Package org.incenp.obofoundry.uberon.util

Class DefaultSpeciesSubsetter

java.lang.Object

org.incenp.obofoundry.uberon.util.DefaultSpeciesSubsetter

All Implemented Interfaces:

ISpeciesSubsetStrategy

public class DefaultSpeciesSubsetter
extends Object
implements ISpeciesSubsetStrategy

The “default” strategy to create a taxon-specific subset.

This strategy is the same as the one implemented by OWLTools’ SpeciesSubsetterUtil class.

Basically, we assert THE_ROOT(s) in_taxon some THE_TAXON, and exclude from the subset all classes that are unsatisfiable because of that assertion.

This may cause some classes to be excluded because they are linked to an unsatisfiable class, even though the link between the two classes does not convey that one cannot exist in a given taxon if the other does not. For example, if C1 shares_ancestor_with some C2 and C2 is unsatisfiable in the considered taxon, then C1 will be unsatisfiable as well, even though it may very well be valid in that taxon. To avoid this, we forcibly remove a handful of “cross-taxon” relationships from the ontology before proceeding.

Field Summary

Fields inherited from interface org.incenp.obofoundry.uberon.util.ISpeciesSubsetStrategy

IN_TAXON

Constructor Summary

Constructors

Constructor	Description
DefaultSpeciesSubsetter()

Method Summary

Modifier and Type	Method	Description
Set<org.semanticweb.owlapi.model.OWLClass>	getSubset(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, Collection<org.semanticweb.owlapi.model.IRI> roots, org.semanticweb.owlapi.model.IRI taxon)	Creates a taxon-specific subset of the given ontology.

Methods inherited from class java.lang.Object

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

Constructor Details

DefaultSpeciesSubsetter

public DefaultSpeciesSubsetter()

Method Details

getSubset

public Set<org.semanticweb.owlapi.model.OWLClass> getSubset(org.semanticweb.owlapi.model.OWLOntology ontology,
 org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
 Collection<org.semanticweb.owlapi.model.IRI> roots,
 org.semanticweb.owlapi.model.IRI taxon)

Description copied from interface: ISpeciesSubsetStrategy

Creates a taxon-specific subset of the given ontology.

Specified by:

getSubset in interface ISpeciesSubsetStrategy

Parameters:

ontology - The ontology to create a subset of.

reasoner - The reasoner to use.

roots - The root classes from which to create the subset; only those classes and their descendants will be considered to create the subset, all ancestors will be ignored; if null, defaults to owl:Thing.

taxon - The ID of the taxon to create the subset for.

Returns:

The set of classes that belong to the subset.