public class NCBIOWL extends NCBIConverter
Modifier and Type | Field and Description |
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protected static OWLDataFactory |
dataFactory
Create OWLAPI utilities: A data factory.
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protected static org.apache.log4j.Logger |
logger
Create a logger.
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protected static OWLOntologyManager |
manager
Create OWLAPI utilities: An ontology manager.
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static HashSet<String> |
ranks
Names of the NCBI ranks.
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static HashMap<String,String> |
synonymTypes
A map from NCBI synonym types to OboInOwl annotation properties.
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Constructor and Description |
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NCBIOWL() |
Modifier and Type | Method and Description |
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static void |
addAltId(OWLOntology ontology,
String merged,
String altId,
OWLAnnotationProperty ap)
Add an alternative identifier for a main term.
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static OWLOntology |
createOWLOntology()
Create and initialize the ontology.
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static OWLOntology |
loadOWLOntology(File inputFile)
Load an ontology from a file.
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static OWLAnnotationProperty |
setupAltIdProperty(OWLOntology ontology)
Setup the alternative identifier annotation property.
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assertSubClass, checkTaxon, createNCBIIRI, createNCBIIRI, createTaxon, getTaxonID
annotate, annotate, annotate, annotate, annotate, annotate, assertSubAnnotationProperty, assertSubClass, createAnnotationProperty, createAnnotationProperty, createAnnotationProperty, declare, getFirstLiteral, getFirstLiteral, getFirstLiteral, initializeFormat, reformatName, synonym, synonym, updateAnnotation
protected static final org.apache.log4j.Logger logger
protected static final OWLDataFactory dataFactory
protected static final OWLOntologyManager manager
public static OWLOntology createOWLOntology() throws OWLOntologyCreationException
OWLOntologyCreationException
Obo2OWLConstants.Obo2OWLVocabulary
public static OWLAnnotationProperty setupAltIdProperty(OWLOntology ontology)
ontology
- addAltId(OWLOntology, String, String, OWLAnnotationProperty)
public static void addAltId(OWLOntology ontology, String merged, String altId, OWLAnnotationProperty ap)
ontology
- merged
- the main termaltId
- the alternate id to be addedap
- annotation property as generated by the setup methodsetupAltIdProperty(OWLOntology)
public static OWLOntology loadOWLOntology(File inputFile) throws OWLOntologyCreationException
inputFile
- the path to the OWL fileOWLOntologyCreationException
- if the ontology can't be loadedCopyright © 2010–2016. All rights reserved.