owltools.mooncat

Class SpeciesSubsetterUtil

java.lang.Object

owltools.mooncat.SpeciesSubsetterUtil

public class SpeciesSubsetterUtil
extends Object

This implements species subsetting (module generation) using OWL reasoning. The procedure is 1. to assert Thing SubClassOf in_taxon some My-taxon-of-interest 2. Remove all unsatisfiable classes. This is a somewhat brutal way of doing things. A more elegant approach would be to test every class (C in_taxon some T), but this would be a little slower. But it avoids stating falsehoods. The current approach requires removing all taxon-crossing relationships first to avoid removing too many (e.g. if C is unsatisfiable, then homologous_to some C is also unsatisfiable, we don't want to remove the homologs). A few of these are hardcoded in the module, but the user should be careful to remove others depending on their ontology. See: https://github.com/obophenotype/uberon/wiki/Taxon-constraints Note that for this approach to work properly, the ontology used needs to be merged with a taxonomy ontology providing relations between taxa, and disjoint classes axioms between sibling taxa (see http://douroucouli.wordpress.com/2012/04/24/taxon-constraints-in-owl/).

Author:

cjm, Frederic Bastian

Field Summary

Fields

Modifier and Type	Field and Description
org.semanticweb.owlapi.reasoner.OWLReasoner	reasoner
org.semanticweb.owlapi.model.OWLClass	rootClass
org.semanticweb.owlapi.model.OWLClass	taxClass
org.semanticweb.owlapi.model.OWLObjectProperty	viewProperty

Constructor Summary

Constructors

Constructor and Description
SpeciesSubsetterUtil(OWLGraphWrapper g) Constructor providing the OWLGraphWrapper wrapping the OWLOntology used for species subsetting.

Method Summary

Methods

Modifier and Type	Method and Description
Collection<List<org.semanticweb.owlapi.model.OWLObject>>	explainTaxonConstraint(Collection<String> clsIds, Collection<String> taxonIds) Provides explanations about the sources of some taxon constraints on the OWLClasses provided through clsIds, related to the taxa provided through taxonIds.
void	removeOtherSpecies()

Methods inherited from class java.lang.Object

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

Field Detail

reasoner

public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner

viewProperty

public org.semanticweb.owlapi.model.OWLObjectProperty viewProperty

taxClass

public org.semanticweb.owlapi.model.OWLClass taxClass

rootClass

public org.semanticweb.owlapi.model.OWLClass rootClass

Constructor Detail

SpeciesSubsetterUtil

public SpeciesSubsetterUtil(OWLGraphWrapper g)

Constructor providing the OWLGraphWrapper wrapping the OWLOntology used for species subsetting. This OWLOntology will be immediately modified to remove relations that could generate incorrect taxon constraints.

Parameters:

g - OWLGraphWrapper wrapping the OWLOntology to use.

Method Detail

removeOtherSpecies

public void removeOtherSpecies()

explainTaxonConstraint

public Collection<List<org.semanticweb.owlapi.model.OWLObject>> explainTaxonConstraint(Collection<String> clsIds,
                                                                              Collection<String> taxonIds)
                                                                                throws IllegalArgumentException

Provides explanations about the sources of some taxon constraints on the OWLClasses provided through clsIds, related to the taxa provided through taxonIds. This method allows to know why a given term, in the OWLOntology provided at instantiation, is defined as existing, or not existing, in some given taxa.

For each requested OWLClass, explanations are provided as paths going from the OWLClass, to a taxon constraint pertinent to any of the requested taxa. A path is represented as a List of OWLObjects. The first OWLObject is always one of the requested OWLClass. Following OWLObjects are either OWLClasses, or anonymous OWLClassExpressions, representing the targets of SubClassOfAxioms. The final OWLObject is either an anonymous OWLClassExpressions representing a "only_in_taxon" relation, or an OWLAnnotation representing a "never_in_taxon" annotation.

If some of the requested OWLClasses are not found in the returned explanations, or their explanations do not cover all requested taxa, it means there is no particular explanation for existence of these OWLClasses in the taxon, they simply exist by default.

Parameters:

clsIds - A Set of Strings that are the OBO-like IDs of the OWLClass for which we want to retrieve explanations about taxon constraints, from the ontology provided at instantiation of this class.

taxonIds - A Set of Strings that are the OBO-like IDs of the taxa for which we want to retrieve explanations about presence or absence of the OWLClasses provided through clsIds.

Returns:

A Collection of Lists of OWLObjects, where each List correspond to a walk explaining a taxon constraint.

Throws:

IllegalArgumentException - If some of the requested OWLClasses or requested taxa could not be found in the ontology provided at instantiation.