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
static Map<String,String>	annotationPropertyMap annotation map

Constructor Summary

Constructors

Constructor and Description
OWLAPIOwl2Obo(OWLOntologyManager translationManager)

Method Summary

Modifier and Type	Method and Description
OBODoc	convert(OWLOntology ont)
static String	getDataVersion(OWLOntology ontology)
static String	getIdentifier(IRI iriId) See table 5.9.2.
static String	getIdentifier(IRI iriId, OWLOntology baseOntology)
String	getIdentifier(OWLObject obj)
static String	getIdentifierFromObject(OWLObject obj, OWLOntology ont) Retrieve the identifier for a given OWLObject.
static String	getIdentifierFromObject(OWLObject obj, OWLOntology ont, String defaultValue) Retrieve the identifier for a given OWLObject.
OWLOntologyManager	getManager()
OBODoc	getObodoc()
static String	getOntologyId(IRI iriObj)
static String	getOntologyId(OWLOntology ontology) if does not match this pattern, then retain original IRI
boolean	getStrictConversion()
Collection<OWLAxiom>	getUntranslatableAxioms()
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(OWLObject obj)
void	setDiscardUntranslatable(boolean discardUntranslatable)
void	setManager(OWLOntologyManager manager)
void	setObodoc(OBODoc obodoc)
void	setStrictConversion(boolean b)

Methods inherited from class java.lang.Object

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

Field Detail

annotationPropertyMap

public static Map<String,String> annotationPropertyMap

annotation map

Constructor Detail

OWLAPIOwl2Obo

public OWLAPIOwl2Obo(OWLOntologyManager translationManager)

Parameters:

translationManager - translationManager

Method Detail

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 OWLOntologyManager getManager()

Returns:

manager

setManager

public void setManager(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(OWLOntology ont)

Parameters:

ont - ont

Returns:

obo doc

getUntranslatableAxioms

public Collection<OWLAxiom> getUntranslatableAxioms()

Returns:

the untranslatableAxioms

getOntologyId

public static String getOntologyId(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(IRI iriObj)

Parameters:

iriObj - iriObj

Returns:

ontology id

getDataVersion

public static String getDataVersion(OWLOntology ontology)

Parameters:

ontology - ontology

Returns:

data version

getIdentifier

public String getIdentifier(OWLObject obj)

Parameters:

obj - obj

Returns:

identifier

getIdentifierFromObject

public static String getIdentifierFromObject(OWLObject obj,
                                             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(OWLObject obj,
                                             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(IRI iriId)

See table 5.9.2. Translation of identifiers

Parameters:

iriId - iriId

Returns:

obo identifier or null

getIdentifier

public static String getIdentifier(IRI iriId,
                                   OWLOntology baseOntology)

Parameters:

iriId - iriId

baseOntology - baseOntology

Returns:

identifier

owlObjectToTag

public static String owlObjectToTag(OWLObject obj)

Parameters:

obj - obj

Returns:

tag for object

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