|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.obolibrary.obo2owl.Obo2Owl
public class Obo2Owl
Field Summary | |
---|---|
static Map<String,org.semanticweb.owlapi.model.IRI> |
annotationPropertyMap
|
static boolean |
DEBUG
|
static String |
DEFAULT_IRI_PREFIX
Deprecated. |
static String |
IRI_PROP_isReversiblePropertyChain
|
Constructor Summary | |
---|---|
Obo2Owl()
|
|
Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
|
Method Summary | |
---|---|
protected void |
add(org.semanticweb.owlapi.model.OWLAxiom axiom)
|
protected void |
addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap,
org.semanticweb.owlapi.model.OWLAnnotationValue v)
|
protected void |
apply(org.semanticweb.owlapi.model.OWLOntologyChange change)
|
org.semanticweb.owlapi.model.OWLOntology |
convert(OBODoc obodoc)
Converts an OBO document to an OWL ontology |
org.semanticweb.owlapi.model.OWLOntology |
convert(OBODoc obodoc,
boolean useFreshManager)
|
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)
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)
See convertURL(String iri, String outFile) |
org.semanticweb.owlapi.model.OWLOntologyManager |
getManager()
|
OBODoc |
getObodoc()
|
protected org.semanticweb.owlapi.model.OWLOntology |
getOwlOntology()
|
org.semanticweb.owlapi.model.IRI |
oboIdToIRI(String id)
|
void |
setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
|
void |
setObodoc(OBODoc obodoc)
|
protected void |
setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)
|
protected org.semanticweb.owlapi.model.OWLAxiom |
trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub,
String tag,
Clause clause)
|
void |
trHeaderFrame(Frame headerFrame)
|
protected org.semanticweb.owlapi.model.OWLAnnotationValue |
trLiteral(Object value)
|
org.semanticweb.owlapi.model.OWLClassExpression |
trRel(String relId,
String classId,
Collection<QualifierValue> quals)
|
static org.semanticweb.owlapi.model.IRI |
trTagToIRI(String tag)
|
org.semanticweb.owlapi.model.OWLClassExpression |
trTermFrame(Frame termFrame)
|
org.semanticweb.owlapi.model.OWLNamedObject |
trTypedefFrame(Frame typedefFrame)
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final boolean DEBUG
@Deprecated public static final String DEFAULT_IRI_PREFIX
public static final String IRI_PROP_isReversiblePropertyChain
public static Map<String,org.semanticweb.owlapi.model.IRI> annotationPropertyMap
Constructor Detail |
---|
public Obo2Owl()
public Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
Method Detail |
---|
public static void convertURL(String iri, String outFile) throws IOException, org.semanticweb.owlapi.model.OWLOntologyCreationException, org.semanticweb.owlapi.model.OWLOntologyStorageException
iri
- outFile
-
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
public static void convertURL(String iri, String outFile, String defaultOnt) throws IOException, org.semanticweb.owlapi.model.OWLOntologyCreationException, org.semanticweb.owlapi.model.OWLOntologyStorageException
convertURL(String iri, String outFile)
iri
- outFile
- defaultOnt
- -- e.g. "go". If the obo file contains no "ontology:" header tag, this is added
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
public org.semanticweb.owlapi.model.OWLOntologyManager getManager()
public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
public OBODoc getObodoc()
public void setObodoc(OBODoc obodoc)
protected org.semanticweb.owlapi.model.OWLOntology getOwlOntology()
protected void setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)
owlOntology
- the owlOntology to setpublic org.semanticweb.owlapi.model.OWLOntology convert(String oboFile) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
oboFile
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc, boolean useFreshManager) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
obodoc
- useFreshManager
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
obodoc
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void trHeaderFrame(Frame headerFrame)
protected void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap, org.semanticweb.owlapi.model.OWLAnnotationValue v)
public org.semanticweb.owlapi.model.OWLClassExpression trTermFrame(Frame termFrame)
public org.semanticweb.owlapi.model.OWLNamedObject trTypedefFrame(Frame typedefFrame)
protected void add(org.semanticweb.owlapi.model.OWLAxiom axiom)
protected void apply(org.semanticweb.owlapi.model.OWLOntologyChange change)
protected org.semanticweb.owlapi.model.OWLAxiom trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub, String tag, Clause clause)
public org.semanticweb.owlapi.model.OWLClassExpression trRel(String relId, String classId, Collection<QualifierValue> quals)
public static org.semanticweb.owlapi.model.IRI trTagToIRI(String tag)
protected org.semanticweb.owlapi.model.OWLAnnotationValue trLiteral(Object value)
public org.semanticweb.owlapi.model.IRI oboIdToIRI(String id)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |