Package org.incenp.obofoundry.uberon.util

Class PreciseSpeciesSubsetter

java.lang.Object

org.incenp.obofoundry.uberon.util.PreciseSpeciesSubsetter

All Implemented Interfaces:

ISpeciesSubsetStrategy

public class PreciseSpeciesSubsetter
extends Object
implements ISpeciesSubsetStrategy

A “precise” strategy to create a taxon-specific subset, as an alternative to the strategy implemented in DefaultSpeciesSubsetter.

For each class C of the ontology below the root(s), we test whether the expression C and in_taxon some THE_TAXON is satisfiable; if it is, then the class is included in the subset.

On Uberon, this is about 4 to 5 times slower than the “default” strategy, but has the advantage that it does not require removing the “cross-taxon” relationships beforehand.

On the other hand, this may fail to exclude classes that are linked to a class that is invalid for the considered taxon, if there is a missing property chain over the in_taxon relation. For example, if we have C1 located_in some C2, and C2 is not valid for the taxon, C1 will still be considered valid because there is (as of September 2024) no property chain between in_taxon and located_in.

Field Summary

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

IN_TAXON

Constructor Summary

Constructors

Constructor	Description
PreciseSpeciesSubsetter()

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

PreciseSpeciesSubsetter

public PreciseSpeciesSubsetter()

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.