org.obolibrary.robot

Class OntologyHelper

java.lang.Object

org.obolibrary.robot.OntologyHelper

public class OntologyHelper
extends Object

Provides convenience methods for working with OWL ontologies.

Author:

James A. Overton

Constructor Summary

Constructors

Constructor and Description
OntologyHelper()

Method Summary

Modifier and Type	Method and Description
static void	addAxiomAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAxiom axiom, org.semanticweb.owlapi.model.IRI propertyIRI, org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an ontology, an axiom, a property IRI, and a value string, add an annotation to this ontology with that property and value.
static void	addAxiomAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAxiom axiom, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) Given an ontology, an axiom, and a set of annotations, annotate the axiom with the annotations in the ontology.
static void	addAxiomAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI propertyIRI, org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an ontology, an annotation property IRI, and an annotation value, annotate all axioms in the ontology with that property and value.
static void	addOntologyAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI propertyIRI, org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an ontology, a property IRI, and a value string, add an annotation to this ontology with that property and value.
static void	addOntologyAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotation annotation) Annotate the ontology with the annotation.
static void	collapseOntology(org.semanticweb.owlapi.model.OWLOntology ontology, int threshold, Set<org.semanticweb.owlapi.model.IRI> precious, boolean repeat) Given an ontology, a threshold, and a set of precious IRIs (or empty set), minimize the input ontology's class hierarchy based on the threshold.
static void	collapseOntology(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.IRI> precious) Given an ontology and a set of IRIs that must be retained, remove intermediate superclasses (classes that only have one child) and update the subclass relationships to preserve structure.
static void	copy(org.semanticweb.owlapi.model.OWLOntology inputOntology, org.semanticweb.owlapi.model.OWLOntology outputOntology, org.semanticweb.owlapi.model.OWLEntity entity, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties) Given input and output ontologies, a target entity, and a set of annotation properties, copy the target entity from the input ontology to the output ontology, along with the specified annotations.
static void	copyAnnotations(org.semanticweb.owlapi.model.OWLOntology inputOntology, org.semanticweb.owlapi.model.OWLOntology outputOntology, org.semanticweb.owlapi.model.OWLEntity entity, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties) Given an input ontology, an output ontology, an entity to copy annotations of, and the annotation properties to copy (or null for all), copy annotations of the entity from the input to the output ontology.
static boolean	extendsAxiomTypes(Class<? extends org.semanticweb.owlapi.model.OWLAxiom> axiom, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes) Given an OWLAxiom class and a set of OWLAxiom classes, determine if the axiom class provided extends at least one of the classes in the set.
static boolean	extendsAxiomTypes(org.semanticweb.owlapi.model.OWLAxiom axiom, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes) Given an OWLAxiom and a set of OWLAxiom class, determine if the axiom's class is an extension of at least one of the given set.
static Set<org.semanticweb.owlapi.model.IRI>	filterExistingTerms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.IRI> IRIs, boolean allowEmpty) Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology.
static Set<org.semanticweb.owlapi.model.IRI>	filterExistingTerms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.IRI> IRIs, boolean allowEmpty, org.semanticweb.owlapi.model.parameters.Imports imports) Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology.
static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom>	getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotationProperty property) Given an ontology, and an optional set of annotation properties, return a set of annotation assertion axioms for those properties, for all subjects.
static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom>	getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotationProperty property, org.semanticweb.owlapi.model.IRI subject) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.
static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom>	getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties, Set<org.semanticweb.owlapi.model.IRI> subjects) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.
static String	getAnnotationString(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotationProperty property, org.semanticweb.owlapi.model.IRI subject) Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.
static String	getAnnotationString(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties, Set<org.semanticweb.owlapi.model.IRI> subjects) Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.
static Set<String>	getAnnotationStrings(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotationProperty property, org.semanticweb.owlapi.model.IRI subject) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.
static Set<String>	getAnnotationStrings(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties, Set<org.semanticweb.owlapi.model.IRI> subjects) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.
static Set<org.semanticweb.owlapi.model.OWLAnnotationValue>	getAnnotationValues(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAnnotationProperty property, org.semanticweb.owlapi.model.IRI subject) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.
static Set<org.semanticweb.owlapi.model.OWLAnnotationValue>	getAnnotationValues(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties, Set<org.semanticweb.owlapi.model.IRI> subjects) Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAnonymousAncestorAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity) Given an ontology, an entity, and an empty set, fill the set with axioms representing any anonymous superclasses in the line of ancestors.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAnonymousDescendantAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity) Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in the descendants of the entity.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAnonymousEquivalentAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity) Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in equivalent entities.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAnonymousParentAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity) Given an ontology and an entity, return a set of axioms only corresponding to anonymous parents.
static Set<org.semanticweb.owlapi.model.OWLEntity>	getEntities(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, return a set of all the entities in its signature.
static Set<org.semanticweb.owlapi.model.OWLEntity>	getEntities(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.IRI> iris) Given an ontology and a set of term IRIs, return a set of entities for those IRIs.
static org.semanticweb.owlapi.model.OWLEntity	getEntity(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI iri) Given an ontology and an IRI, get the OWLEntity object represented by the IRI.
static org.semanticweb.owlapi.model.OWLEntity	getEntity(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI iri, boolean allowNull) Given an ontology, an IRI, and a boolean specifying if a null return value is allowed, get the OWLEntity object represented by the IRI.
static Set<org.semanticweb.owlapi.model.IRI>	getIRIs(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, return a set of IRIs for all the entities in its signature.
static Set<org.semanticweb.owlapi.model.IRI>	getIRIsInSignature(org.semanticweb.owlapi.model.OWLAxiom axiom) Given an OWLAxiom, return all the IRIs in the signature.
static Function<org.semanticweb.owlapi.model.OWLNamedObject,String>	getLabelFunction(org.semanticweb.owlapi.model.OWLOntology ontology, boolean useIriAsDefault) Generates a function that returns a label string for any named object in the ontology
static Map<String,org.semanticweb.owlapi.model.IRI>	getLabelIRIs(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, return a map from rdfs:label to IRIs.
static Map<org.semanticweb.owlapi.model.IRI,String>	getLabels(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, return a map from IRIs to rdfs:labels.
static Set<org.semanticweb.owlapi.model.OWLObject>	getNamedObjects(org.semanticweb.owlapi.model.OWLAxiom axiom) Get all named OWLObjects associated with an axiom.
static Set<org.semanticweb.owlapi.model.OWLObject>	getNamedObjects(org.semanticweb.owlapi.model.OWLOntology ontology) Get all named OWLObjects from an input ontology.
static Set<org.semanticweb.owlapi.model.OWLObject>	getObjects(org.semanticweb.owlapi.model.OWLAxiom axiom) Get all OWLObjects associated with an axiom.
static Set<org.semanticweb.owlapi.model.OWLObject>	getObjects(org.semanticweb.owlapi.model.OWLOntology ontology) Get all OWLObjects from an input ontology.
static org.semanticweb.owlapi.model.OWLDatatype	getType(org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an annotation value, return its datatype, or null.
static org.semanticweb.owlapi.model.IRI	getTypeIRI(org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an annotation value, return the IRI of its datatype, or null.
static String	getValue(org.semanticweb.owlapi.model.OWLAnnotation annotation) Given an OWLAnnotation, return its value as a string.
static String	getValue(org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom axiom) Given an OWLAnnotationAssertionAxiom, return its value as a string.
static String	getValue(org.semanticweb.owlapi.model.OWLAnnotationValue value) Given an OWLAnnotationValue, return its value as a string.
static String	getValue(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) Given a set of OWLAnnotations, return the first string value as determined by natural string sorting.
static Set<String>	getValues(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) Given a set of OWLAnnotations, return a set of their value strings.
static void	removeImports(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, remove the import declarations.
static void	removeOntologyAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology) Remove all annotations on this ontology.
static String	renderManchester(org.semanticweb.owlapi.model.OWLObject object, org.semanticweb.owlapi.util.ShortFormProvider provider) Render a Manchester string for an OWLObject.
static String	renderManchester(org.semanticweb.owlapi.model.OWLObject object, org.semanticweb.owlapi.util.ShortFormProvider provider, RendererType rt) Render a Manchester string for an OWLObject.
static void	setOntologyIRI(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI ontologyIRI, org.semanticweb.owlapi.model.IRI versionIRI) Set the ontology IRI and version IRI.
static void	setOntologyIRI(org.semanticweb.owlapi.model.OWLOntology ontology, String ontologyIRIString, String versionIRIString) Set the ontology IRI and version IRI using strings.
static void	trimOntology(org.semanticweb.owlapi.model.OWLOntology ontology) Given an ontology, remove any dangling entities.

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyHelper

public OntologyHelper()

Method Detail

addAxiomAnnotation

public static void addAxiomAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology,
                                      org.semanticweb.owlapi.model.OWLAxiom axiom,
                                      org.semanticweb.owlapi.model.IRI propertyIRI,
                                      org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an ontology, an axiom, a property IRI, and a value string, add an annotation to this ontology with that property and value.

Note that as axioms are immutable, the axiom is removed and replaced with a new one.

Parameters:

ontology - the ontology to modify

axiom - the axiom to annotate

propertyIRI - the IRI of the property to add

value - the IRI or literal value to add

addAxiomAnnotation

public static void addAxiomAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology,
                                      org.semanticweb.owlapi.model.OWLAxiom axiom,
                                      Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

Given an ontology, an axiom, and a set of annotations, annotate the axiom with the annotations in the ontology.

Note that as axioms are immutable, the axiom is removed and replaced with a new one.

Parameters:

ontology - the ontology to modify

axiom - the axiom to annotate

annotations - the set of annotation to add to the axiom

addAxiomAnnotations

public static void addAxiomAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology,
                                       org.semanticweb.owlapi.model.IRI propertyIRI,
                                       org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an ontology, an annotation property IRI, and an annotation value, annotate all axioms in the ontology with that property and value.

Parameters:

ontology - the ontology to modify

propertyIRI - the IRI of the property to add

value - the IRI or literal value to add

addOntologyAnnotation

public static void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology,
                                         org.semanticweb.owlapi.model.IRI propertyIRI,
                                         org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an ontology, a property IRI, and a value string, add an annotation to this ontology with that property and value.

Parameters:

ontology - the ontology to modify

propertyIRI - the IRI of the property to add

value - the IRI or literal value to add

addOntologyAnnotation

public static void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLOntology ontology,
                                         org.semanticweb.owlapi.model.OWLAnnotation annotation)

Annotate the ontology with the annotation.

Parameters:

ontology - the ontology to modify

annotation - the annotation to add

collapseOntology

public static void collapseOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                    Set<org.semanticweb.owlapi.model.IRI> precious)
                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an ontology and a set of IRIs that must be retained, remove intermediate superclasses (classes that only have one child) and update the subclass relationships to preserve structure. The ontology passed in is updated. Do not perform collapse multiple times (some intermediate classes will remain after only one pass).

Parameters:

ontology - ontology to remove intermediates in

precious - set of OWLEntities that should not be removed

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problem creating ontology

collapseOntology

public static void collapseOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                    int threshold,
                                    Set<org.semanticweb.owlapi.model.IRI> precious,
                                    boolean repeat)
                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an ontology, a threshold, and a set of precious IRIs (or empty set), minimize the input ontology's class hierarchy based on the threshold. The threshold is the minimum number of child classes that an intermediate class should have. Any intermediate class that has less than the threshold number of children will be removed and its children will become children of the next level up. Bottom-level and top-level classes are not removed. Any class with an IRI in the precious set is not removed. If not repeat, collapse will only be performed once, meaning that some intermediate classes may remain.

Parameters:

ontology - OWLOntology to minimize

threshold - minimum number of child classes

precious - set of IRIs to keep

repeat - if true, repeat collapsing until no intermediate classes remain

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problem creating copy to span gaps

copy

public static void copy(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                        org.semanticweb.owlapi.model.OWLOntology outputOntology,
                        org.semanticweb.owlapi.model.OWLEntity entity,
                        Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)

Given input and output ontologies, a target entity, and a set of annotation properties, copy the target entity from the input ontology to the output ontology, along with the specified annotations. If the entity is already in the outputOntology, then return without making any changes. The input ontology is not changed.

Parameters:

inputOntology - the ontology to copy from

outputOntology - the ontology to copy to

entity - the target entity that will have its ancestors copied

annotationProperties - the annotations to copy

copyAnnotations

public static void copyAnnotations(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                   org.semanticweb.owlapi.model.OWLOntology outputOntology,
                                   org.semanticweb.owlapi.model.OWLEntity entity,
                                   Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)

Given an input ontology, an output ontology, an entity to copy annotations of, and the annotation properties to copy (or null for all), copy annotations of the entity from the input to the output ontology.

Parameters:

inputOntology - OWLOntology to copy from

outputOntology - OWLOntology to copy to

entity - OWLEntity to copy annotations of

annotationProperties - Set of annotation properties to copy, or null for all

filterExistingTerms

public static Set<org.semanticweb.owlapi.model.IRI> filterExistingTerms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        Set<org.semanticweb.owlapi.model.IRI> IRIs,
                                                                        boolean allowEmpty)

Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology. Always include terms in imports.

Parameters:

ontology - the ontology to check for IRIs

IRIs - Set of IRIs to filter

allowEmpty - boolean specifying if an empty set can be returned

Returns:

Set of filtered IRIs

filterExistingTerms

public static Set<org.semanticweb.owlapi.model.IRI> filterExistingTerms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        Set<org.semanticweb.owlapi.model.IRI> IRIs,
                                                                        boolean allowEmpty,
                                                                        org.semanticweb.owlapi.model.parameters.Imports imports)

Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology. Maybe include terms in imports.

Parameters:

ontology - the ontology to check for IRIs

IRIs - Set of IRIs to filter

allowEmpty - boolean specifying if an empty set can be returned

imports - Imports INCLUDED or EXCLUDED

Returns:

Set of filtered IRIs

getNamedObjects

public static Set<org.semanticweb.owlapi.model.OWLObject> getNamedObjects(org.semanticweb.owlapi.model.OWLOntology ontology)

Get all named OWLObjects from an input ontology.

Parameters:

ontology - OWLOntology to retrieve objects from

Returns:

set of objects

getNamedObjects

public static Set<org.semanticweb.owlapi.model.OWLObject> getNamedObjects(org.semanticweb.owlapi.model.OWLAxiom axiom)

Get all named OWLObjects associated with an axiom. This is builds on getSignature() by including annotation subjects, properties, and values.

Parameters:

axiom - The axiom to check

Returns:

The set of objects

getIRIsInSignature

public static Set<org.semanticweb.owlapi.model.IRI> getIRIsInSignature(org.semanticweb.owlapi.model.OWLAxiom axiom)

Given an OWLAxiom, return all the IRIs in the signature. This is an add-on to the getSignature method to include OWLAnnotationAssertionAxioms.

Parameters:

axiom - OWLAxiom to get signature of

Returns:

IRIs used in OWLAxiom

getObjects

public static Set<org.semanticweb.owlapi.model.OWLObject> getObjects(org.semanticweb.owlapi.model.OWLOntology ontology)

Get all OWLObjects from an input ontology.

Parameters:

ontology - OWLOntology to retrieve objects from

Returns:

set of objects

getObjects

public static Set<org.semanticweb.owlapi.model.OWLObject> getObjects(org.semanticweb.owlapi.model.OWLAxiom axiom)

Get all OWLObjects associated with an axiom. This is builds on getSignature() by including anonymous objects.

Parameters:

axiom - The axiom to check

Returns:

The set of objects

getAnonymousAncestorAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAnonymousAncestorAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                    org.semanticweb.owlapi.model.OWLEntity entity)

Given an ontology, an entity, and an empty set, fill the set with axioms representing any anonymous superclasses in the line of ancestors.

Parameters:

ontology - the ontology to search

entity - the entity to search ancestors of

Returns:

set of OWLAxioms

getAnonymousDescendantAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAnonymousDescendantAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                      org.semanticweb.owlapi.model.OWLEntity entity)

Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in the descendants of the entity. Includes supers and equivalents.

Parameters:

ontology - the ontology to search

entity - the entity to search descendants of

Returns:

set of OWLAxioms

getAnonymousEquivalentAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAnonymousEquivalentAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                      org.semanticweb.owlapi.model.OWLEntity entity)

Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in equivalent entities.

Parameters:

ontology - the ontology to search

entity - the entity to search equivalents of

Returns:

set of OWLAxioms

getAnonymousParentAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAnonymousParentAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                  org.semanticweb.owlapi.model.OWLEntity entity)

Given an ontology and an entity, return a set of axioms only corresponding to anonymous parents.

Parameters:

ontology - the ontology to search

entity - the entity to search parents of

Returns:

set of OWLAxioms

getAnnotationAxioms

public static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom> getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                org.semanticweb.owlapi.model.OWLAnnotationProperty property)

Given an ontology, and an optional set of annotation properties, return a set of annotation assertion axioms for those properties, for all subjects.

Parameters:

ontology - the ontology to search (including imports closure)

property - an annotation property

Returns:

a filtered set of annotation assertion axioms

getAnnotationAxioms

public static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom> getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                org.semanticweb.owlapi.model.OWLAnnotationProperty property,
                                                                                                org.semanticweb.owlapi.model.IRI subject)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

property - an annotation property

subject - an annotation subject IRIs

Returns:

a filtered set of annotation assertion axioms

getAnnotationAxioms

public static Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom> getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                                Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties,
                                                                                                Set<org.semanticweb.owlapi.model.IRI> subjects)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

properties - a set of annotation properties, or null if all properties should be included

subjects - a set of annotation subject IRIs, or null if all subjects should be included

Returns:

a filtered set of annotation assertion axioms

getAnnotationString

public static String getAnnotationString(org.semanticweb.owlapi.model.OWLOntology ontology,
                                         org.semanticweb.owlapi.model.OWLAnnotationProperty property,
                                         org.semanticweb.owlapi.model.IRI subject)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

property - an annotation property

subject - an annotation subject IRIs

Returns:

the first annotation string

getAnnotationString

public static String getAnnotationString(org.semanticweb.owlapi.model.OWLOntology ontology,
                                         Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties,
                                         Set<org.semanticweb.owlapi.model.IRI> subjects)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

properties - a set of annotation properties, or null if all properties should be included

subjects - a set of annotation subject IRIs, or null if all subjects should be included

Returns:

the first annotation string

getAnnotationStrings

public static Set<String> getAnnotationStrings(org.semanticweb.owlapi.model.OWLOntology ontology,
                                               org.semanticweb.owlapi.model.OWLAnnotationProperty property,
                                               org.semanticweb.owlapi.model.IRI subject)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

property - an annotation property

subject - an annotation subject IRIs

Returns:

a filtered set of annotation strings

getAnnotationStrings

public static Set<String> getAnnotationStrings(org.semanticweb.owlapi.model.OWLOntology ontology,
                                               Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties,
                                               Set<org.semanticweb.owlapi.model.IRI> subjects)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

properties - a set of annotation properties, or null if all properties should be included

subjects - a set of annotation subject IRIs, or null if all subjects should be included

Returns:

a filtered set of annotation strings

getAnnotationValues

public static Set<org.semanticweb.owlapi.model.OWLAnnotationValue> getAnnotationValues(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                       org.semanticweb.owlapi.model.OWLAnnotationProperty property,
                                                                                       org.semanticweb.owlapi.model.IRI subject)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

property - an annotation property

subject - an annotation subject IRIs

Returns:

a filtered set of annotation values

getAnnotationValues

public static Set<org.semanticweb.owlapi.model.OWLAnnotationValue> getAnnotationValues(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                       Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> properties,
                                                                                       Set<org.semanticweb.owlapi.model.IRI> subjects)

Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.

Parameters:

ontology - the ontology to search (including imports closure)

properties - a set of annotation properties, or null if all properties should be included

subjects - a set of annotation subject IRIs, or null if all subjects should be included

Returns:

a filtered set of annotation values

getEntity

public static org.semanticweb.owlapi.model.OWLEntity getEntity(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                               org.semanticweb.owlapi.model.IRI iri)
                                                        throws Exception

Given an ontology and an IRI, get the OWLEntity object represented by the IRI. If it does not exist in the ontology, throw an exception.

Parameters:

ontology - OWLOntology to retrieve from

iri - IRI to get type of

Returns:

OWLEntity

Throws:

Exception - if IRI is not in ontology

getEntity

public static org.semanticweb.owlapi.model.OWLEntity getEntity(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                               org.semanticweb.owlapi.model.IRI iri,
                                                               boolean allowNull)
                                                        throws Exception

Given an ontology, an IRI, and a boolean specifying if a null return value is allowed, get the OWLEntity object represented by the IRI.

Parameters:

ontology - OWLOntology to retrieve from

iri - IRI to get type of

allowNull - if true, do not throw exception if IRI does not exist in ontology

Returns:

OWLEntity

Throws:

Exception - if allowNull is false and IRI is not in ontology

getEntities

public static Set<org.semanticweb.owlapi.model.OWLEntity> getEntities(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                      Set<org.semanticweb.owlapi.model.IRI> iris)

Given an ontology and a set of term IRIs, return a set of entities for those IRIs. The input ontology is not changed.

Parameters:

ontology - the ontology to search

iris - the IRIs of the entities to find

Returns:

a set of OWLEntities with the given IRIs

getEntities

public static Set<org.semanticweb.owlapi.model.OWLEntity> getEntities(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, return a set of all the entities in its signature.

Parameters:

ontology - the ontology to search

Returns:

a set of all entities in the ontology

getIRIs

public static Set<org.semanticweb.owlapi.model.IRI> getIRIs(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, return a set of IRIs for all the entities in its signature.

Parameters:

ontology - the ontology to search

Returns:

a set of IRIs for all entities in the ontology

getLabelFunction

public static Function<org.semanticweb.owlapi.model.OWLNamedObject,String> getLabelFunction(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                            boolean useIriAsDefault)

Generates a function that returns a label string for any named object in the ontology

Parameters:

ontology - to use

useIriAsDefault - if true then label-less classes will return IRI

Returns:

function mapping object to label

getLabelIRIs

public static Map<String,org.semanticweb.owlapi.model.IRI> getLabelIRIs(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, return a map from rdfs:label to IRIs. Includes labels asserted in for all imported ontologies. Duplicates overwrite existing with a warning.

Parameters:

ontology - the ontology to use

Returns:

a map from label strings to IRIs

getLabels

public static Map<org.semanticweb.owlapi.model.IRI,String> getLabels(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, return a map from IRIs to rdfs:labels. Includes labels asserted in for all imported ontologies. If there are multiple labels, use the alphanumerically first.

Parameters:

ontology - the ontology to use

Returns:

a map from IRIs to label strings

getType

public static org.semanticweb.owlapi.model.OWLDatatype getType(org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an annotation value, return its datatype, or null.

Parameters:

value - the value to check

Returns:

the datatype, or null if the value has none

getTypeIRI

public static org.semanticweb.owlapi.model.IRI getTypeIRI(org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an annotation value, return the IRI of its datatype, or null.

Parameters:

value - the value to check

Returns:

the IRI of the datatype, or null if the value has none

getValue

public static String getValue(org.semanticweb.owlapi.model.OWLAnnotationValue value)

Given an OWLAnnotationValue, return its value as a string.

Parameters:

value - the OWLAnnotationValue to get the string value of

Returns:

the string value

getValue

public static String getValue(org.semanticweb.owlapi.model.OWLAnnotation annotation)

Given an OWLAnnotation, return its value as a string.

Parameters:

annotation - the OWLAnnotation to get the string value of

Returns:

the string value

getValue

public static String getValue(org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom axiom)

Given an OWLAnnotationAssertionAxiom, return its value as a string.

Parameters:

axiom - the OWLAnnotationAssertionAxiom to get the string value of

Returns:

the string value

getValue

public static String getValue(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

Given a set of OWLAnnotations, return the first string value as determined by natural string sorting.

Parameters:

annotations - a set of OWLAnnotations to get the value of

Returns:

the first string value

getValues

public static Set<String> getValues(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

Given a set of OWLAnnotations, return a set of their value strings.

Parameters:

annotations - a set of OWLAnnotations to get the value of

Returns:

a set of the value strings

extendsAxiomTypes

public static boolean extendsAxiomTypes(org.semanticweb.owlapi.model.OWLAxiom axiom,
                                        Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)

Given an OWLAxiom and a set of OWLAxiom class, determine if the axiom's class is an extension of at least one of the given set.

Parameters:

axiom - the OWLAxiom to check

axiomTypes - classes of axioms desired

Returns:

true if axiom is an instantiation of one of the classes in set

extendsAxiomTypes

public static boolean extendsAxiomTypes(Class<? extends org.semanticweb.owlapi.model.OWLAxiom> axiom,
                                        Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)

Given an OWLAxiom class and a set of OWLAxiom classes, determine if the axiom class provided extends at least one of the classes in the set.

Parameters:

axiom - the OWLAxiom class to check

axiomTypes - classes of axioms desired

Returns:

true if axiom class extends one of the classes in set

removeImports

public static void removeImports(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, remove the import declarations.

Parameters:

ontology - OWLOntology to remove imports from

removeOntologyAnnotations

public static void removeOntologyAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology)

Remove all annotations on this ontology. Just annotations on the ontology itself, not annotations on its classes, etc.

Parameters:

ontology - the ontology to modify

renderManchester

public static String renderManchester(org.semanticweb.owlapi.model.OWLObject object,
                                      org.semanticweb.owlapi.util.ShortFormProvider provider)

Render a Manchester string for an OWLObject.

Parameters:

object - OWLObject to render

provider - ShortFormProvider to resolve entities

Returns:

String rendering of OWLObject based on renderer type

renderManchester

public static String renderManchester(org.semanticweb.owlapi.model.OWLObject object,
                                      org.semanticweb.owlapi.util.ShortFormProvider provider,
                                      RendererType rt)

Render a Manchester string for an OWLObject. The RendererType will determine what Manchester OWL Syntax renderer will be created.

Parameters:

object - OWLObject to render

provider - ShortFormProvider to resolve entities

rt - RendererType to use to render Manchester

Returns:

String rendering of OWLObject based on renderer type

setOntologyIRI

public static void setOntologyIRI(org.semanticweb.owlapi.model.OWLOntology ontology,
                                  String ontologyIRIString,
                                  String versionIRIString)

Set the ontology IRI and version IRI using strings.

Parameters:

ontology - the ontology to change

ontologyIRIString - the ontology IRI string, or null for no change

versionIRIString - the version IRI string, or null for no change

setOntologyIRI

public static void setOntologyIRI(org.semanticweb.owlapi.model.OWLOntology ontology,
                                  org.semanticweb.owlapi.model.IRI ontologyIRI,
                                  org.semanticweb.owlapi.model.IRI versionIRI)

Set the ontology IRI and version IRI.

Parameters:

ontology - the ontology to change

ontologyIRI - the new ontology IRI, or null for no change

versionIRI - the new version IRI, or null for no change

trimOntology

public static void trimOntology(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, remove any dangling entities.

Parameters:

ontology - the ontology to trim