Package org.obolibrary.robot

Class RelatedObjectsHelper

java.lang.Object

org.obolibrary.robot.RelatedObjectsHelper

public class RelatedObjectsHelper
extends Object

Convenience methods to get related entities for a set of IRIs. Allowed relation options are: - ancestors - descendants - disjoints - domains - equivalents - inverses - ranges - types

Author:

Becky Tauber

Constructor Summary

Constructors

Constructor	Description
RelatedObjectsHelper()

Method Summary

Modifier and Type	Method	Description
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms, Set<org.semanticweb.owlapi.model.OWLObject> objects, List<String> axiomSelectors, List<String> baseNamespaces, boolean partial, boolean namedOnly)	Filter a set of OWLAxioms based on the provided arguments.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterAxiomsByAxiomType(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean partial, boolean namedOnly)	Given a set of OWLAxioms, a set of OWLObjects, a set of OWLAxiom Classes, a partial boolean, and a named-only boolean, return a set of OWLAxioms based on OWLAxiom type.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterCompleteAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean namedOnly)	Given a st of axioms, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterExternalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms, List<String> baseNamespaces)	Given a list of base namespaces and a set of axioms, return only the axioms that DO NOT have a subject in the base namespaces.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterInternalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms, List<String> baseNamespaces)	Given a list of base namespaces and a set of axioms, return only the axioms that have a subject in the base namespaces.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterPartialAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean namedOnly)	Given a set of axioms, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	filterTautologicalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms, boolean structural)	Given a set of OWLAxioms and a structural boolean, filter for tautological axioms, i.e., those that would be true in any ontology.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return the annotation axioms for all objects.
protected static Set<org.semanticweb.owlapi.model.OWLAnnotation>	getAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String annotation)	Given an IOHelper and an annotation as CURIE=..., return the OWLAnnotation object(s).
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean partial, boolean signature)	Deprecated. replaced by filterAxiomsByAxiomType(Set, Set, Set, boolean, boolean)
static Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>>	getAxiomValues(String axiomSelector)	Given a string axiom selector, return the OWLAxiom Class type(s) or null.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getCompleteAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)	Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getCompleteAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean namedOnly)	Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getPartialAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)	Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	getPartialAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes, boolean namedOnly)	Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLObject>	select(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String selector)	Given an ontology, a set of objects, and a selector, return the related objects related to the set of OWL objects based on the selector.
static Set<org.semanticweb.owlapi.model.OWLObject>	select(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, List<String> selectors)	Given an ontology, a set of objects, and a list of selector strings, return the objects related to the set of OWLObjects based on the set of selectors.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectAncestors(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all ancestors (recursively) of those objects.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectAnnotationProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of annotation properties from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectAnonymous(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of anonymous objects from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectChildren(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return the children of the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectClasses(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of OWLClasses from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectComplement(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all objects contained in the ontology that are NOT in the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectCURIE(IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String selector)	Given an IOHelper, a set of objects, and a selector string for CURIE pattern, return a set of objects matching that CURIE pattern.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectDataProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of OWLDataProperties from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectDescendants(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all descendants (recursively) of those objects.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectDomains(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all domains of any properties in the set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectEquivalents(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all equivalent objects of the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectGroups(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, List<List<String>> selectorGroups)	Given an ontology, a set of objects, and a list of select groups (as lists), return the objects related to the set of OWLObjects based on each set of selectors.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectIndividuals(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of OWLIndividuals from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectInstances(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, select all the instances of the classes in the set of objects.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectIRI(Set<org.semanticweb.owlapi.model.OWLObject> objects, String selector)	Given a set of objects, and a selector string (IRI pattern in angle brackets), select all the objects that have an IRI matching that pattern.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectNamed(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of named objects from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectObjectProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of OWLObjectProperties from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectParents(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return the parent objects of all objects in the set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectPattern(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String annotationPattern)	Given an ontology, a set of objects, and a pattern to match annotations to, return a set of objects that are annotated with the matching annotation.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given a set of objects, return a set of all OWLProperties from the starting set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectRanges(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return all ranges of any properties in the set.
static Set<org.semanticweb.owlapi.model.OWLObject>	selectTypes(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, return a set of all the types of the individuals in that set.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology, List<String> baseNamespaces, Set<org.semanticweb.owlapi.model.OWLObject> objects, boolean excludeAnonymous, boolean internal, boolean external)	Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects)	Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLObject> objects, boolean excludeAnonymous)	Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.

Methods inherited from class java.lang.Object

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

Constructor Detail

RelatedObjectsHelper

public RelatedObjectsHelper()

Method Detail

getAnnotationAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAnnotationAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                             Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return the annotation axioms for all objects.

Parameters:

ontology - OWLOntology to get annotations from

objects - OWLObjects to get annotations of

Returns:

set of OWLAxioms

filterAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms,
                                                                      Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                      List<String> axiomSelectors,
                                                                      List<String> baseNamespaces,
                                                                      boolean partial,
                                                                      boolean namedOnly)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Filter a set of OWLAxioms based on the provided arguments.

Parameters:

inputAxioms - Set of OWLAxioms to filter

objects - Set of OWLObjects to get axioms for

axiomSelectors - List of string selectors for types of axioms

baseNamespaces - List of string base namespaces used for internal/external selections

partial - if true, get any axiom containing at least one OWLObject from objects

namedOnly - if true, ignore anonymous OWLObjects in axioms

Returns:

set of filtered OWLAxioms

Throws:

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

filterAxiomsByAxiomType

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterAxiomsByAxiomType(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms,
                                                                                 Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                                 Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                                 boolean partial,
                                                                                 boolean namedOnly)

Given a set of OWLAxioms, a set of OWLObjects, a set of OWLAxiom Classes, a partial boolean, and a named-only boolean, return a set of OWLAxioms based on OWLAxiom type. The axiom is added to the set if it is an instance of an OWLAxiom Class in the axiomTypes set. If partial, return any axioms that use at least one object from the objects set. Otherwise, only return axioms that use objects in the set. If namedOnly, only consider named OWLObjects in the axioms and ignore any anonymous objects when selecting the axioms.

Parameters:

axioms - set of OWLAxioms to filter

objects - set of OWLObjects to get axioms for

axiomTypes - set of OWLAxiom Classes that determines what type of axioms will be selected

partial - if true, include all axioms that use at least one OWLObject from objects

namedOnly - if true, ignore anonymous OWLObjects used in axioms

Returns:

set of filtered axioms

filterCompleteAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterCompleteAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms,
                                                                              Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                              Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                              boolean namedOnly)

Given a st of axioms, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.

Parameters:

inputAxioms - Set of OWLAxioms to filter

objects - Set of objects to match in axioms

axiomTypes - OWLAxiom types to return

namedOnly - when true, consider only named OWLObjects

Returns:

Set of OWLAxioms containing only the OWLObjects

filterExternalAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterExternalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms,
                                                                              List<String> baseNamespaces)

Given a list of base namespaces and a set of axioms, return only the axioms that DO NOT have a subject in the base namespaces.

Parameters:

axioms - set of OWLAxioms

baseNamespaces - list of base namespaces

Returns:

external OWLAxioms

filterInternalAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterInternalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms,
                                                                              List<String> baseNamespaces)

Given a list of base namespaces and a set of axioms, return only the axioms that have a subject in the base namespaces.

Parameters:

axioms - set of OWLAxioms

baseNamespaces - list of base namespaces

Returns:

internal OWLAxioms

filterPartialAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterPartialAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> inputAxioms,
                                                                             Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                             Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                             boolean namedOnly)

Given a set of axioms, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.

Parameters:

inputAxioms - Set of OWLAxioms to filter

objects - Set of OWLObjects to match in axioms

axiomTypes - OWLAxiom types to return

namedOnly - when true, only consider named OWLObjects

Returns:

Set of OWLAxioms containing at least one of the OWLObjects

filterTautologicalAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> filterTautologicalAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms,
                                                                                  boolean structural)
                                                                           throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given a set of OWLAxioms and a structural boolean, filter for tautological axioms, i.e., those that would be true in any ontology.

Parameters:

axioms - set of OWLAxioms to filter

structural - if true, only filter for structural tautological axioms based on a hard-coded set of patterns (e.g., X subClassOf owl:Thing, owl:Nothing subClassOf X, X subClassOf X)

Returns:

tautological OWLAxioms from original set

Throws:

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

getAxioms

@Deprecated
public static Set<org.semanticweb.owlapi.model.OWLAxiom> getAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                   Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                   Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                   boolean partial,
                                                                   boolean signature)

Deprecated.

replaced by filterAxiomsByAxiomType(Set, Set, Set, boolean, boolean)

Parameters:

ontology - OWLOntology to get axioms from

objects - OWLObjects to get axioms about

axiomTypes - Set of OWLAxiom Classes that are the types of OWLAxioms to return

partial - if true, return any OWLAxiom that has at least one OWLObject from objects

signature - if true, ignore anonymous OWLObjects in axioms

Returns:

axioms from ontology based on options

getAxiomValues

public static Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> getAxiomValues(String axiomSelector)

Given a string axiom selector, return the OWLAxiom Class type(s) or null. The selector is either a special keyword that represents a set of axiom classes or the name of an OWLAxiom Class.

Parameters:

axiomSelector - string option to get the OWLAxiom Class type or types for

Returns:

set of OWLAxiom Class types based on the string option

getCompleteAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getCompleteAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                           Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                           Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)

Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects. Prefer filterCompleteAxioms(Set, Set, Set, boolean).

Parameters:

ontology - OWLOntology to get axioms from

objects - Set of objects to match in axioms

axiomTypes - OWLAxiom types to return

Returns:

Set of OWLAxioms containing only the OWLObjects

getCompleteAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getCompleteAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                           Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                           Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                           boolean namedOnly)

Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects. Prefer filterCompleteAxioms(Set, Set, Set, boolean).

Parameters:

ontology - OWLOntology to get axioms from

objects - Set of objects to match in axioms

axiomTypes - OWLAxiom types to return

namedOnly - when true, consider only named OWLObjects

Returns:

Set of OWLAxioms containing only the OWLObjects

getPartialAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getPartialAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                          Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                          Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes)

Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects. Prefer filterPartialAxioms(Set, Set, Set, boolean).

Parameters:

ontology - OWLOntology to get axioms from

objects - Set of objects to match in axioms

axiomTypes - OWLAxiom types to return

Returns:

Set of OWLAxioms containing at least one of the OWLObjects

getPartialAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> getPartialAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                          Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                          Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> axiomTypes,
                                                                          boolean namedOnly)

Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects. Prefer filterPartialAxioms(Set, Set, Set, boolean).

Parameters:

ontology - OWLOntology to get axioms from

objects - Set of objects to match in axioms

axiomTypes - OWLAxiom types to return

namedOnly - when true, only consider named OWLObjects

Returns:

Set of OWLAxioms containing at least one of the OWLObjects

selectGroups

public static Set<org.semanticweb.owlapi.model.OWLObject> selectGroups(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                       IOHelper ioHelper,
                                                                       Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                       List<List<String>> selectorGroups)
                                                                throws Exception

Given an ontology, a set of objects, and a list of select groups (as lists), return the objects related to the set of OWLObjects based on each set of selectors. Each selector group will build on the previous group.

Parameters:

ontology - OWLOntology to get related objects from

ioHelper - IOHelper to use for prefixes

objects - Set of objects to start with

selectorGroups - types of related objects to return

Returns:

Set of related objects

Throws:

Exception - on annotation pattern issue

select

public static Set<org.semanticweb.owlapi.model.OWLObject> select(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                 IOHelper ioHelper,
                                                                 Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                 List<String> selectors)
                                                          throws Exception

Given an ontology, a set of objects, and a list of selector strings, return the objects related to the set of OWLObjects based on the set of selectors.

Parameters:

ontology - OWLOntology to get related objects from

ioHelper - IOHelper to use for prefixes

objects - Set of objects to start with

selectors - types of related objects to return

Returns:

Set of related objects

Throws:

Exception - on annotation pattern issue

select

public static Set<org.semanticweb.owlapi.model.OWLObject> select(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                 IOHelper ioHelper,
                                                                 Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                 String selector)
                                                          throws Exception

Given an ontology, a set of objects, and a selector, return the related objects related to the set of OWL objects based on the selector.

Parameters:

ontology - OWLOntology to get related objects from

ioHelper - IOHelper to use for prefixes

objects - Set of objects to start with

selector - type of related objects to return

Returns:

Set of related objects

Throws:

Exception - on annotation pattern issue

selectAncestors

public static Set<org.semanticweb.owlapi.model.OWLObject> selectAncestors(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                          Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all ancestors (recursively) of those objects.

Parameters:

ontology - OWLOntology to retrieve ancestors from

objects - OWLObjects to retrieve ancestors of

Returns:

set of ancestors of the starting set

selectAnnotationProperties

public static Set<org.semanticweb.owlapi.model.OWLObject> selectAnnotationProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of annotation properties from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of OWLAnnotationProperties from the starting set

selectAnonymous

public static Set<org.semanticweb.owlapi.model.OWLObject> selectAnonymous(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of anonymous objects from the starting set. Valid for classes and individuals.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of anonymous objects from the starting set

selectChildren

public static Set<org.semanticweb.owlapi.model.OWLObject> selectChildren(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                         Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return the children of the starting set.

Parameters:

ontology - OWLOntology to retrieve children from

objects - Set of OWLObjects to get children of

Returns:

set of children of the starting set

selectClasses

public static Set<org.semanticweb.owlapi.model.OWLObject> selectClasses(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of OWLClasses from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of OWLClasses from the starting set

selectComplement

public static Set<org.semanticweb.owlapi.model.OWLObject> selectComplement(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                           Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all objects contained in the ontology that are NOT in the starting set.

Parameters:

ontology - OWLOntology to retrieve complement objects from

objects - Set of OWLObjects to get the complement of

Returns:

complement set of OWLObjects

selectCURIE

public static Set<org.semanticweb.owlapi.model.OWLObject> selectCURIE(IOHelper ioHelper,
                                                                      Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                      String selector)

Given an IOHelper, a set of objects, and a selector string for CURIE pattern, return a set of objects matching that CURIE pattern.

Parameters:

ioHelper - the IOHelper to resolve names

objects - the set of objects to filter

selector - the CURIE selector string

Returns:

the subset of objects that match the CURIE selector

selectDataProperties

public static Set<org.semanticweb.owlapi.model.OWLObject> selectDataProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of OWLDataProperties from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of OWLDataProperties from the starting set

selectDescendants

public static Set<org.semanticweb.owlapi.model.OWLObject> selectDescendants(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                            Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all descendants (recursively) of those objects.

Parameters:

ontology - OWLOntology to retrieve descendants from

objects - Set of OWLObjects to get descendants of

Returns:

set of descendants of the starting set

selectDomains

public static Set<org.semanticweb.owlapi.model.OWLObject> selectDomains(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all domains of any properties in the set.

Parameters:

ontology - OWLOntology to retrieve domains from

objects - OWLObjects to retrieve domains of

Returns:

set of domains of the starting set

selectEquivalents

public static Set<org.semanticweb.owlapi.model.OWLObject> selectEquivalents(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                            Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all equivalent objects of the starting set.

Parameters:

ontology - OWLOntology to retrieve equivalents from

objects - Set of OWLObjects to get equivalents of

Returns:

set of equivalent OWLObjects

selectIndividuals

public static Set<org.semanticweb.owlapi.model.OWLObject> selectIndividuals(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of OWLIndividuals from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of OWLIndividuals from the starting set

selectInstances

public static Set<org.semanticweb.owlapi.model.OWLObject> selectInstances(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                          Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, select all the instances of the classes in the set of objects.

Parameters:

ontology - OWLOntology to retrieve instances from

objects - Set of OWLObjects to get instances of

Returns:

set of instances as OWLObjects

selectIRI

public static Set<org.semanticweb.owlapi.model.OWLObject> selectIRI(Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                    String selector)

Given a set of objects, and a selector string (IRI pattern in angle brackets), select all the objects that have an IRI matching that pattern.

Parameters:

objects - Set of OWLObjects to look through

selector - IRI pattern to match (enclosed in angle brackets, using ? or * wildcards)

Returns:

set of IRIs that match the selector pattern

selectNamed

public static Set<org.semanticweb.owlapi.model.OWLObject> selectNamed(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of named objects from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of named objects from the starting set

selectObjectProperties

public static Set<org.semanticweb.owlapi.model.OWLObject> selectObjectProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of OWLObjectProperties from the starting set.

Parameters:

objects - Set of OWLObjects to filter

Returns:

subset of OWLObjectProperties from the starting set

selectParents

public static Set<org.semanticweb.owlapi.model.OWLObject> selectParents(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return the parent objects of all objects in the set.

Parameters:

ontology - OWLOntology to retrieve parents from

objects - set of OWLObjects to get parents of

Returns:

set of parent objects

selectPattern

public static Set<org.semanticweb.owlapi.model.OWLObject> selectPattern(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        IOHelper ioHelper,
                                                                        Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                        String annotationPattern)
                                                                 throws Exception

Given an ontology, a set of objects, and a pattern to match annotations to, return a set of objects that are annotated with the matching annotation.

Parameters:

ontology - OWLOntology to get annotations from

ioHelper - IOHelper to use for prefixes

objects - Set of OWLObjects to filter

annotationPattern - annotation to filter OWLObjects on

Returns:

subset of OWLObjects matching the annotation pattern

Throws:

Exception - on issue getting literal annotations

selectProperties

public static Set<org.semanticweb.owlapi.model.OWLObject> selectProperties(Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given a set of objects, return a set of all OWLProperties from the starting set.

Parameters:

objects - Set of OWLObjects to filter OWLProperties of

Returns:

subset of OWLProperties from the starting set

selectRanges

public static Set<org.semanticweb.owlapi.model.OWLObject> selectRanges(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                       Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return all ranges of any properties in the set.

Parameters:

ontology - OWLOntology to retrieve ranges from

objects - OWLObjects to retrieve ranges of

Returns:

set of ranges of the starting set

selectTypes

public static Set<org.semanticweb.owlapi.model.OWLObject> selectTypes(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                      Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, return a set of all the types of the individuals in that set.

Parameters:

ontology - OWLOntology to retrieve types from

objects - Set of OWLObjects to get the types of

Returns:

set of types (OWLClass or OWLClassExpression)

spanGaps

public static Set<org.semanticweb.owlapi.model.OWLAxiom> spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                  Set<org.semanticweb.owlapi.model.OWLObject> objects)

Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.

Parameters:

ontology - input OWLOntology

objects - set of Objects to build hierarchy

Returns:

set of OWLAxioms to maintain hierarchy

spanGaps

public static Set<org.semanticweb.owlapi.model.OWLAxiom> spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                  Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                  boolean excludeAnonymous)

Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.

Parameters:

ontology - input OWLOntology

objects - set of Objects to build hierarchy

excludeAnonymous - when true, span across anonymous nodes

Returns:

set of OWLAxioms to maintain hierarchy

spanGaps

public static Set<org.semanticweb.owlapi.model.OWLAxiom> spanGaps(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                  List<String> baseNamespaces,
                                                                  Set<org.semanticweb.owlapi.model.OWLObject> objects,
                                                                  boolean excludeAnonymous,
                                                                  boolean internal,
                                                                  boolean external)

Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.

Parameters:

ontology - input OWLOntology

baseNamespaces - list of base namespaces as strings

objects - set of Objects to build hierarchy

excludeAnonymous - when true, span across anonymous nodes

internal - when true, only preserve structure between internal nodes defined by base namespaces

external - when true, only preserve structure between external nodes defined by base namespaces

Returns:

set of OWLAxioms to maintain hierarchy

getAnnotations

protected static Set<org.semanticweb.owlapi.model.OWLAnnotation> getAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                IOHelper ioHelper,
                                                                                String annotation)
                                                                         throws Exception

Given an IOHelper and an annotation as CURIE=..., return the OWLAnnotation object(s).

Parameters:

ontology - OWLOntology to get annotations from

ioHelper - IOHelper to get IRI

annotation - String input

Returns:

set of OWLAnnotations

Throws:

Exception - on issue getting literal annotation