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,IRI>	ANNOTATIONPROPERTYMAP The annotation property map.
static String	IRI_PROP_ISREVERSIBLEPROPERTYCHAIN The Constant IRI_PROP_isReversiblePropertyChain.

Constructor Summary

Constructors

Constructor and Description
OWLAPIObo2Owl(OWLOntologyManager manager)

Method Summary

Modifier and Type	Method and Description
OWLOntology	convert(OBODoc doc) Convert.
OWLOntology	convert(OBODoc doc, OWLOntology in) Convert.
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, 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, OWLOntologyManager manager) See.
OWLOntologyManager	getManager() Gets the manager.
OBODoc	getObodoc() Gets the obodoc.
IRI	oboIdToIRI_load(String id) Obo id to iri.
IRI	oboIdToIRI(String id) Obo id to iri.
void	setManager(OWLOntologyManager manager) Sets the manager.
void	setObodoc(OBODoc obodoc) Sets the obodoc.
void	trHeaderFrame(Frame headerFrame) Translate header frame.
OWLClassExpression	trRel(String relId, String classId, Collection<QualifierValue> quals) Translate rel.
static IRI	trTagToIRI(String tag) Translate tag to iri.
OWLClassExpression	trTermFrame(Frame termFrame) Translate term frame.
Set<OWLAxiom>	trTermFrameClauses(OWLClass cls, Collection<Clause> clauses, String t) Translate term frame clauses.
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,IRI> ANNOTATIONPROPERTYMAP

The annotation property map.

Constructor Detail

OWLAPIObo2Owl

public OWLAPIObo2Owl(OWLOntologyManager manager)

Parameters:

manager - the manager

Method Detail

convertURL

public static void convertURL(@Nonnull
                              String iri,
                              @Nonnull
                              String outFile,
                              @Nonnull
                              OWLOntologyManager manager)
                       throws IOException,
                              OWLOntologyCreationException,
                              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.

OWLOntologyCreationException - the OWL ontology creation exception

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
                              OWLOntologyManager manager)
                       throws IOException,
                              OWLOntologyCreationException,
                              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.

OWLOntologyCreationException - the OWL ontology creation exception

OWLOntologyStorageException - the OWL ontology storage exception

OBOFormatParserException - the OBO format parser exception convertURL(String iri, String outFile, OWLOntologyManager manager)

getManager

public OWLOntologyManager getManager()

Gets the manager.

Returns:

the manager

setManager

public void setManager(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 OWLOntology convert(@Nonnull
                           String oboFile)
                    throws 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:

OWLOntologyCreationException - the OWL ontology creation exception

convert

@Nonnull
public OWLOntology convert(OBODoc doc)
                             throws OWLOntologyCreationException

Convert.

Parameters:

doc - the obodoc

Returns:

ontology

Throws:

OWLOntologyCreationException - the OWL ontology creation exception

convert

public OWLOntology convert(OBODoc doc,
                           @Nonnull
                           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 OWLClassExpression trTermFrame(@Nonnull
                                      Frame termFrame)

Translate term frame.

Parameters:

termFrame - the term frame

Returns:

the OWL class expression

trTermFrameClauses

@Nonnull
public Set<OWLAxiom> trTermFrameClauses(@Nonnull
                                                 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 OWLNamedObject trTypedefFrame(@Nonnull
                                               Frame typedefFrame)

Translate typedef frame.

Parameters:

typedefFrame - the typedef frame

Returns:

the OWL named object

trRel

public 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 IRI trTagToIRI(String tag)

Translate tag to iri.

Parameters:

tag - the tag

Returns:

the iri

oboIdToIRI

@Nonnull
public IRI oboIdToIRI(@Nonnull
                               String id)

Obo id to iri.

Parameters:

id - the id

Returns:

the iri

oboIdToIRI_load

@Nonnull
public IRI oboIdToIRI_load(@Nonnull
                                    String id)

Obo id to iri.

Parameters:

id - the id

Returns:

the iri