerFactory - the factory to create a reasoner instance from

Throws:

OntologyLogicException - if the ontology contains unsatisfiable classes, properties or inconsistencies

org.semanticweb.owlapi.model.OWLOntologyCreationException - if ontology cannot be created

InvalidReferenceException - if the reference checker fails

reason

public static void reason(org.semanticweb.owlapi.model.OWLOntology ontology,
                          org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                          Map<String,String> options)
                   throws OntologyLogicException,
                          org.semanticweb.owlapi.model.OWLOntologyCreationException,
                          InvalidReferenceException

Given an ontology, a reasoner factory, and a map of options, return the ontology with inferred axioms added after reasoning.

Parameters:

ontology - the ontology to reason over

reasonerFactory - the factory to create a reasoner instance from

options - a map of option strings, or null

Throws:

OntologyLogicException - if the ontology contains unsatisfiable classes, properties or inconsistencies

org.semanticweb.owlapi.model.OWLOntologyCreationException - if ontology cannot be created

InvalidReferenceException - if the reference checker fails

getTautologyChecker

public static org.semanticweb.owlapi.reasoner.OWLReasoner getTautologyChecker(boolean structural)
                                                                       throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Create a tautology checker.

Parameters:

structural - if true, return null - we do not need a checker for the structural patterns

Returns:

new OWLReasoner for empty ontology or null

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on issue creating empty ontology

isTautological

public static boolean isTautological(org.semanticweb.owlapi.model.OWLAxiom axiom,
                                     org.semanticweb.owlapi.reasoner.OWLReasoner tautologyChecker,
                                     boolean structural)

Given an OWLAxiom, a tautology checker reasoner, and a boolean, determine if the axiom is a tautology.

Parameters:

axiom - OWLAxiom to check

tautologyChecker - OWLReasoner for empty ontology

structural - if true, only check for hard-coded structural patterns (checker can be null)

Returns:

true if axiom is tautological

removeRedundantSubClassAxioms

public static void removeRedundantSubClassAxioms(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)

Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.

Example: genotyping assay - asserted in dev: assay - inferred by reasoner: analyte assay - asserted after fill: assay, analyte assay - asserted after removeRedundantSubClassAxioms: analyte assay

Parameters:

reasoner - an OWL reasoner, initialized with a root ontology; the ontology will be modified

removeRedundantSubClassAxioms

public static void removeRedundantSubClassAxioms(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                 Map<String,String> options)

Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.

Example: genotyping assay - asserted in dev: assay - inferred by reasoner: analyte assay - asserted after fill: assay, analyte assay - asserted after removeRedundantSubClassAxioms: analyte assay

Parameters:

reasoner - an OWL reasoner, initialized with a root ontology; the ontology will be modified

options - map of options for reasoning