org.obolibrary.obo2owl

Class OWLAPIObo2Owl

java.lang.Object

org.obolibrary.obo2owl.OWLAPIObo2Owl

public class OWLAPIObo2Owl
extends Object

The Class OWLAPIObo2Owl.

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,org.semanticweb.owlapi.model.IRI>	ANNOTATIONPROPERTYMAP The annotation property map.
protected Set<org.semanticweb.owlapi.model.OWLAnnotationProperty>	apToDeclare The ap to declare.
protected Map<String,org.semanticweb.owlapi.model.OWLClass>	clsToDeclare The cls to declar.
protected String	defaultIDSpace The default id space.
protected org.semanticweb.owlapi.model.OWLDataFactory	fac The fac.
protected Map<String,String>	idSpaceMap The id space map.
static String	IRI_PROP_ISREVERSIBLEPROPERTYCHAIN The Constant IRI_PROP_isReversiblePropertyChain.
protected org.semanticweb.owlapi.model.OWLOntologyManager	manager The manager.
protected OBODoc	obodoc The obodoc.
protected org.semanticweb.owlapi.model.OWLOntology	owlOntology The owl ontology.
protected Map<String,org.semanticweb.owlapi.model.OWLAnnotationProperty>	typedefToAnnotationProperty The typedef to annotation property.

Constructor Summary

Constructors

Constructor and Description
OWLAPIObo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager) Instantiates a new oWLAPI obo2 owl.

Method Summary

Modifier and Type	Method and Description
protected void	add(org.semanticweb.owlapi.model.OWLAxiom axiom) Adds the.
protected void	add(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms) Adds the.
protected void	addDeclaredAnnotationProperties(Collection<org.semanticweb.owlapi.model.OWLAnnotationProperty> declaredProperties) Adds the declared annotation properties.
protected void	addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap, org.semanticweb.owlapi.model.OWLAnnotationValue v, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) Adds the ontology annotation.
protected void	addPropertyValueHeaders(Collection<Clause> clauses) Adds the property value headers.
protected void	apply(List<org.semanticweb.owlapi.model.OWLOntologyChange> changes) Apply the changes.
protected void	apply(org.semanticweb.owlapi.model.OWLOntologyChange change) Apply the change.
org.semanticweb.owlapi.model.OWLOntology	convert(OBODoc doc) Convert.
org.semanticweb.owlapi.model.OWLOntology	convert(OBODoc doc, org.semanticweb.owlapi.model.OWLOntology in) Convert.
org.semanticweb.owlapi.model.OWLOntology	convert(String oboFile) Creates an OBOFormatParser object to parse a file and then converts it using the convert method.
static void	convertURL(String iri, String outFile, org.semanticweb.owlapi.model.OWLOntologyManager manager) Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML.
static void	convertURL(String iri, String outFile, String defaultOnt, org.semanticweb.owlapi.model.OWLOntologyManager manager) See.
protected String	getDefaultIDSpace() Gets the default id space.
protected static String	getIdPrefix(String x) Gets the id prefix.
org.semanticweb.owlapi.model.OWLOntologyManager	getManager() Gets the manager.
OBODoc	getObodoc() Gets the obodoc.
protected org.semanticweb.owlapi.model.OWLOntology	getOwlOntology() Gets the owl ontology.
protected static boolean	getQVBoolean(String q, Collection<QualifierValue> quals) Gets the qV boolean.
protected static Integer	getQVInt(String q, Collection<QualifierValue> quals) Gets the qV int.
protected static String	getQVString(String q, Collection<QualifierValue> quals) Gets the qV string.
protected static String	getURI(String path) Gets the uri.
protected void	init(org.semanticweb.owlapi.model.OWLOntologyManager m) Init
protected static Map<String,org.semanticweb.owlapi.model.IRI>	initAnnotationPropertyMap() Table 5.8 Translation of Annotation Vocabulary.
protected String	mapPropId(String id) See section "header macros" and treat-xrefs-as-equivalent.
org.semanticweb.owlapi.model.IRI	oboIdToIRI(String id) Obo id to iri.
protected void	postProcess(org.semanticweb.owlapi.model.OWLOntology ontology) perform any necessary post-processing.
void	setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager) Sets the manager.
void	setObodoc(OBODoc obodoc) Sets the obodoc.
protected void	setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology) Sets the owl ontology.
protected org.semanticweb.owlapi.model.OWLOntology	tr(org.semanticweb.owlapi.model.OWLOntology in) Tr.
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trAnnotationProp(String relId) Tr annotation prop.
protected Set<org.semanticweb.owlapi.model.OWLAnnotation>	trAnnotations(Clause clause) Tr annotations.
protected void	trAnnotations(Clause clause, Set<org.semanticweb.owlapi.model.OWLAnnotation> anns) Tr annotations.
protected Set<? extends org.semanticweb.owlapi.model.OWLAnnotation>	trAnnotations(Collection<Clause> clauses) Tr annotations.
protected Set<org.semanticweb.owlapi.model.OWLAxiom>	translateAltIds(Collection<Clause> clauses, org.semanticweb.owlapi.model.IRI replacedBy, boolean isClass) Generate axioms for the alternate identifiers of an OWLClass or OWLObjectProperty.
protected String	translateShorthandIdToExpandedId(String id) Translate shorthand id to expanded id.
protected org.semanticweb.owlapi.model.OWLClassExpression	trClass(Object v) Tr class.
protected org.semanticweb.owlapi.model.OWLClass	trClass(String classId) Tr class.
protected org.semanticweb.owlapi.model.OWLAxiom	trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub, String tag, Clause clause) Tr generic clause.
protected org.semanticweb.owlapi.model.OWLAxiom	trGenericClause(org.semanticweb.owlapi.model.OWLNamedObject e, String tag, Clause clause) Tr generic clause.
void	trHeaderFrame(Frame headerFrame) Tr header frame.
protected org.semanticweb.owlapi.model.OWLIndividual	trIndividual(String instId) Tr individual.
protected org.semanticweb.owlapi.model.OWLAxiom	trIntersectionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses) Tr intersection of.
protected org.semanticweb.owlapi.model.OWLAnnotationValue	trLiteral(Object inputValue) Tr literal.
protected org.semanticweb.owlapi.model.OWLObjectPropertyExpression	trObjectProp(Object v) Tr object prop.
protected org.semanticweb.owlapi.model.OWLObjectProperty	trObjectProp(String relId) Tr object prop.
org.semanticweb.owlapi.model.OWLClassExpression	trRel(String relId, String classId, Collection<QualifierValue> quals) Tr rel.
protected static org.semanticweb.owlapi.model.OWLAxiom	trRelationIntersectionOf(String id, org.semanticweb.owlapi.model.OWLProperty p, Collection<Clause> clauses) Tr relation intersection of.
protected static org.semanticweb.owlapi.model.OWLAxiom	trRelationUnionOf(String id, org.semanticweb.owlapi.model.OWLProperty p, Collection<Clause> clauses) Tr relation union of.
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trSynonymType(String type) Tr synonym type.
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trTagToAnnotationProp(String tag) Tr tag to annotation prop.
static org.semanticweb.owlapi.model.IRI	trTagToIRI(String tag) Tr tag to iri.
protected org.semanticweb.owlapi.model.OWLAxiom	trTermClause(org.semanticweb.owlapi.model.OWLClass cls, String tag, Clause clause) #5.2
org.semanticweb.owlapi.model.OWLClassExpression	trTermFrame(Frame termFrame) Tr term frame.
Set<org.semanticweb.owlapi.model.OWLAxiom>	trTermFrameClauses(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses, String t) Tr term frame clauses.
protected org.semanticweb.owlapi.model.OWLAxiom	trTypedefClause(org.semanticweb.owlapi.model.OWLObjectProperty p, String tag, Clause clause) Tr typedef clause.
org.semanticweb.owlapi.model.OWLNamedObject	trTypedefFrame(Frame typedefFrame) Tr typedef frame.
protected org.semanticweb.owlapi.model.OWLNamedObject	trTypedefToAnnotationProperty(Frame typedefFrame) Tr typedef to annotation property.
protected org.semanticweb.owlapi.model.OWLAxiom	trUnionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses) Tr union of.

Methods inherited from class java.lang.Object

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

Field Detail

IRI_PROP_ISREVERSIBLEPROPERTYCHAIN

public static final String IRI_PROP_ISREVERSIBLEPROPERTYCHAIN

The Constant IRI_PROP_isReversiblePropertyChain.

See Also:

Constant Field Values

defaultIDSpace

protected String defaultIDSpace

The default id space.

manager

protected org.semanticweb.owlapi.model.OWLOntologyManager manager

The manager.

owlOntology

protected org.semanticweb.owlapi.model.OWLOntology owlOntology

The owl ontology.

fac

protected org.semanticweb.owlapi.model.OWLDataFactory fac

The fac.

obodoc

protected OBODoc obodoc

The obodoc.

idSpaceMap

protected final Map<String,String> idSpaceMap

The id space map.

ANNOTATIONPROPERTYMAP

public static final Map<String,org.semanticweb.owlapi.model.IRI> ANNOTATIONPROPERTYMAP

The annotation property map.

apToDeclare

protected final Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> apToDeclare

The ap to declare.

clsToDeclare

protected final Map<String,org.semanticweb.owlapi.model.OWLClass> clsToDeclare

The cls to declar.

typedefToAnnotationProperty

protected final Map<String,org.semanticweb.owlapi.model.OWLAnnotationProperty> typedefToAnnotationProperty

The typedef to annotation property.

Constructor Detail

OWLAPIObo2Owl

public OWLAPIObo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)

Instantiates a new oWLAPI obo2 owl.

Parameters:

manager - the manager

Method Detail

init

protected void init(org.semanticweb.owlapi.model.OWLOntologyManager m)

Init

Parameters:

m - the manager

convertURL

public static void convertURL(String iri,
                              String outFile,
                              org.semanticweb.owlapi.model.OWLOntologyManager manager)
                       throws IOException,
                              org.semanticweb.owlapi.model.OWLOntologyCreationException,
                              org.semanticweb.owlapi.model.OWLOntologyStorageException

Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML.

Parameters:

iri - the iri

outFile - the out file

manager - manager to use

Throws:

IOException - Signals that an I/O exception has occurred.

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

org.semanticweb.owlapi.model.OWLOntologyStorageException - the oWL ontology storage exception

OBOFormatParserException - the oBO format parser exception

convertURL

public static void convertURL(String iri,
                              String outFile,
                              String defaultOnt,
                              org.semanticweb.owlapi.model.OWLOntologyManager manager)
                       throws IOException,
                              org.semanticweb.owlapi.model.OWLOntologyCreationException,
                              org.semanticweb.owlapi.model.OWLOntologyStorageException

See.

Parameters:

iri - the iri

outFile - the out file

defaultOnt - -- e.g. "go". If the obo file contains no "ontology:" header tag, this is added

manager - the manager to be used

Throws:

IOException - Signals that an I/O exception has occurred.

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

org.semanticweb.owlapi.model.OWLOntologyStorageException - the oWL ontology storage exception

OBOFormatParserException - the oBO format parser exception convertURL(String iri, String outFile, OWLOntologyManager manager)

initAnnotationPropertyMap

protected static Map<String,org.semanticweb.owlapi.model.IRI> initAnnotationPropertyMap()

Table 5.8 Translation of Annotation Vocabulary.

Returns:

property map

getManager

public org.semanticweb.owlapi.model.OWLOntologyManager getManager()

Gets the manager.

Returns:

the manager

setManager

public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)

Sets the manager.

Parameters:

manager - the new manager

getObodoc

public OBODoc getObodoc()

Gets the obodoc.

Returns:

the obodoc

setObodoc

public void setObodoc(OBODoc obodoc)

Sets the obodoc.

Parameters:

obodoc - the new obodoc

getOwlOntology

protected org.semanticweb.owlapi.model.OWLOntology getOwlOntology()

Gets the owl ontology.

Returns:

the owlOntology

setOwlOntology

protected void setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)

Sets the owl ontology.

Parameters:

owlOntology - the owlOntology to set

convert

public org.semanticweb.owlapi.model.OWLOntology convert(String oboFile)
                                                 throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Creates an OBOFormatParser object to parse a file and then converts it using the convert method.

Parameters:

oboFile - the obo file

Returns:

ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

convert

public org.semanticweb.owlapi.model.OWLOntology convert(OBODoc doc)
                                                 throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Convert.

Parameters:

doc - the obodoc

Returns:

ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

convert

public org.semanticweb.owlapi.model.OWLOntology convert(OBODoc doc,
                                                        org.semanticweb.owlapi.model.OWLOntology in)
                                                 throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Convert.

Parameters:

doc - the obodoc

in - the in

Returns:

the oWL ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

tr

protected org.semanticweb.owlapi.model.OWLOntology tr(org.semanticweb.owlapi.model.OWLOntology in)
                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Tr.

Parameters:

in - the in

Returns:

the oWL ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - the oWL ontology creation exception

postProcess

protected void postProcess(org.semanticweb.owlapi.model.OWLOntology ontology)

perform any necessary post-processing. currently this only includes the experimental logical-definitions-view-property

Parameters:

ontology - the ontology

getURI

protected static String getURI(String path)

Gets the uri.

Parameters:

path - the path

Returns:

the uri

trHeaderFrame

public void trHeaderFrame(Frame headerFrame)

Tr header frame.

Parameters:

headerFrame - the header frame

addPropertyValueHeaders

protected void addPropertyValueHeaders(Collection<Clause> clauses)

Adds the property value headers.

Parameters:

clauses - the clauses

addOntologyAnnotation

protected void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap,
                                     org.semanticweb.owlapi.model.OWLAnnotationValue v,
                                     Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

Adds the ontology annotation.

Parameters:

ap - the ap

v - the v

annotations - the annotations

trTermFrame

public org.semanticweb.owlapi.model.OWLClassExpression trTermFrame(Frame termFrame)

Tr term frame.

Parameters:

termFrame - the term frame

Returns:

the oWL class expression

translateAltIds

protected Set<org.semanticweb.owlapi.model.OWLAxiom> translateAltIds(Collection<Clause> clauses,
                                                                     org.semanticweb.owlapi.model.IRI replacedBy,
                                                                     boolean isClass)

Generate axioms for the alternate identifiers of an OWLClass or OWLObjectProperty.

Parameters:

clauses - collection of alt_id clauses

replacedBy - IRI of the entity

isClass - set to true if the alt_id is represents a class, false in case of an property

Returns:

set of axioms generated for the alt_id clauses

trTermFrameClauses

public Set<org.semanticweb.owlapi.model.OWLAxiom> trTermFrameClauses(org.semanticweb.owlapi.model.OWLClass cls,
                                                                     Collection<Clause> clauses,
                                                                     String t)

Tr term frame clauses.

Parameters:

cls - the cls

clauses - the clauses

t - the t

Returns:

the sets the

trTypedefToAnnotationProperty

protected org.semanticweb.owlapi.model.OWLNamedObject trTypedefToAnnotationProperty(Frame typedefFrame)

Tr typedef to annotation property.

Parameters:

typedefFrame - the typedef frame

Returns:

the oWL named object

trTypedefFrame

public org.semanticweb.owlapi.model.OWLNamedObject trTypedefFrame(Frame typedefFrame)

Tr typedef frame.

Parameters:

typedefFrame - the typedef frame

Returns:

the oWL named object

trRelationUnionOf

protected static org.semanticweb.owlapi.model.OWLAxiom trRelationUnionOf(String id,
                                                                         org.semanticweb.owlapi.model.OWLProperty p,
                                                                         Collection<Clause> clauses)

Tr relation union of.

Parameters:

id - the id

p - the p

clauses - the clauses

Returns:

the oWL axiom

trRelationIntersectionOf

protected static org.semanticweb.owlapi.model.OWLAxiom trRelationIntersectionOf(String id,
                                                                                org.semanticweb.owlapi.model.OWLProperty p,
                                                                                Collection<Clause> clauses)

Tr relation intersection of.

Parameters:

id - the id

p - the p

clauses - the clauses

Returns:

the oWL axiom

trUnionOf

protected org.semanticweb.owlapi.model.OWLAxiom trUnionOf(org.semanticweb.owlapi.model.OWLClass cls,
                                                          Collection<Clause> clauses)

Tr union of.

Parameters:

cls - the cls

clauses - the clauses

Returns:

the oWL axiom

trIntersectionOf

protected org.semanticweb.owlapi.model.OWLAxiom trIntersectionOf(org.semanticweb.owlapi.model.OWLClass cls,
                                                                 Collection<Clause> clauses)

Tr intersection of.

Parameters:

cls - the cls

clauses - the clauses

Returns:

the oWL axiom

add

protected void add(org.semanticweb.owlapi.model.OWLAxiom axiom)

Adds the.

Parameters:

axiom - the axiom

add

protected void add(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms)

Adds the.

Parameters:

axioms - the axioms

apply

protected void apply(org.semanticweb.owlapi.model.OWLOntologyChange change)

Apply the change.

Parameters:

change - the change

apply

protected void apply(List<org.semanticweb.owlapi.model.OWLOntologyChange> changes)

Apply the changes.

Parameters:

changes - the changes

trTermClause

protected org.semanticweb.owlapi.model.OWLAxiom trTermClause(org.semanticweb.owlapi.model.OWLClass cls,
                                                             String tag,
                                                             Clause clause)

#5.2

Parameters:

cls - the cls

tag - the tag

clause - the clause

Returns:

axiom

trTypedefClause

protected org.semanticweb.owlapi.model.OWLAxiom trTypedefClause(org.semanticweb.owlapi.model.OWLObjectProperty p,
                                                                String tag,
                                                                Clause clause)

Tr typedef clause.

Parameters:

p - the p

tag - the tag

clause - the clause

Returns:

the oWL axiom

trGenericClause

protected org.semanticweb.owlapi.model.OWLAxiom trGenericClause(org.semanticweb.owlapi.model.OWLNamedObject e,
                                                                String tag,
                                                                Clause clause)

Tr generic clause.

Parameters:

e - the e

tag - the tag

clause - the clause

Returns:

the oWL axiom

trGenericClause

protected org.semanticweb.owlapi.model.OWLAxiom trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub,
                                                                String tag,
                                                                Clause clause)

Tr generic clause.

Parameters:

sub - the sub

tag - the tag

clause - the clause

Returns:

the oWL axiom

trSynonymType

protected org.semanticweb.owlapi.model.OWLAnnotationProperty trSynonymType(String type)

Tr synonym type.

Parameters:

type - the type

Returns:

the oWL annotation property

trAnnotations

protected Set<org.semanticweb.owlapi.model.OWLAnnotation> trAnnotations(Clause clause)

Tr annotations.

Parameters:

clause - the clause

Returns:

the sets the

trAnnotations

protected void trAnnotations(Clause clause,
                             Set<org.semanticweb.owlapi.model.OWLAnnotation> anns)

Tr annotations.

Parameters:

clause - the clause

anns - the anns

trAnnotations

protected Set<? extends org.semanticweb.owlapi.model.OWLAnnotation> trAnnotations(Collection<Clause> clauses)

Tr annotations.

Parameters:

clauses - the clauses

Returns:

the set of annotations

trRel

public org.semanticweb.owlapi.model.OWLClassExpression trRel(String relId,
                                                             String classId,
                                                             Collection<QualifierValue> quals)

Tr rel.

Parameters:

relId - the rel id

classId - the class id

quals - the quals

Returns:

the oWL class expression

getQVString

protected static String getQVString(String q,
                                    Collection<QualifierValue> quals)

Gets the qV string.

Parameters:

q - the q

quals - the quals

Returns:

the qV string

getQVBoolean

protected static boolean getQVBoolean(String q,
                                      Collection<QualifierValue> quals)

Gets the qV boolean.

Parameters:

q - the q

quals - the quals

Returns:

the qV boolean

getQVInt

protected static Integer getQVInt(String q,
                                  Collection<QualifierValue> quals)

Gets the qV int.

Parameters:

q - the q

quals - the quals

Returns:

the qV int

trClass

protected org.semanticweb.owlapi.model.OWLClass trClass(String classId)

Tr class.

Parameters:

classId - the class id

Returns:

the oWL class

trClass

protected org.semanticweb.owlapi.model.OWLClassExpression trClass(Object v)

Tr class.

Parameters:

v - the v

Returns:

the oWL class expression

mapPropId

protected String mapPropId(String id)

See section "header macros" and treat-xrefs-as-equivalent.

Parameters:

id - the id

Returns:

mapped id

getIdPrefix

protected static String getIdPrefix(String x)

Gets the id prefix.

Parameters:

x - the x

Returns:

the id prefix

trIndividual

protected org.semanticweb.owlapi.model.OWLIndividual trIndividual(String instId)

Tr individual.

Parameters:

instId - the inst id

Returns:

the oWL individual

trTagToIRI

public static org.semanticweb.owlapi.model.IRI trTagToIRI(String tag)

Tr tag to iri.

Parameters:

tag - the tag

Returns:

the iri

trTagToAnnotationProp

protected org.semanticweb.owlapi.model.OWLAnnotationProperty trTagToAnnotationProp(String tag)

Tr tag to annotation prop.

Parameters:

tag - the tag

Returns:

the oWL annotation property

addDeclaredAnnotationProperties

protected void addDeclaredAnnotationProperties(Collection<org.semanticweb.owlapi.model.OWLAnnotationProperty> declaredProperties)

Adds the declared annotation properties.

Parameters:

declaredProperties - the declared properties

trAnnotationProp

protected org.semanticweb.owlapi.model.OWLAnnotationProperty trAnnotationProp(String relId)

Tr annotation prop.

Parameters:

relId - the rel id

Returns:

the oWL annotation property

trObjectProp

protected org.semanticweb.owlapi.model.OWLObjectProperty trObjectProp(String relId)

Tr object prop.

Parameters:

relId - the rel id

Returns:

the oWL object property

trObjectProp

protected org.semanticweb.owlapi.model.OWLObjectPropertyExpression trObjectProp(Object v)

Tr object prop.

Parameters:

v - the v

Returns:

the oWL object property expression

trLiteral

protected org.semanticweb.owlapi.model.OWLAnnotationValue trLiteral(Object inputValue)

Tr literal.

Parameters:

inputValue - the value

Returns:

the oWL annotation value

oboIdToIRI

public org.semanticweb.owlapi.model.IRI oboIdToIRI(String id)

Obo id to iri.

Parameters:

id - the id

Returns:

the iri

translateShorthandIdToExpandedId

protected String translateShorthandIdToExpandedId(String id)

Translate shorthand id to expanded id.

Parameters:

id - the id

Returns:

the string

getDefaultIDSpace

protected String getDefaultIDSpace()

Gets the default id space.

Returns:

the default id space