owltools.cli

Class BioChebiGenerator

java.lang.Object

owltools.cli.BioChebiGenerator

public class BioChebiGenerator
extends Object

Methods for creating the BioChEBI wrapper file for ChEBI. The wrapper creates the GCIs equivalences from ChEBI in GO.

Constructor Summary

Constructors

Constructor and Description
BioChebiGenerator(Map<org.semanticweb.owlapi.model.OWLObjectProperty,Set<org.semanticweb.owlapi.model.OWLObjectProperty>> expansionMap)

Method Summary

Methods

Modifier and Type	Method and Description
static org.semanticweb.owlapi.model.OWLOntology	createBioChebi(File bioChebiTemplateFile, String ignoredSubset) Create the GCIs for BioChEBI.
static void	createBioChebi(OWLGraphWrapper graph, Set<org.semanticweb.owlapi.model.OWLClass> ignoredClasses) Create the GCIs for BioChEBI.
static void	createBioChebi(OWLGraphWrapper graph, String ignoredSubset) Create the GCIs for BioChEBI.
void	expand(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLClass> ignoredClasses) Create the GCIs for BioChEBI.
static void	main(String[] args) Main method.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioChebiGenerator

public BioChebiGenerator(Map<org.semanticweb.owlapi.model.OWLObjectProperty,Set<org.semanticweb.owlapi.model.OWLObjectProperty>> expansionMap)

Parameters:

expansionMap -

Method Detail

expand

public void expand(org.semanticweb.owlapi.model.OWLOntology ontology,
          Set<org.semanticweb.owlapi.model.OWLClass> ignoredClasses)

Create the GCIs for BioChEBI. Add the axioms into the given ontology.

Parameters:

ontology -

ignoredClasses -

createBioChebi

public static org.semanticweb.owlapi.model.OWLOntology createBioChebi(File bioChebiTemplateFile,
                                                      String ignoredSubset)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Create the GCIs for BioChEBI. Use the given ontology file as template.

Parameters:

bioChebiTemplateFile -

ignoredSubset - optional subset for ignored classes

Returns:

ontology

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

createBioChebi

public static void createBioChebi(OWLGraphWrapper graph,
                  String ignoredSubset)
                           throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Create the GCIs for BioChEBI. Add the axioms into the given ontology graph.

Parameters:

graph -

ignoredSubset - optional subset for ignored classes

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

createBioChebi

public static void createBioChebi(OWLGraphWrapper graph,
                  Set<org.semanticweb.owlapi.model.OWLClass> ignoredClasses)

Create the GCIs for BioChEBI. Add the axioms into the given ontology graph.

Parameters:

graph -

ignoredClasses - options set of ignored classes

main

public static void main(String[] args)
                 throws Exception

Main method. For testing purposes ONLY!

Parameters:

args -

Throws:

Exception