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.
static String	IRI_PROP_ISREVERSIBLEPROPERTYCHAIN The Constant IRI_PROP_isReversiblePropertyChain.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
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.
org.semanticweb.owlapi.model.OWLOntologyManager	getManager() Gets the manager.
OBODoc	getObodoc() Gets the obodoc.
org.semanticweb.owlapi.model.IRI	oboIdToIRI_load(String id) Obo id to iri.
org.semanticweb.owlapi.model.IRI	oboIdToIRI(String id) Obo id to iri.
void	setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager) Sets the manager.
void	setObodoc(OBODoc obodoc) Sets the obodoc.
void	trHeaderFrame(Frame headerFrame) Translate header frame.
org.semanticweb.owlapi.model.OWLClassExpression	trRel(String relId, String classId, Collection<QualifierValue> quals) Translate rel.
static org.semanticweb.owlapi.model.IRI	trTagToIRI(String tag) Translate tag to iri.
org.semanticweb.owlapi.model.OWLClassExpression	trTermFrame(Frame termFrame) Translate term frame.
Set<org.semanticweb.owlapi.model.OWLAxiom>	trTermFrameClauses(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses, String t) Translate term frame clauses.
org.semanticweb.owlapi.model.OWLNamedObject	trTypedefFrame(Frame typedefFrame) Translate typedef frame.

Methods inherited from class java.lang.Object

equals, 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

ANNOTATIONPROPERTYMAP

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

The annotation property map.

Constructor Detail

OWLAPIObo2Owl

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

Parameters:

manager - the manager

Method Detail

convertURL

public static void convertURL(@Nonnull
                              String iri,
                              @Nonnull
                              String outFile,
                              @Nonnull
                              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,
                              @Nonnull
                              String outFile,
                              String defaultOnt,
                              @Nonnull
                              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)

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

convert

public org.semanticweb.owlapi.model.OWLOntology convert(@Nonnull
                                                        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

@Nonnull
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,
                                                        @Nonnull
                                                        org.semanticweb.owlapi.model.OWLOntology in)

Convert.

Parameters:

doc - the obodoc

in - the in

Returns:

the OWL ontology

trHeaderFrame

public void trHeaderFrame(@Nonnull
                          Frame headerFrame)

Translate header frame.

Parameters:

headerFrame - the header frame

trTermFrame

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

Translate term frame.

Parameters:

termFrame - the term frame

Returns:

the OWL class expression

trTermFrameClauses

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

Translate term frame clauses.

Parameters:

cls - the cls

clauses - the clauses

t - the t

Returns:

the sets the

trTypedefFrame

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

Translate typedef frame.

Parameters:

typedefFrame - the typedef frame

Returns:

the OWL named object

trRel

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

Translate rel.

Parameters:

relId - the rel id

classId - the class id

quals - the quals

Returns:

the OWL class expression

trTagToIRI

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

Translate tag to iri.

Parameters:

tag - the tag

Returns:

the iri

oboIdToIRI

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

Obo id to iri.

Parameters:

id - the id

Returns:

the iri

oboIdToIRI_load

@Nonnull
public org.semanticweb.owlapi.model.IRI oboIdToIRI_load(@Nonnull
                                                                 String id)

Obo id to iri.

Parameters:

id - the id

Returns:

the iri