owltools.gaf
Class EcoTools

java.lang.Object
  extended by owltools.gaf.EcoTools

public class EcoTools
extends Object

Methods to simplify the work with the evidence code ontology (ECO).


Constructor Summary
EcoTools()
           
 
Method Summary
static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco, Set<String> goCodes)
          Retrieve the ECO classes for the given GO annotation codes.
static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco, String... goCodes)
          Retrieve the ECO classes for the given GO annotation codes.
static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes, OWLGraphWrapper eco)
           
static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes, OWLGraphWrapper eco, boolean includeDescendants)
          Retrieve the set of codes for a given set of ECO classes.
static OWLGraphWrapper loadECO(ParserWrapper pw)
          Load the evidence code ontology (ECO) from its default PURL.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

EcoTools

public EcoTools()
Method Detail

loadECO

public static OWLGraphWrapper loadECO(ParserWrapper pw)
                               throws IOException,
                                      org.semanticweb.owlapi.model.OWLOntologyCreationException
Load the evidence code ontology (ECO) from its default PURL.

Parameters:
pw -
Returns:
eco ontology graph
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException

getClassesForGoCodes

public static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco,
                                                                              String... goCodes)
Retrieve the ECO classes for the given GO annotation codes.

Parameters:
eco -
goCodes -
Returns:
set of ECO classes

getClassesForGoCodes

public static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco,
                                                                              Set<String> goCodes)
Retrieve the ECO classes for the given GO annotation codes.

Parameters:
eco -
goCodes -
Returns:
set of ECO classes

getCodes

public static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
                                   OWLGraphWrapper eco)

getCodes

public static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
                                   OWLGraphWrapper eco,
                                   boolean includeDescendants)
Retrieve the set of codes for a given set of ECO classes. Option: include sub classes of all the classes. Uses a reasoner to infer the sub classes.

Parameters:
classes -
eco -
includeDescendants - set to true if sub classes should be included
Returns:
set of codes potentially used for the given ECO classes


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