Package org.incenp.obofoundry.odk

Class NormalizeCommand

java.lang.Object

org.incenp.obofoundry.odk.BasePlugin

org.incenp.obofoundry.odk.NormalizeCommand

All Implemented Interfaces:

org.obolibrary.robot.Command

public class NormalizeCommand
extends BasePlugin

A command to perform various “normalisation” operations on an ontology.

Available normalization operations currently include:

• injecting SubAnnotationPropertyOf axioms to ensure that IRIs representing subsets (used as the value of oboInOwl#inSubset annotations) are subproperties of oboInOwl#SubsetProperty;
• likewise, injecting SubAnnotationPropertyOf axioms to ensure that IRIs representing synonym types (used as the value of oboInOwl#hasSynonymType annotations) are subproperties of oboInOwl#SynonymTypeProperty;
• merging logically equivalent axioms, that differ only by their annotation sets;
• injecting a dc:source ontology annotation derived from the version IRI.

Field Summary

Fields inherited from class org.incenp.obofoundry.odk.BasePlugin

ioHelper, options

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor	Description
NormalizeCommand()

Method Summary

Modifier and Type	Method	Description
static void	injectDeclarations(org.semanticweb.owlapi.model.OWLOntology ontology, Set<String> prefixes, boolean forSubsets, boolean forSynonyms)	Inject SubAnnotationPropertyOf axioms for IRIs representing subsets or synonyms.
static void	mergeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology)	Merges all logically equivalent axioms in the given ontology.
void	performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line)	Performs whatever operation the command is supposed to do.

Methods inherited from class org.incenp.obofoundry.odk.BasePlugin

execute, getDescription, getIRI, getName, getOptions, getUsage, main, readFile, readFileAsIRIs

Methods inherited from class java.lang.Object

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

Constructor Details

NormalizeCommand

public NormalizeCommand()

Method Details

performOperation

public void performOperation(org.obolibrary.robot.CommandState state,
 org.apache.commons.cli.CommandLine line)
                      throws Exception

Description copied from class: BasePlugin

Performs whatever operation the command is supposed to do.

Specified by:

performOperation in class BasePlugin

Parameters:

state - The internal state of ROBOT.

line - The command line used to invoke the command.

Throws:

Exception - If any error occurs when attempting to execute the operation.

mergeAxioms

public static void mergeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology)

Merges all logically equivalent axioms in the given ontology. Logically equivalent axioms, in the context of this command, refers to axioms that differ only by their annotations.

Parameters:

ontology - The ontology whose logically equivalent axioms are to be merged. Axioms from the imports closure are not processed.

injectDeclarations

public static void injectDeclarations(org.semanticweb.owlapi.model.OWLOntology ontology,
 Set<String> prefixes,
 boolean forSubsets,
 boolean forSynonyms)

Inject SubAnnotationPropertyOf axioms for IRIs representing subsets or synonyms.

Parameters:

ontology - The ontology in which axioms should be injected. When collecting the IRIs used as subsets or synonym types, annotation axioms from the imports closure are not taken into account.

prefixes - A set of IRI prefixes; axioms will only be injected for IRIs that start with one of the given prefixes. May be null to force injecting axioms for all IRIs regardless of their namespace.

forSubsets - If true, inject axioms to declare subset properties.

forSynonyms - If true, inject axioms to declare synonym type properties.