org.obolibrary.obo2owl

Class OWLAPIOwl2Obo

java.lang.Object

org.obolibrary.obo2owl.OWLAPIOwl2Obo

public class OWLAPIOwl2Obo
extends Object

owlapi version of Owl2Obo

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	OWLAPIOwl2Obo.UntranslatableAxiomException untranslatable axiom exception

Field Summary

Fields

Modifier and Type	Field and Description
protected Pattern	absoulteURLPattern
static Map<String,String>	annotationPropertyMap annotation map
protected Set<org.semanticweb.owlapi.model.OWLAnnotationProperty>	apToDeclare
protected boolean	discardUntranslatable
protected org.semanticweb.owlapi.model.OWLDataFactory	fac
protected Map<String,String>	idSpaceMap
protected org.semanticweb.owlapi.model.OWLOntologyManager	manager
protected OBODoc	obodoc
protected String	ontologyId
protected org.semanticweb.owlapi.model.OWLOntology	owlOntology
protected boolean	strictConversion
protected Set<org.semanticweb.owlapi.model.OWLAxiom>	untranslatableAxioms

Constructor Summary

Constructors

Constructor and Description
OWLAPIOwl2Obo(org.semanticweb.owlapi.model.OWLOntologyManager translationManager)

Method Summary

Modifier and Type	Method and Description
protected void	add(Frame f)
protected void	addQualifiers(Clause c, Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers)
OBODoc	convert(org.semanticweb.owlapi.model.OWLOntology ont)
protected Clause	createRelationshipClauseWithCardinality(org.semanticweb.owlapi.model.OWLObjectCardinalityRestriction restriction, String fillerId, Set<QualifierValue> qvs, org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)
protected Clause	createRelationshipClauseWithRestrictions(org.semanticweb.owlapi.model.OWLQuantifiedObjectRestriction r, String fillerId, Set<QualifierValue> qvs, org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)
protected void	error(org.semanticweb.owlapi.model.OWLAxiom ax)
protected void	error(String message)
protected void	error(String message, org.semanticweb.owlapi.model.OWLAxiom ax)
static String	getDataVersion(org.semanticweb.owlapi.model.OWLOntology ontology)
static String	getIdentifier(org.semanticweb.owlapi.model.IRI iriId) See table 5.9.2.
static String	getIdentifier(org.semanticweb.owlapi.model.IRI iriId, org.semanticweb.owlapi.model.OWLOntology baseOntology)
String	getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)
static String	getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont) Retrieve the identifier for a given OWLObject.
static String	getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont, String defaultValue) Retrieve the identifier for a given OWLObject.
protected String	getIdentifierUsingBaseOntology(org.semanticweb.owlapi.model.IRI iriId)
org.semanticweb.owlapi.model.OWLOntologyManager	getManager()
OBODoc	getObodoc()
static String	getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)
static String	getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology) if does not match this pattern, then retain original IRI
boolean	getStrictConversion()
protected Frame	getTermFrame(org.semanticweb.owlapi.model.OWLClass entity)
protected Frame	getTypedefFrame(org.semanticweb.owlapi.model.OWLEntity entity)
Collection<org.semanticweb.owlapi.model.OWLAxiom>	getUntranslatableAxioms()
protected String	getValue(org.semanticweb.owlapi.model.OWLAnnotationValue annVal, String tag)
protected boolean	handleDuplicateClause(Frame frame, Clause clause) Handle a duplicate clause in a frame during translation.
protected void	handleSynonym(Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers, String scope, Clause clause, Set<org.semanticweb.owlapi.model.OWLAnnotation> unprocessedQualifiers)
protected void	init()
protected static HashMap<String,String>	initAnnotationPropertyMap()
boolean	isDiscardUntranslatable()
static List<Clause>	normalizeRelationshipClauses(List<Clause> clauses) Join clauses and its QualifierValue which have the same relationship type and target.
static String	owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)
protected void	preProcess()
void	setDiscardUntranslatable(boolean discardUntranslatable)
void	setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
void	setObodoc(OBODoc obodoc)
void	setStrictConversion(boolean b)
protected OBODoc	tr()
protected void	tr(org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom aanAx, Frame frame)
protected boolean	tr(org.semanticweb.owlapi.model.OWLAnnotationProperty prop, org.semanticweb.owlapi.model.OWLAnnotationValue annVal, Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers, Frame frame)
protected void	tr(org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLClassAssertionAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLDeclarationAxiom axiom)
protected void	tr(org.semanticweb.owlapi.model.OWLDisjointClassesAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLOntology ontology)
protected void	tr(org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom ax)
protected void	tr(org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom ax)
protected boolean	trGenericPropertyValue(org.semanticweb.owlapi.model.OWLAnnotationProperty prop, org.semanticweb.owlapi.model.OWLAnnotationValue annVal, Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers, Frame frame)
protected void	trNaryPropertyAxiom(org.semanticweb.owlapi.model.OWLNaryPropertyAxiom<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> ax, String tag)
protected boolean	trObjectProperty(org.semanticweb.owlapi.model.OWLObjectProperty prop, String tag, Boolean value, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
protected boolean	trObjectProperty(org.semanticweb.owlapi.model.OWLObjectProperty prop, String tag, String value, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

Methods inherited from class java.lang.Object

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

Field Detail

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

untranslatableAxioms

protected Set<org.semanticweb.owlapi.model.OWLAxiom> untranslatableAxioms

idSpaceMap

protected Map<String,String> idSpaceMap

annotationPropertyMap

public static Map<String,String> annotationPropertyMap

annotation map

apToDeclare

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

ontologyId

protected String ontologyId

strictConversion

protected boolean strictConversion

discardUntranslatable

protected boolean discardUntranslatable

absoulteURLPattern

protected Pattern absoulteURLPattern

Constructor Detail

OWLAPIOwl2Obo

public OWLAPIOwl2Obo(org.semanticweb.owlapi.model.OWLOntologyManager translationManager)

Parameters:

translationManager - translationManager

Method Detail

init

protected void init()

initAnnotationPropertyMap

protected static HashMap<String,String> initAnnotationPropertyMap()

setStrictConversion

public void setStrictConversion(boolean b)

Parameters:

b - strict conversion

getStrictConversion

public boolean getStrictConversion()

Returns:

strict conversion

isDiscardUntranslatable

public boolean isDiscardUntranslatable()

Returns:

the discardUntranslatable

setDiscardUntranslatable

public void setDiscardUntranslatable(boolean discardUntranslatable)

Parameters:

discardUntranslatable - the discardUntranslatable to set

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:

obo doc

setObodoc

public void setObodoc(OBODoc obodoc)

Parameters:

obodoc - obodoc

convert

public OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ont)

Parameters:

ont - ont

Returns:

obo doc

getUntranslatableAxioms

public Collection<org.semanticweb.owlapi.model.OWLAxiom> getUntranslatableAxioms()

Returns:

the untranslatableAxioms

tr

protected OBODoc tr()

Returns:

translated obodoc

preProcess

protected void preProcess()

add

protected void add(Frame f)

trObjectProperty

protected boolean trObjectProperty(org.semanticweb.owlapi.model.OWLObjectProperty prop,
                                   String tag,
                                   String value,
                                   Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

trObjectProperty

protected boolean trObjectProperty(org.semanticweb.owlapi.model.OWLObjectProperty prop,
                                   String tag,
                                   Boolean value,
                                   Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)

trNaryPropertyAxiom

protected void trNaryPropertyAxiom(org.semanticweb.owlapi.model.OWLNaryPropertyAxiom<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> ax,
                                   String tag)

tr

protected void tr(org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom aanAx,
                  Frame frame)

tr

protected boolean tr(org.semanticweb.owlapi.model.OWLAnnotationProperty prop,
                     org.semanticweb.owlapi.model.OWLAnnotationValue annVal,
                     Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers,
                     Frame frame)

handleSynonym

protected void handleSynonym(Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers,
                             String scope,
                             Clause clause,
                             Set<org.semanticweb.owlapi.model.OWLAnnotation> unprocessedQualifiers)

handleDuplicateClause

protected boolean handleDuplicateClause(Frame frame,
                                        Clause clause)

Handle a duplicate clause in a frame during translation.

Parameters:

frame - frame

clause - clause

Returns:

true if the clause is to be marked as redundant and will not be added to the

trGenericPropertyValue

protected boolean trGenericPropertyValue(org.semanticweb.owlapi.model.OWLAnnotationProperty prop,
                                         org.semanticweb.owlapi.model.OWLAnnotationValue annVal,
                                         Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers,
                                         Frame frame)

getValue

protected String getValue(org.semanticweb.owlapi.model.OWLAnnotationValue annVal,
                          String tag)

addQualifiers

protected void addQualifiers(Clause c,
                             Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers)

getOntologyId

public static String getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)

if does not match this pattern, then retain original IRI

Parameters:

ontology - ontology

Returns:

The OBO ID of the ontology

getOntologyId

public static String getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)

Parameters:

iriObj - iriObj

Returns:

ontology id

getDataVersion

public static String getDataVersion(org.semanticweb.owlapi.model.OWLOntology ontology)

Parameters:

ontology - ontology

Returns:

data version

tr

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

tr

protected void tr(org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLDisjointClassesAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLDeclarationAxiom axiom)

getIdentifier

public String getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)

Parameters:

obj - obj

Returns:

identifier

getIdentifierFromObject

public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                             org.semanticweb.owlapi.model.OWLOntology ont,
                                             String defaultValue)

Retrieve the identifier for a given OWLObject. This methods uses also shorthand hints to resolve the identifier. Should the translation process encounter a problem or not find an identifier the defaultValue is returned.

Parameters:

obj - the OWLObject to resolve

ont - the target ontology

defaultValue - the value to return in case of an error or no id

Returns:

identifier or the default value

getIdentifierFromObject

public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                             org.semanticweb.owlapi.model.OWLOntology ont)
                                      throws OWLAPIOwl2Obo.UntranslatableAxiomException

Retrieve the identifier for a given OWLObject. This methods uses also shorthand hints to resolve the identifier. Should the translation process encounter an unexpected axiom an OWLAPIOwl2Obo.UntranslatableAxiomException is thrown.

Parameters:

obj - the OWLObject to resolve

ont - the target ontology

Returns:

identifier or null

Throws:

OWLAPIOwl2Obo.UntranslatableAxiomException - UntranslatableAxiomException

getIdentifier

public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)

See table 5.9.2. Translation of identifiers

Parameters:

iriId - iriId

Returns:

obo identifier or null

getIdentifierUsingBaseOntology

protected String getIdentifierUsingBaseOntology(org.semanticweb.owlapi.model.IRI iriId)

getIdentifier

public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId,
                                   org.semanticweb.owlapi.model.OWLOntology baseOntology)

Parameters:

iriId - iriId

baseOntology - baseOntology

Returns:

identifier

owlObjectToTag

public static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)

Parameters:

obj - obj

Returns:

tag for object

getTermFrame

protected Frame getTermFrame(org.semanticweb.owlapi.model.OWLClass entity)

getTypedefFrame

protected Frame getTypedefFrame(org.semanticweb.owlapi.model.OWLEntity entity)

tr

protected void tr(org.semanticweb.owlapi.model.OWLClassAssertionAxiom ax)

tr

protected void tr(org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)

createRelationshipClauseWithRestrictions

protected Clause createRelationshipClauseWithRestrictions(org.semanticweb.owlapi.model.OWLQuantifiedObjectRestriction r,
                                                          String fillerId,
                                                          Set<QualifierValue> qvs,
                                                          org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)

createRelationshipClauseWithCardinality

protected Clause createRelationshipClauseWithCardinality(org.semanticweb.owlapi.model.OWLObjectCardinalityRestriction restriction,
                                                         String fillerId,
                                                         Set<QualifierValue> qvs,
                                                         org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)

normalizeRelationshipClauses

public static List<Clause> normalizeRelationshipClauses(List<Clause> clauses)

Join clauses and its QualifierValue which have the same relationship type and target. Try to resolve conflicts for multiple statements. E.g., min=2 and min=3 is resolved to min=2, or max=2 and max=4 is resolved to max=4. It will not merge conflicting exact cardinality statements. TODO How to merge "all_some", and "all_only"?

Parameters:

clauses - clauses

Returns:

normalized list of Clause

error

protected void error(String message,
                     org.semanticweb.owlapi.model.OWLAxiom ax)

error

protected void error(org.semanticweb.owlapi.model.OWLAxiom ax)

error

protected void error(String message)