org.obolibrary.obo2owl

Class OWLAPIObo2Owl

java.lang.Object

org.obolibrary.obo2owl.OWLAPIObo2Owl

public class OWLAPIObo2Owl
extends Object

OWLAPI version of Obo2Owl

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,org.semanticweb.owlapi.model.IRI>	annotationPropertyMap
protected Set<org.semanticweb.owlapi.model.OWLAnnotationProperty>	apToDeclare
protected Map<String,org.semanticweb.owlapi.model.OWLClass>	clsToDeclar
protected String	defaultIDSpace
protected org.semanticweb.owlapi.model.OWLDataFactory	fac
protected Map<String,String>	idSpaceMap
static String	IRI_PROP_isReversiblePropertyChain reversible property chain iri
protected org.semanticweb.owlapi.model.OWLOntologyManager	manager
protected OBODoc	obodoc
protected org.semanticweb.owlapi.model.OWLOntology	owlOntology
protected Map<String,org.semanticweb.owlapi.model.OWLAnnotationProperty>	typedefToAnnotationProperty

Constructor Summary

Constructors

Constructor and Description
OWLAPIObo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)

Method Summary

Modifier and Type	Method and Description
protected void	add(org.semanticweb.owlapi.model.OWLAxiom axiom)
protected void	add(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms)
protected void	addDeclaredAnnotationProperties(Collection<org.semanticweb.owlapi.model.OWLAnnotationProperty> declaredProperties)
protected void	addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap, org.semanticweb.owlapi.model.OWLAnnotationValue v, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
protected void	addPropertyValueHeaders(Collection<Clause> clauses)
protected void	apply(List<org.semanticweb.owlapi.model.OWLOntologyChange> changes)
protected void	apply(org.semanticweb.owlapi.model.OWLOntologyChange change)
org.semanticweb.owlapi.model.OWLOntology	convert(OBODoc doc)
org.semanticweb.owlapi.model.OWLOntology	convert(OBODoc doc, org.semanticweb.owlapi.model.OWLOntology in)
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 convertURL(String iri, String outFile, OWLOntologyManager manager)
protected String	getDefaultIDSpace()
protected String	getIdPrefix(String x)
org.semanticweb.owlapi.model.OWLOntologyManager	getManager()
OBODoc	getObodoc()
protected org.semanticweb.owlapi.model.OWLOntology	getOwlOntology()
protected Boolean	getQVBoolean(String q, Collection<QualifierValue> quals)
protected Integer	getQVInt(String q, Collection<QualifierValue> quals)
protected String	getQVString(String q, Collection<QualifierValue> quals)
protected String	getURI(String path)
protected void	init(org.semanticweb.owlapi.model.OWLOntologyManager m)
protected static HashMap<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)
protected void	postProcess(org.semanticweb.owlapi.model.OWLOntology ontology) perform any necessary post-processing.
void	setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
void	setObodoc(OBODoc obodoc)
protected void	setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)
protected org.semanticweb.owlapi.model.OWLOntology	tr(org.semanticweb.owlapi.model.OWLOntology in)
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trAnnotationProp(String relId)
protected Set<org.semanticweb.owlapi.model.OWLAnnotation>	trAnnotations(Clause clause)
protected void	trAnnotations(Clause clause, Set<org.semanticweb.owlapi.model.OWLAnnotation> anns)
protected Set<? extends org.semanticweb.owlapi.model.OWLAnnotation>	trAnnotations(Collection<Clause> clauses)
protected String	translateShorthandIdToExpandedId(String id)
protected org.semanticweb.owlapi.model.OWLClassExpression	trClass(Object v)
protected org.semanticweb.owlapi.model.OWLClass	trClass(String classId)
protected org.semanticweb.owlapi.model.OWLAxiom	trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub, String tag, Clause clause)
protected org.semanticweb.owlapi.model.OWLAxiom	trGenericClause(org.semanticweb.owlapi.model.OWLNamedObject e, String tag, Clause clause)
void	trHeaderFrame(Frame headerFrame)
protected org.semanticweb.owlapi.model.OWLIndividual	trIndividual(String instId)
protected org.semanticweb.owlapi.model.OWLAxiom	trIntersectionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses)
protected org.semanticweb.owlapi.model.OWLAnnotationValue	trLiteral(Object value)
protected org.semanticweb.owlapi.model.OWLObjectPropertyExpression	trObjectProp(Object v)
protected org.semanticweb.owlapi.model.OWLObjectProperty	trObjectProp(String relId)
org.semanticweb.owlapi.model.OWLClassExpression	trRel(String relId, String classId, Collection<QualifierValue> quals)
protected org.semanticweb.owlapi.model.OWLAxiom	trRelationIntersectionOf(String id, org.semanticweb.owlapi.model.OWLProperty<?,?> p, Collection<Clause> clauses)
protected org.semanticweb.owlapi.model.OWLAxiom	trRelationUnionOf(String id, org.semanticweb.owlapi.model.OWLProperty<?,?> p, Collection<Clause> clauses)
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trSynonymType(String type)
protected org.semanticweb.owlapi.model.OWLAnnotationProperty	trTagToAnnotationProp(String tag)
static org.semanticweb.owlapi.model.IRI	trTagToIRI(String tag)
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)
Set<org.semanticweb.owlapi.model.OWLAxiom>	trTermFrameClauses(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses, String t)
protected org.semanticweb.owlapi.model.OWLAxiom	trTypedefClause(org.semanticweb.owlapi.model.OWLObjectProperty p, String tag, Clause clause)
org.semanticweb.owlapi.model.OWLNamedObject	trTypedefFrame(Frame typedefFrame)
protected org.semanticweb.owlapi.model.OWLNamedObject	trTypedefToAnnotationProperty(Frame typedefFrame)
protected org.semanticweb.owlapi.model.OWLAxiom	trUnionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses)

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

reversible property chain iri

See Also:

Constant Field Values

defaultIDSpace

protected String defaultIDSpace

manager

protected org.semanticweb.owlapi.model.OWLOntologyManager manager

owlOntology

protected org.semanticweb.owlapi.model.OWLOntology owlOntology

fac

protected org.semanticweb.owlapi.model.OWLDataFactory fac

obodoc

protected OBODoc obodoc

idSpaceMap

protected final Map<String,String> idSpaceMap

annotationPropertyMap

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

apToDeclare

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

clsToDeclar

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

typedefToAnnotationProperty

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

Constructor Detail

OWLAPIObo2Owl

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

Parameters:

manager - manager

Method Detail

init

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

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,
                              OBOFormatParserException

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 - iri

outFile - outFile

manager - manager to use

Throws:

IOException - IOException

org.semanticweb.owlapi.model.OWLOntologyCreationException - OWLOntologyCreationException

org.semanticweb.owlapi.model.OWLOntologyStorageException - OWLOntologyStorageException

OBOFormatParserException - OBOFormatParserException

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,
                              OBOFormatParserException

See convertURL(String iri, String outFile, OWLOntologyManager manager)

Parameters:

iri - iri

outFile - outFile

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

manager - the manager to be used

Throws:

IOException - IOException

org.semanticweb.owlapi.model.OWLOntologyCreationException - OWLOntologyCreationException

org.semanticweb.owlapi.model.OWLOntologyStorageException - OWLOntologyStorageException

OBOFormatParserException - OBOFormatParserException

initAnnotationPropertyMap

protected static HashMap<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()

Returns:

manager

setManager

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

Parameters:

manager - manager

getObodoc

public OBODoc getObodoc()

Returns:

obodoc

setObodoc

public void setObodoc(OBODoc obodoc)

Parameters:

obodoc - obodoc

getOwlOntology

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

Returns:

the owlOntology

setOwlOntology

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

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 - oboFile

Returns:

ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - OWLOntologyCreationException

convert

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

Parameters:

doc - obodoc

Returns:

ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - OWLOntologyCreationException

convert

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

Parameters:

doc - obodoc

in - in

Returns:

converted ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - OWLOntologyCreationException

tr

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

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

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 - ontology

getURI

protected String getURI(String path)

trHeaderFrame

public void trHeaderFrame(Frame headerFrame)

Parameters:

headerFrame - headerFrame

addPropertyValueHeaders

protected void addPropertyValueHeaders(Collection<Clause> clauses)

addOntologyAnnotation

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

trTermFrame

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

Parameters:

termFrame - termFrame

Returns:

term frame class

trTermFrameClauses

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

Parameters:

cls - cls

clauses - clauses

t - t

Returns:

term frame axioms

trTypedefToAnnotationProperty

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

trTypedefFrame

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

Parameters:

typedefFrame - typedefFrame

Returns:

typedef frame

trRelationUnionOf

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

trRelationIntersectionOf

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

trUnionOf

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

trIntersectionOf

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

add

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

add

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

apply

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

apply

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

trTermClause

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

#5.2

Parameters:

cls - cls

tag - tag

clause - clause

Returns:

axiom

trTypedefClause

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

trGenericClause

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

trGenericClause

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

trSynonymType

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

trAnnotations

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

trAnnotations

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

trAnnotations

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

trRel

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

Parameters:

relId - relId

classId - classId

quals - quals

Returns:

relation

getQVString

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

getQVBoolean

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

getQVInt

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

trClass

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

trClass

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

mapPropId

protected String mapPropId(String id)

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

Parameters:

id - id

Returns:

mapped id

getIdPrefix

protected String getIdPrefix(String x)

trIndividual

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

trTagToIRI

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

Parameters:

tag - tag

Returns:

iri for tag

trTagToAnnotationProp

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

addDeclaredAnnotationProperties

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

trAnnotationProp

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

trObjectProp

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

trObjectProp

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

trLiteral

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

oboIdToIRI

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

Parameters:

id - id

Returns:

iri for id

translateShorthandIdToExpandedId

protected String translateShorthandIdToExpandedId(String id)

getDefaultIDSpace

protected String getDefaultIDSpace()