public class NCBIConverter extends OWLConverter
Modifier and Type | Field and Description |
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protected static org.apache.log4j.Logger |
logger
Create a logger.
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Constructor and Description |
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NCBIConverter() |
Modifier and Type | Method and Description |
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protected static OWLSubClassOfAxiom |
assertSubClass(OWLOntology ontology,
OWLClass child,
String parentID)
Convenience method for asserting a subClass relation between
a parent and child class in an ontology.
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static Boolean |
checkTaxon(OWLOntology ontology,
OWLClass taxon)
Check to make sure that this taxon has the required properties.
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protected static IRI |
createNCBIIRI(int id)
Create an NCBI taxon IRI from an NCBI ID integer.
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protected static IRI |
createNCBIIRI(String id)
Create an NCBI taxon IRI from an NCBI ID string.
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static OWLClass |
createTaxon(OWLOntology ontology,
String id)
Create a class for an NCBI Taxonomy ID and add it to the ontology.
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static String |
getTaxonID(OWLClass taxon)
Get the NCBI Taxonomy ID of an OWL Class.
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annotate, annotate, annotate, annotate, annotate, annotate, assertSubAnnotationProperty, assertSubClass, createAnnotationProperty, createAnnotationProperty, createAnnotationProperty, declare, getFirstLiteral, getFirstLiteral, getFirstLiteral, initializeFormat, reformatName, synonym, synonym, updateAnnotation
protected static IRI createNCBIIRI(String id)
id
- the ID stringprotected static IRI createNCBIIRI(int id)
id
- the numeric IDprotected static OWLSubClassOfAxiom assertSubClass(OWLOntology ontology, OWLClass child, String parentID)
ontology
- the current ontologychild
- the child classparentID
- the NCBI ID of the parent classpublic static String getTaxonID(OWLClass taxon)
taxon
- the classpublic static OWLClass createTaxon(OWLOntology ontology, String id)
ontology
- the current ontologyid
- the NCBI Taxonomy ID, will be expanded into an IRI of the
form http://purl.obolibrary.org/obo/NCBITaxon_1public static Boolean checkTaxon(OWLOntology ontology, OWLClass taxon)
ontology
- the current ontologytaxon
- the subjectCopyright © 2010–2016. All rights reserved.