org.obolibrary.obo2owl

Class OWLAPIOwl2Obo

java.lang.Object

org.obolibrary.obo2owl.OWLAPIOwl2Obo

public class OWLAPIOwl2Obo
extends Object

The Class OWLAPIOwl2Obo.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	OWLAPIOwl2Obo.UntranslatableAxiomException The Class UntranslatableAxiomException.

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,String>	ANNOTATIONPROPERTYMAP The annotation property map.

Constructor Summary

Constructors

Constructor and Description
OWLAPIOwl2Obo(org.semanticweb.owlapi.model.OWLOntologyManager translationManager) Instantiates a new OWLAPI owl2 obo.

Method Summary

Modifier and Type	Method and Description
OBODoc	convert(org.semanticweb.owlapi.model.OWLOntology ont) Convert.
static String	getDataVersion(org.semanticweb.owlapi.model.OWLOntology ontology) Gets the data version.
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.PrefixManager pm) See table 5.9.2.
String	getIdentifier(org.semanticweb.owlapi.model.OWLObject obj) Gets the identifier.
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, org.semanticweb.owlapi.model.PrefixManager pm) 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.
org.semanticweb.owlapi.model.OWLOntologyManager	getManager() Gets the manager.
OBODoc	getObodoc() Gets the obodoc.
static String	getOntologyId(org.semanticweb.owlapi.model.IRI iriObj) Gets the ontology id.
static String	getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology) E.g.
boolean	getStrictConversion() Gets the strict conversion.
Collection<org.semanticweb.owlapi.model.OWLAxiom>	getUntranslatableAxioms() Gets the untranslatable axioms.
boolean	isDiscardUntranslatable() Checks if is discard untranslatable.
boolean	isMuteUntranslatableAxioms()
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) Owl object to tag.
static String	owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.PrefixManager pm) Owl object to tag.
void	setDiscardUntranslatable(boolean discardUntranslatable) Sets the discard untranslatable.
void	setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager) Sets the manager.
void	setMuteUntranslatableAxioms(boolean muteUntranslatableAxioms)
void	setObodoc(OBODoc obodoc) Sets the obodoc.
void	setPrefixManager(org.semanticweb.owlapi.model.PrefixManager manager)
void	setStrictConversion(boolean b) Sets the strict conversion.

Methods inherited from class java.lang.Object

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

Field Detail

ANNOTATIONPROPERTYMAP

@Nonnull
public static final Map<String,String> ANNOTATIONPROPERTYMAP

The annotation property map.

Constructor Detail

OWLAPIOwl2Obo

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

Instantiates a new OWLAPI owl2 obo.

Parameters:

translationManager - the translation manager

Method Detail

setStrictConversion

public void setStrictConversion(boolean b)

Sets the strict conversion.

Parameters:

b - the new strict conversion

getStrictConversion

public boolean getStrictConversion()

Gets the strict conversion.

Returns:

the strict conversion

isDiscardUntranslatable

public boolean isDiscardUntranslatable()

Checks if is discard untranslatable.

Returns:

the discard untranslatable flag

setDiscardUntranslatable

public void setDiscardUntranslatable(boolean discardUntranslatable)

Sets the discard untranslatable.

Parameters:

discardUntranslatable - the value for discard untranslatable to set

getManager

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

Gets the manager.

Returns:

the manager

setManager

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

Sets the manager.

Parameters:

manager - the new manager

getObodoc

@Nonnull
public OBODoc getObodoc()

Gets the obodoc.

Returns:

the obodoc

setObodoc

public void setObodoc(@Nonnull
                      OBODoc obodoc)

Sets the obodoc.

Parameters:

obodoc - the new obodoc

setPrefixManager

public void setPrefixManager(@Nonnull
                             org.semanticweb.owlapi.model.PrefixManager manager)

convert

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

Convert.

Parameters:

ont - the ontology

Returns:

the OBO doc

getUntranslatableAxioms

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

Gets the untranslatable axioms.

Returns:

the untranslatable axioms

getOntologyId

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

E.g. http://purl.obolibrary.org/obo/go.owl to "go"
if does not match this pattern, then retain original IRI

Parameters:

ontology - the ontology

Returns:

The OBO ID of the ontology

getOntologyId

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

Gets the ontology id.

Parameters:

iriObj - the iri

Returns:

the ontology id

getDataVersion

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

Gets the data version.

Parameters:

ontology - the ontology

Returns:

the data version

getIdentifier

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

Gets the identifier.

Parameters:

obj - the object

Returns:

the identifier

isMuteUntranslatableAxioms

public boolean isMuteUntranslatableAxioms()

Returns:

true if untranslatable axioms should not be logged

setMuteUntranslatableAxioms

public void setMuteUntranslatableAxioms(boolean muteUntranslatableAxioms)

Parameters:

muteUntranslatableAxioms - true disables logging

getIdentifierFromObject

@Nonnull
public static String getIdentifierFromObject(@Nonnull
                                                      org.semanticweb.owlapi.model.OWLObject obj,
                                                      @Nonnull
                                                      org.semanticweb.owlapi.model.OWLOntology ont,
                                                      @Nonnull
                                                      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

@Nullable
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                                       @Nonnull
                                                       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

Parameters:

obj - the OWLObject to resolve

ont - the target ontology

Returns:

identifier or null

Throws:

OWLAPIOwl2Obo.UntranslatableAxiomException - the untranslatable axiom exception OWLAPIOwl2Obo.UntranslatableAxiomException is thrown.

getIdentifierFromObject

@Nullable
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                                       @Nonnull
                                                       org.semanticweb.owlapi.model.OWLOntology ont,
                                                       @Nonnull
                                                       org.semanticweb.owlapi.model.PrefixManager pm)
                                                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

Parameters:

obj - the OWLObject to resolve

ont - the target ontology

pm - PrefixManager to pass through for IRI compaction

Returns:

identifier or null

Throws:

OWLAPIOwl2Obo.UntranslatableAxiomException - the untranslatable axiom exception OWLAPIOwl2Obo.UntranslatableAxiomException is thrown.

getIdentifier

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

See table 5.9.2. Translation of identifiers

Parameters:

iriId - the iri id

Returns:

obo identifier or null

getIdentifier

@Nullable
public static String getIdentifier(@Nullable
                                             org.semanticweb.owlapi.model.IRI iriId,
                                             @Nonnull
                                             org.semanticweb.owlapi.model.PrefixManager pm)

See table 5.9.2. Translation of identifiers

Parameters:

iriId - the iri id

pm - PrefixManager to pass through for IRI compaction

Returns:

obo identifier or null

owlObjectToTag

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

Owl object to tag.

Parameters:

obj - the object

Returns:

the string

owlObjectToTag

@Nullable
public static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj,
                                              @Nonnull
                                              org.semanticweb.owlapi.model.PrefixManager pm)

Owl object to tag.

Parameters:

obj - the object

pm - PrefixManager to pass through for IRI compaction

Returns:

the string

normalizeRelationshipClauses

@Nonnull
public static List<Clause> normalizeRelationshipClauses(@Nonnull
                                                                 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 - the clauses

Returns:

normalized list of Clause