Package org.obolibrary.robot

Class ReduceOperation

java.lang.Object

org.obolibrary.robot.ReduceOperation

public class ReduceOperation
extends Object

Reason over an ontology and remove redundant SubClassOf axioms

Every axiom A = SubClassOf(C D) is tested (C or D are permitted to be anonymous, e.g. SomeValuesFrom)

If there already exists an axiom SubClassOf(C Z), where Z is entailed to be a proper SubClassOf of D (direct or indirect), then A is redundant, and removed.

Implementation

Because an OWL reasoner will only return named (non-anonymous) superclasses, we add a pre-processing step, where for each class C appearing in either LHS or RHS of a SubClassOf expression, if C is anonymous, we create a named class C' and add a temporary axioms EquivalentClasses(C' C), which is later removed as a post-processing step. When performing reasoner tests, we can then substitute C for C'

GENERAL CLASS INCLUSION AXIOMS

We make a special additional case of redunancy, as in the following example: 1. (hand and part-of some human) SubClassOf part-of some forelimb 2. hand SubClassOf part-of some forelimb Here we treat axiom 1 as redundant, but this is not detected by the algorithm above, because there is no explicit SubClassOf axiom between the GCI LHS and 'human'. We therefore extend the test above and first find all superclasses of anonymous LHSs, and then test for these

Author:

Chris Mungall

Constructor Summary

Constructors

Constructor	Description
ReduceOperation()

Method Summary

Modifier and Type	Method	Description
static Map<String,String>	getDefaultOptions()	Return a map from option name to default option value, for all the available reasoner options.
static void	reduce(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory)	Remove redundant SubClassOf axioms.
static void	reduce(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory, Map<String,String> options)	Remove redundant SubClassOf axioms.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReduceOperation

public ReduceOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return a map from option name to default option value, for all the available reasoner options.

Returns:

a map with default values for all available options

reduce

public static void reduce(org.semanticweb.owlapi.model.OWLOntology ontology,
                          org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory)
                   throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Remove redundant SubClassOf axioms.

Parameters:

ontology - The ontology to reduce.

reasonerFactory - The reasoner factory to use.

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on ontology problem

reduce

public static void reduce(org.semanticweb.owlapi.model.OWLOntology ontology,
                          org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory,
                          Map<String,String> options)
                   throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Remove redundant SubClassOf axioms.

Parameters:

ontology - The ontology to reduce.

reasonerFactory - The reasoner factory to use.

options - A map of options for the operation.

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException - on ontology problem