Package org.obolibrary.robot

Class MireotOperation

java.lang.Object

org.obolibrary.robot.MireotOperation

public class MireotOperation
extends Object

Implements several variations on MIREOT, as first described in "MIREOT: The minimum information to reference an external ontology term" (link).

Author:

James A. Overton

Constructor Summary

Constructors

Constructor	Description
MireotOperation()

Method Summary

Modifier and Type	Method	Description
static org.semanticweb.owlapi.model.OWLOntology	getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.IRI> lowerIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)	Given an ontology, a set of upper-level IRIs, a set of lower-level IRIs, and a set of annotation properties, return a new ontology with just the named ancestors of those terms, their subclass relations, and the selected annotations.
static org.semanticweb.owlapi.model.OWLOntology	getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.IRI> lowerIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties, boolean annotateSource, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)	Deprecated. replaced by getAncestors(OWLOntology, Set, Set, Set)
static org.semanticweb.owlapi.model.OWLOntology	getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.IRI> lowerIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties, Map<String,String> options, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> inputSourceMap)	Given an input ontology, a set of upper IRIs, a set of lower IRIs, a set of annotation properties (or null for all), and a map of extract options, get the ancestors of the lower IRIs up to the upper IRIs.
static Set<org.semanticweb.owlapi.model.OWLAnnotationProperty>	getDefaultAnnotationProperties()	Get a set of default annotation properties.
static org.semanticweb.owlapi.model.OWLOntology	getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)	Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations.
static org.semanticweb.owlapi.model.OWLOntology	getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties, boolean annotateSource, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)	Deprecated. replaced by getDescendants(OWLOntology, Set, Set, Map, Map)
static org.semanticweb.owlapi.model.OWLOntology	getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology, Set<org.semanticweb.owlapi.model.IRI> upperIRIs, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties, Map<String,String> options, Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> inputSourceMap)	Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations.

Methods inherited from class java.lang.Object

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

Constructor Detail

MireotOperation

public MireotOperation()

Method Detail

getDefaultAnnotationProperties

public static Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> getDefaultAnnotationProperties()

Get a set of default annotation properties. Currenly includes only RDFS label.

Returns:

a set of annotation properties

getAncestors

public static org.semanticweb.owlapi.model.OWLOntology getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                    Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                    Set<org.semanticweb.owlapi.model.IRI> lowerIRIs,
                                                                    Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)
                                                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an ontology, a set of upper-level IRIs, a set of lower-level IRIs, and a set of annotation properties, return a new ontology with just the named ancestors of those terms, their subclass relations, and the selected annotations. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

upperIRIs - ancestors will be copied up to and including these terms

lowerIRIs - copy these terms and their superclasses

annotationProperties - the annotation properties to copy; if null, all will be copied

Returns:

a new ontology with the target terms and their named ancestors

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating new ontology

getAncestors

public static org.semanticweb.owlapi.model.OWLOntology getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                    Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                    Set<org.semanticweb.owlapi.model.IRI> lowerIRIs,
                                                                    Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties,
                                                                    Map<String,String> options,
                                                                    Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> inputSourceMap)
                                                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an input ontology, a set of upper IRIs, a set of lower IRIs, a set of annotation properties (or null for all), and a map of extract options, get the ancestors of the lower IRIs up to the upper IRIs. Include the specified annotation properties.

Parameters:

inputOntology - OWLOntology to extract from

upperIRIs - top level IRIs

lowerIRIs - bottom level IRIs

annotationProperties - annotation properties to copy, or null for all

options - map of extract options or null

inputSourceMap - map of source IRIs to targets

Returns:

extracted module

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating the new ontology

getAncestors

@Deprecated
public static org.semanticweb.owlapi.model.OWLOntology getAncestors(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                    Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                    Set<org.semanticweb.owlapi.model.IRI> lowerIRIs,
                                                                    Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties,
                                                                    boolean annotateSource,
                                                                    Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)
                                                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Deprecated.

replaced by getAncestors(OWLOntology, Set, Set, Set)

Given an ontology, a set of upper-level IRIs, a set of lower-level IRIs, a set of annotation properties, and a boolean indiciating if rdfs:isDefinedBy should be added to copied classes, return a new ontology with just the named ancestors of those terms, their subclass relations, and the selected annotations. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

upperIRIs - ancestors will be copied up to and including these terms

lowerIRIs - copy these terms and their superclasses

annotationProperties - the annotation properties to copy; if null, all will be copied

annotateSource - if true, annotate copied classes with rdfs:isDefinedBy

sourceMap - map of term IRI to source IRI

Returns:

a new ontology with the target terms and their named ancestors

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating new ontology

getDescendants

public static org.semanticweb.owlapi.model.OWLOntology getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                      Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                      Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

upperIRIs - these terms and their descendants will be copied

annotationProperties - the annotation properties to copy; if null, all will be copied

Returns:

a new ontology with the target terms and their named ancestors

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating new ontology

getDescendants

public static org.semanticweb.owlapi.model.OWLOntology getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                      Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                      Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties,
                                                                      Map<String,String> options,
                                                                      Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> inputSourceMap)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

upperIRIs - these terms and their descendants will be copied

annotationProperties - the annotation properties to copy; if null, all will be copied

options - map of options

inputSourceMap - map of source IRIs (or null)

Returns:

a new ontology with the target terms and their named ancestors

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating new ontology

getDescendants

@Deprecated
public static org.semanticweb.owlapi.model.OWLOntology getDescendants(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                      Set<org.semanticweb.owlapi.model.IRI> upperIRIs,
                                                                      Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> annotationProperties,
                                                                      boolean annotateSource,
                                                                      Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> sourceMap)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Deprecated.

replaced by getDescendants(OWLOntology, Set, Set, Map, Map)

Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations. The input ontology is not changed.

Parameters:

inputOntology - the ontology to extract from

upperIRIs - these terms and their descendants will be copied

annotationProperties - the annotation properties to copy; if null, all will be copied

annotateSource - if true, annotate copied classes with rdfs:isDefinedBy

sourceMap - map of term IRI to source IRI

Returns:

a new ontology with the target terms and their named ancestors

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on problems creating new ontology