Package org.obolibrary.robot

Class ExtractOperation

java.lang.Object

org.obolibrary.robot.ExtractOperation

public class ExtractOperation
extends Object

Extract a set of OWLEntities from the input ontology to an output ontology. Uses the OWLAPI's SyntacticLocalityModuleExtractor (SLME).

Author:

James A. Overton

Constructor Summary

Constructors

Constructor	Description
ExtractOperation()

Method Summary

Modifier and Type	Method	Description
static org.semanticweb.owlapi.model.OWLOntology	extract(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> terms, org.semanticweb.owlapi.model.IRI outputIRI, uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType)	Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME) with default options.
static org.semanticweb.owlapi.model.OWLOntology	extract(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> terms, org.semanticweb.owlapi.model.IRI outputIRI, uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType, Map<String,String> options)
static org.semanticweb.owlapi.model.OWLOntology	extract(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> terms, org.semanticweb.owlapi.model.IRI outputIRI, uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType, Map<String,String> options, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)	Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME).
static org.semanticweb.owlapi.model.OWLOntology	extractSubset(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> terms, org.semanticweb.owlapi.model.IRI outputIRI, Map<String,String> options, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap, org.semanticweb.owlapi.model.parameters.Imports imports)	Extracts a materialized sub-ontology from the given ontology that only contains the given terms and the relations between them.
static Map<String,String>	getDefaultOptions()	Return a map from option name to default option value.
protected static org.semanticweb.owlapi.model.OWLAnnotationAxiom	getIsDefinedBy(org.semanticweb.owlapi.model.OWLEntity entity, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)	Given an OWLEntity, return an OWLAnnotationAssertionAxiom indicating the source ontology with rdfs:isDefinedBy.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractOperation

public ExtractOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return a map from option name to default option value.

Returns:

a map with default values for all available options

extract

public static org.semanticweb.owlapi.model.OWLOntology extract(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                               Set<org.semanticweb.owlapi.model.IRI> terms,
                                                               org.semanticweb.owlapi.model.IRI outputIRI,
                                                               uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType)
                                                        throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME) with default options. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

terms - a set of IRIs for terms to extract

outputIRI - the OntologyIRI of the new ontology

moduleType - determines the type of extraction; defaults to STAR

Returns:

a new ontology (with a new manager)

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on any OWLAPI problem

extract

public static org.semanticweb.owlapi.model.OWLOntology extract(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                               Set<org.semanticweb.owlapi.model.IRI> terms,
                                                               org.semanticweb.owlapi.model.IRI outputIRI,
                                                               uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType,
                                                               Map<String,String> options)
                                                        throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

extract

public static org.semanticweb.owlapi.model.OWLOntology extract(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                               Set<org.semanticweb.owlapi.model.IRI> terms,
                                                               org.semanticweb.owlapi.model.IRI outputIRI,
                                                               uk.ac.manchester.cs.owlapi.modularity.ModuleType moduleType,
                                                               Map<String,String> options,
                                                               Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)
                                                        throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME). The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

terms - a set of IRIs for terms to extract

outputIRI - the OntologyIRI of the new ontology

moduleType - determines the type of extraction; defaults to STAR

options - map of extract options

sourceMap - map of term IRI to source IRI, or null (only used with annotate-with-source)

Returns:

a new ontology (with a new manager)

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on any OWLAPI problem

extractSubset

public static org.semanticweb.owlapi.model.OWLOntology extractSubset(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                     Set<org.semanticweb.owlapi.model.IRI> terms,
                                                                     org.semanticweb.owlapi.model.IRI outputIRI,
                                                                     Map<String,String> options,
                                                                     Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap,
                                                                     org.semanticweb.owlapi.model.parameters.Imports imports)
                                                              throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Extracts a materialized sub-ontology from the given ontology that only contains the given terms and the relations between them. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

terms - a set of IRIs for terms to extract

outputIRI - the OntologyIRI of the new ontology

options - map of extract options

sourceMap - map of term IRI to source IRI, or null (only used with annotate-with-source)

imports - handle imports option (default: include)

Returns:

a new ontology (with a new manager)

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on any OWLAPI problem

getIsDefinedBy

protected static org.semanticweb.owlapi.model.OWLAnnotationAxiom getIsDefinedBy(org.semanticweb.owlapi.model.OWLEntity entity,
                                                                                Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)

Given an OWLEntity, return an OWLAnnotationAssertionAxiom indicating the source ontology with rdfs:isDefinedBy.

Parameters:

entity - entity to get source of

sourceMap - map of term IRI to source IRI, or null

Returns:

OWLAnnotationAssertionAxiom with rdfs:isDefinedBy as the property