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A

addAltId(OWLOntology, String, String, OWLAnnotationProperty) - Static method in class owltools.ncbi.NCBIOWL
Add an alternative identifier for a main term.
annotate(OWLOntology, OWLEntity, OWLAnnotationProperty, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology.
annotate(OWLOntology, OWLEntity, String, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property.
annotate(OWLOntology, OWLEntity, String, String) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property and a string literal.
annotate(OWLOntology, OWLEntity, String, boolean) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property and an Boolean literal.
annotate(OWLOntology, String, IRI) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology itself, taking a CURIE for the property and an Boolean literal.
annotate(OWLOntology, String, String) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding an annotation assertion to the ontology itself, taking a CURIE for the property and an Boolean literal.
assertSubAnnotationProperty(OWLOntology, OWLAnnotationProperty, OWLAnnotationProperty) - Static method in class owltools.ncbi.OWLConverter
Convenience method for asserting a subAnnotationProperty relation between a parent and child property in an ontology.
assertSubClass(OWLOntology, OWLClass, String) - Static method in class owltools.ncbi.NCBIConverter
Convenience method for asserting a subClass relation between a parent and child class in an ontology.
assertSubClass(OWLOntology, OWLClass, OWLClass) - Static method in class owltools.ncbi.OWLConverter
Convenience method for asserting a subClass relation between a parent and child class in an ontology.

C

checkAxioms(String, String) - Static method in class owltools.ncbi.NCBI2OWL
Load an ontology from a file and then print a list of its axioms.
checkTaxon(OWLOntology, OWLClass) - Static method in class owltools.ncbi.NCBIConverter
Check to make sure that this taxon has the required properties.
convertToOWL(String, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL
Read a data file and create an OWL representation.
convertToOWL(String, String, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL
Read a data file, create an OWL representation, and save an OWL file.
convertToOWL(String, String, InputStream, InputStream, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL
Read a data file, create an OWL representation, and save an OWL file.
createAnnotationProperty(OWLOntology, IRI) - Static method in class owltools.ncbi.OWLConverter
Create an annotation property and add it to the ontology.
createAnnotationProperty(OWLOntology, String) - Static method in class owltools.ncbi.OWLConverter
Convenience method taking a string CURIE instead of an IRI.
createAnnotationProperty(OWLOntology, Obo2OWLConstants.Obo2OWLVocabulary) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding and labelling OboInOwl annotation properties with its rdfs:label.
createNCBIIRI(String) - Static method in class owltools.ncbi.NCBIConverter
Create an NCBI taxon IRI from an NCBI ID string.
createNCBIIRI(int) - Static method in class owltools.ncbi.NCBIConverter
Create an NCBI taxon IRI from an NCBI ID integer.
createOWLOntology() - Static method in class owltools.ncbi.NCBIOWL
Create and initialize the ontology.
createTaxon(OWLOntology, String) - Static method in class owltools.ncbi.NCBIConverter
Create a class for an NCBI Taxonomy ID and add it to the ontology.

D

dataFactory - Static variable in class owltools.ncbi.NCBIOWL
Create OWLAPI utilities: A data factory.
declare(OWLOntology, OWLEntity) - Static method in class owltools.ncbi.OWLConverter
Convenience method for adding a declaration axiom to the ontology.

E

error(String) - Static method in class owltools.ncbi.NCBI2OWL
 

F

format - Static variable in class owltools.ncbi.OWLConverter
Create OWLAPI utilities: An ontology format.

G

getFirstLiteral(OWLOntology, OWLEntity, OWLAnnotationProperty) - Static method in class owltools.ncbi.OWLConverter
Convenience method to get the first string literal of an annotation property.
getFirstLiteral(OWLOntology, OWLEntity, IRI) - Static method in class owltools.ncbi.OWLConverter
Convenience method to get the first string literal of an annotation property.
getFirstLiteral(OWLOntology, OWLEntity, String) - Static method in class owltools.ncbi.OWLConverter
Convenience method to get the first string literal of an annotation property.
getTaxonID(OWLClass) - Static method in class owltools.ncbi.NCBIConverter
Get the NCBI Taxonomy ID of an OWL Class.

H

handleLine(OWLOntology, Map<String, List<OWLClass>>, OWLClass, String, int) - Static method in class owltools.ncbi.NCBI2OWL
Handle one line of the data file.

I

IAO - Static variable in class owltools.ncbi.OWLConverter
Define the base IRI for Information Artifact Ontology (IAO) terms.
initializeFormat() - Static method in class owltools.ncbi.OWLConverter
Initialize the format with standard default prefixes (rdf, rdfs, xsd, owl) and with the prefixes we will use (obo, oio, iao).

L

loadOWLOntology(File) - Static method in class owltools.ncbi.NCBIOWL
Load an ontology from a file.
logger - Static variable in class owltools.ncbi.NCBI2OWL
Create a logger.
logger - Static variable in class owltools.ncbi.NCBIConverter
Create a logger.
logger - Static variable in class owltools.ncbi.NCBIOWL
Create a logger.
logger - Static variable in class owltools.ncbi.OWLConverter
Create a logger.

M

main(String[]) - Static method in class owltools.ncbi.NCBI2OWL
Handle command-line arguments when this class is used in an executable Jar file.
manager - Static variable in class owltools.ncbi.NCBIOWL
Create OWLAPI utilities: An ontology manager.

N

NCBI - Static variable in class owltools.ncbi.OWLConverter
Define the base IRI for NCBI Taxonomy terms.
NCBI2OWL - Class in owltools.ncbi
Provides static methods for converting NCBI Taxonomy data files into OWL format.
NCBI2OWL() - Constructor for class owltools.ncbi.NCBI2OWL
 
NCBIConverter - Class in owltools.ncbi
Provides common methods for working with NCBI.
NCBIConverter() - Constructor for class owltools.ncbi.NCBIConverter
 
NCBIOWL - Class in owltools.ncbi
Provides static methods for creating and initializing an OWLOntology into which taxa can be inserted.
NCBIOWL() - Constructor for class owltools.ncbi.NCBIOWL
 

O

OBO - Static variable in class owltools.ncbi.OWLConverter
Define the base IRI for Open Biomedical Ontologies (OBO).
OIO - Static variable in class owltools.ncbi.OWLConverter
Define the base IRI for OboInOwl terms.
OWLConverter - Class in owltools.ncbi
Provides common methods for converting data into Web Ontology Language (OWL) format using OWLAPI.
OWLConverter() - Constructor for class owltools.ncbi.OWLConverter
 
owltools.ncbi - package owltools.ncbi
 

P

parseLine(String, int) - Static method in class owltools.ncbi.NCBI2OWL
Parse a line of the data file into a pair of strings: the field name and the field value.
printAxioms(OWLOntology, String) - Static method in class owltools.ncbi.NCBI2OWL
Print string representations of all the axioms in an ontology, one axiom statement per line.

R

ranks - Static variable in class owltools.ncbi.NCBIOWL
Names of the NCBI ranks.
reformatName(String) - Static method in class owltools.ncbi.OWLConverter
Reformat names for use in IRIs.

S

setupAltIdProperty(OWLOntology) - Static method in class owltools.ncbi.NCBIOWL
Setup the alternative identifier annotation property.
synonym(OWLOntology, OWLEntity, OWLAnnotationValue, OWLAnnotationProperty, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter
Add an synonym annotation, plus an annotation on that annotation that specified the type of synonym.
synonym(OWLOntology, OWLEntity, String, String, String) - Static method in class owltools.ncbi.OWLConverter
Add an synonym annotation, plus an annotation on that annotation that specified the type of synonym.
synonymTypes - Static variable in class owltools.ncbi.NCBIOWL
A map from NCBI synonym types to OboInOwl annotation properties.

U

updateAnnotation(OWLOntology, OWLEntity, String, String) - Static method in class owltools.ncbi.OWLConverter
 
usage - Static variable in class owltools.ncbi.NCBI2OWL
Command line usage information.
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