public class OWLConverter extends Object
Modifier and Type | Field and Description |
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protected static org.semanticweb.owlapi.formats.RDFXMLDocumentFormat |
format
Create OWLAPI utilities: An ontology format.
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protected static String |
IAO
Define the base IRI for Information Artifact Ontology (IAO) terms.
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protected static org.apache.log4j.Logger |
logger
Create a logger.
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protected static String |
NCBI
Define the base IRI for NCBI Taxonomy terms.
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protected static String |
OBO
Define the base IRI for Open Biomedical Ontologies (OBO).
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protected static String |
OIO
Define the base IRI for OboInOwl terms.
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Constructor and Description |
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OWLConverter() |
Modifier and Type | Method and Description |
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protected static OWLAnnotationAssertionAxiom |
annotate(OWLOntology ontology,
OWLEntity subject,
OWLAnnotationProperty property,
OWLAnnotationValue value)
Convenience method for adding an annotation assertion to the
ontology.
|
protected static OWLAnnotationAssertionAxiom |
annotate(OWLOntology ontology,
OWLEntity subject,
String propertyCURIE,
boolean value)
Convenience method for adding an annotation assertion to the
ontology, taking a CURIE for the property and an Boolean literal.
|
protected static OWLAnnotationAssertionAxiom |
annotate(OWLOntology ontology,
OWLEntity subject,
String propertyCURIE,
OWLAnnotationValue value)
Convenience method for adding an annotation assertion to the
ontology, taking a CURIE for the property.
|
protected static OWLAnnotationAssertionAxiom |
annotate(OWLOntology ontology,
OWLEntity subject,
String propertyCURIE,
String value)
Convenience method for adding an annotation assertion to the
ontology, taking a CURIE for the property and a string literal.
|
protected static OWLAnnotation |
annotate(OWLOntology ontology,
String propertyCURIE,
IRI value)
Convenience method for adding an annotation assertion to the
ontology itself, taking a CURIE for the property and an Boolean literal.
|
protected static OWLAnnotation |
annotate(OWLOntology ontology,
String propertyCURIE,
String value)
Convenience method for adding an annotation assertion to the
ontology itself, taking a CURIE for the property and an Boolean literal.
|
protected static OWLSubAnnotationPropertyOfAxiom |
assertSubAnnotationProperty(OWLOntology ontology,
OWLAnnotationProperty child,
OWLAnnotationProperty parent)
Convenience method for asserting a subAnnotationProperty relation
between a parent and child property in an ontology.
|
protected static OWLSubClassOfAxiom |
assertSubClass(OWLOntology ontology,
OWLClass child,
OWLClass parent)
Convenience method for asserting a subClass relation between
a parent and child class in an ontology.
|
protected static OWLAnnotationProperty |
createAnnotationProperty(OWLOntology ontology,
IRI iri)
Create an annotation property and add it to the ontology.
|
protected static OWLAnnotationProperty |
createAnnotationProperty(OWLOntology ontology,
org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary term)
Convenience method for adding and labelling OboInOwl annotation
properties with its rdfs:label.
|
protected static OWLAnnotationProperty |
createAnnotationProperty(OWLOntology ontology,
String curie)
Convenience method taking a string CURIE instead of an IRI.
|
protected static OWLDeclarationAxiom |
declare(OWLOntology ontology,
OWLEntity subject)
Convenience method for adding a declaration axiom to the ontology.
|
protected static String |
getFirstLiteral(OWLOntology ontology,
OWLEntity subject,
IRI propertyIRI)
Convenience method to get the first string literal of an
annotation property.
|
protected static String |
getFirstLiteral(OWLOntology ontology,
OWLEntity taxon,
OWLAnnotationProperty property)
Convenience method to get the first string literal of an
annotation property.
|
protected static String |
getFirstLiteral(OWLOntology ontology,
OWLEntity subject,
String propertyCURIE)
Convenience method to get the first string literal of an
annotation property.
|
protected static org.semanticweb.owlapi.formats.RDFXMLDocumentFormat |
initializeFormat()
Initialize the format with standard default prefixes
(rdf, rdfs, xsd, owl) and with the prefixes we will use
(obo, oio, iao).
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protected static String |
reformatName(String name)
Reformat names for use in IRIs.
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protected static OWLAnnotationAssertionAxiom |
synonym(OWLOntology ontology,
OWLEntity subject,
OWLAnnotationValue type,
OWLAnnotationProperty property,
OWLAnnotationValue value)
Add an synonym annotation, plus an annotation on that annotation
that specified the type of synonym.
|
protected static OWLAnnotationAssertionAxiom |
synonym(OWLOntology ontology,
OWLEntity subject,
String typeCURIE,
String propertyCURIE,
String value)
Add an synonym annotation, plus an annotation on that annotation
that specified the type of synonym.
|
protected static OWLAnnotationAssertionAxiom |
updateAnnotation(OWLOntology ontology,
OWLEntity subject,
String propertyCURIE,
String value) |
protected static final String OBO
protected static final String OIO
protected static final String IAO
protected static final String NCBI
protected static final org.apache.log4j.Logger logger
protected static org.semanticweb.owlapi.formats.RDFXMLDocumentFormat format
protected static org.semanticweb.owlapi.formats.RDFXMLDocumentFormat initializeFormat()
protected static String reformatName(String name)
name
- the string to reformatprotected static OWLAnnotationProperty createAnnotationProperty(OWLOntology ontology, IRI iri)
ontology
- the current ontologyiri
- the IRI for the annotation propertyprotected static OWLAnnotationProperty createAnnotationProperty(OWLOntology ontology, String curie)
ontology
- the current ontologycurie
- will be expanded using the format.getIRI methodprotected static OWLAnnotationProperty createAnnotationProperty(OWLOntology ontology, org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary term)
ontology
- the current ontologyterm
- the Obo2Owl term to useObo2OWLConstants.Obo2OWLVocabulary
protected static OWLDeclarationAxiom declare(OWLOntology ontology, OWLEntity subject)
ontology
- the current ontologysubject
- the entity for which the declaration will be addedprotected static OWLAnnotationAssertionAxiom annotate(OWLOntology ontology, OWLEntity subject, OWLAnnotationProperty property, OWLAnnotationValue value)
ontology
- the current ontologysubject
- the subject of the annotationproperty
- the annotation propertyvalue
- the annotation valueprotected static OWLAnnotationAssertionAxiom annotate(OWLOntology ontology, OWLEntity subject, String propertyCURIE, OWLAnnotationValue value)
ontology
- the current ontologysubject
- the subject of the annotationpropertyCURIE
- will be expanded to the full annotation
property IRIvalue
- the annotation valueprotected static OWLAnnotationAssertionAxiom annotate(OWLOntology ontology, OWLEntity subject, String propertyCURIE, String value)
ontology
- the current ontologysubject
- the subject of the annotationpropertyCURIE
- will be expanded to the full annotation
property IRIvalue
- the literal value of the annotationprotected static OWLAnnotationAssertionAxiom annotate(OWLOntology ontology, OWLEntity subject, String propertyCURIE, boolean value)
ontology
- the current ontologysubject
- the subject of the annotationpropertyCURIE
- will be expanded to the full annotation
property IRIvalue
- the literal value of the annotationprotected static OWLAnnotation annotate(OWLOntology ontology, String propertyCURIE, IRI value)
ontology
- the current ontologypropertyCURIE
- will be expanded to the full annotation
property IRIvalue
- the literal value of the annotationprotected static OWLAnnotation annotate(OWLOntology ontology, String propertyCURIE, String value)
ontology
- the current ontologypropertyCURIE
- will be expanded to the full annotation
property IRIvalue
- the literal value of the annotationprotected static OWLAnnotationAssertionAxiom updateAnnotation(OWLOntology ontology, OWLEntity subject, String propertyCURIE, String value)
protected static OWLAnnotationAssertionAxiom synonym(OWLOntology ontology, OWLEntity subject, OWLAnnotationValue type, OWLAnnotationProperty property, OWLAnnotationValue value)
ontology
- the current ontologysubject
- the subject of the annotationtype
- the IRI of the type of synonymproperty
- the IRI of the annotation property.value
- the literal value of the synonymprotected static OWLAnnotationAssertionAxiom synonym(OWLOntology ontology, OWLEntity subject, String typeCURIE, String propertyCURIE, String value)
ontology
- the current ontologysubject
- the subject of the annotationtypeCURIE
- a CURIE string for the type of synonympropertyCURIE
- a CURIE string for the propertyvalue
- the string value of the synonymprotected static OWLSubClassOfAxiom assertSubClass(OWLOntology ontology, OWLClass child, OWLClass parent)
ontology
- the current ontologychild
- the child classparent
- the parent classprotected static OWLSubAnnotationPropertyOfAxiom assertSubAnnotationProperty(OWLOntology ontology, OWLAnnotationProperty child, OWLAnnotationProperty parent)
ontology
- the current ontologychild
- the child propertyparent
- the parent propertyprotected static String getFirstLiteral(OWLOntology ontology, OWLEntity taxon, OWLAnnotationProperty property)
ontology
- the current ontologytaxon
- the subjectproperty
- the propertyprotected static String getFirstLiteral(OWLOntology ontology, OWLEntity subject, IRI propertyIRI)
ontology
- the current ontologysubject
- the subjectpropertyIRI
- the property IRIprotected static String getFirstLiteral(OWLOntology ontology, OWLEntity subject, String propertyCURIE)
ontology
- the current ontologysubject
- the subjectpropertyCURIE
- the property CURIECopyright © 2010–2016. All rights reserved.