# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1333025362 -7200
# Node ID 7e6604a5ee557f86cebd4fbd07518733ea2dab15
# Parent  d0722148cb59afbd6917247a562ae56563fd5193
New query tool added

diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/README
--- a/OPPL/README	Thu Mar 22 14:37:46 2012 +0100
+++ b/OPPL/README	Thu Mar 29 14:49:22 2012 +0200
@@ -10,21 +10,25 @@
 /galaxy-dist/tool-data/shared/jars/:
 
 oppl_galaxy_tool.jar
-oppl_galax_lib/
+inference.jar
+query.jar
+oppl_galaxy_lib/
+inference_lib/
+query_lib/
 FaCT++-linux-v1.5.2/ 
 FaCT++-OSX-v1.5.2/
-inference.jar
-inference_lib/ 
-
+ 
 3.- Create directory /galaxy-dist/tools/OPPL/
 
-4.- Copy oppl.xml and inference.xml to /galaxy-dist/tools/OPPL/
+4.- Copy oppl.xml, inference.xml and query.xml to
+/galaxy-dist/tools/OPPL/
 
 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
 
   <section name="Ontology Pre Processor Language" id="oppl">
     <tool file="OPPL/oppl.xml"/>
     <tool file="OPPL/inference.xml"/>
+    <tool file="OPPL/query.xml"/>
   </section>
 
 6.- Start Galaxy.
@@ -34,24 +38,28 @@
 FORESEEN FEATURES
 =================
 
-OPPL:
+General (OPPL, Inference, Query):
 
 - Support for processing ontologies that import other ontologies loaded
 in galaxy.
 
-- Rendering definition (URI fragment, label, etc).
+- Entities rendering definition (URI fragment, rdfs:label, QName, etc).
+
+- OWLLink and Racer support.
+
+
+OPPL:
 
 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
 cell).
 
-- OWLLink and Racer support.
+- Other output formats apart from RDF/XML.
 
 
 Inference:
 
-- DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals,
-...
-
+- Support for DataPropertyAssertion, DataPropertyHierarchy,
+DifferentIndividuals, ...
 
 
 
@@ -87,10 +95,11 @@
 
 Copyright (c) 2011 Mikel Egaña Aranguren. 
 
-(OPPL|Inference)-Galaxy is free software: you can redistribute it and/or
-modify it under the terms of the GNU General Public License as published
-by the Free Software Foundation, either version 3 of the License, or (at
-your option) any later version.
+(OPPL|Inference|Query)-Galaxy 
+is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your
+option) any later version.
 
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query.jar
Binary file OPPL/query.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/query.xml	Thu Mar 29 14:49:22 2012 +0200
@@ -0,0 +1,73 @@
+<tool id="query" name="Perform an OWL query against an ontology" version="1.0.1">
+	<description>It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology</description>
+
+	<!-- DEFAULT SETTINGS -->
+	
+	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
+
+	<command>
+		java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
+	</command>
+	
+	<!-- FACT++ -->
+	
+	<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
+	<!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
+	
+	<!--<command>
+		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
+	</commadn>-->
+	
+
+	<inputs>
+		<param format="text" name="ontology" type="data" label="Input ontology file"/>
+		<param name="query" type="text" size="100" value="" label="Query" />
+		<param name="reasoner" type="select" label="Choose reasoner">
+			<option value="Pellet" selected="true">Pellet</option>
+			<option value="HermiT">HermiT</option>
+			<option value="FaCTPlusPlus">FaCT++</option>
+		</param>
+		<param name="answer_type" type="select" label="Choose answer type">
+			<option value="Descendants">Descendant classes</option>
+			<option value="DirectSubClasses" selected="true">Direct sub-classes</option>
+			<option value="Ancestors">Ancestor classes</option>
+			<option value="DirectSuperClasses">Direct super-classes</option>
+			<option value="EquivalentClasses">Equivalent classes</option>
+			<option value="Individuals">Individuals</option>
+		</param>
+		<param name="answer_format" type="select" label="Choose how to render the retrieved entities">
+			<option value="URI" selected="true">URI</option>
+			<option value="URIfragment">URI fragment</option>
+			<option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="text" name="output" />
+	</outputs>
+	<tests>
+		<test>
+			<param name="input" value="OWLQueryGalaxyTest.owl"/>
+			<param name="query" value="p some d"/>
+			<param name="reasoner" value="Pellet"/>
+			<param name="answer_type" value="DirectSubClasses"/>
+			<param name="answer_format" value="URIfragment"/>
+			<output name="out_file" file="query_result"/>	
+		</test>
+	</tests>
+	<help>
+
+**About Query-Galaxy**
+
+  Query-Galaxy can be used to execute a DL query against an OWL ontology (e.g. GO_0007049 or part_of some GO_0007049). The result is a list of entities from the target ontology. How those entities relate to the query can be chosen (A DL query is just an anonymous OWL Class).
+
+**Formats**
+
+  Inference-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is a list of terms.
+
+**Contact**
+
+  Please send any request or comment to mikel.egana.aranguren@gmail.com.
+
+	</help>
+
+</tool>
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar
Binary file OPPL/query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/HermiT.jar
Binary file OPPL/query_lib/HermiT.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/antlr-runtime-3.2.jar
Binary file OPPL/query_lib/antlr-runtime-3.2.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/aterm-java-1.6.jar
Binary file OPPL/query_lib/aterm-java-1.6.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/commons-logging-1.1.1.jar
Binary file OPPL/query_lib/commons-logging-1.1.1.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/jgrapht-jdk1.5.jar
Binary file OPPL/query_lib/jgrapht-jdk1.5.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/junit-4.8.2.jar
Binary file OPPL/query_lib/junit-4.8.2.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/junit.jar
Binary file OPPL/query_lib/junit.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/log4j-1.2.15.jar
Binary file OPPL/query_lib/log4j-1.2.15.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/oboformat.jar
Binary file OPPL/query_lib/oboformat.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/org.coode.oppl-API.jar
Binary file OPPL/query_lib/org.coode.oppl-API.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/owlapi-bin.jar
Binary file OPPL/query_lib/owlapi-bin.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/owlapi-bin_2.jar
Binary file OPPL/query_lib/owlapi-bin_2.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/owllink-bin.jar
Binary file OPPL/query_lib/owllink-bin.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/parsers.jar
Binary file OPPL/query_lib/parsers.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-core.jar
Binary file OPPL/query_lib/pellet-core.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-datatypes.jar
Binary file OPPL/query_lib/pellet-datatypes.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-el.jar
Binary file OPPL/query_lib/pellet-el.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-owlapiv3.jar
Binary file OPPL/query_lib/pellet-owlapiv3.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-query.jar
Binary file OPPL/query_lib/pellet-query.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/query_lib/pellet-rules.jar
Binary file OPPL/query_lib/pellet-rules.jar has changed
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/src/GalaxyOWLAPI.java
--- a/OPPL/src/GalaxyOWLAPI.java	Thu Mar 22 14:37:46 2012 +0100
+++ b/OPPL/src/GalaxyOWLAPI.java	Thu Mar 29 14:49:22 2012 +0200
@@ -10,10 +10,16 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
+import java.util.Set;
 
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
+import org.coode.parsers.BidirectionalShortFormProviderAdapter;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.expression.OWLEntityChecker;
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
 import org.semanticweb.owlapi.model.AddAxiom;
@@ -22,16 +28,20 @@
 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyChange;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.semanticweb.owlapi.reasoner.InferenceType;
+import org.semanticweb.owlapi.reasoner.NodeSet;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
@@ -41,8 +51,10 @@
 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
 import org.semanticweb.owlapi.util.OWLEntityRenamer;
 import org.semanticweb.owlapi.util.OWLOntologyMerger;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
 import org.semanticweb.owlapi.vocab.OWL2Datatype;
 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+import org.semanticweb.owlapi.reasoner.Node;
 
 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
 
@@ -103,7 +115,47 @@
 		IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl");
 		ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
 	}
-
+	
+	public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
+		Set<OWLOntology> importsClosure = ontology.getImportsClosure();
+		BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());
+        OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
+		ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr);
+		MOSparser.setOWLEntityChecker(entityChecker);
+		return MOSparser.parseClassExpression();
+	}
+	
+	public Set<OWLNamedIndividual> getIndividuals (OWLClassExpression expr){
+		return (reasoner.getInstances(expr, false)).getFlattened();
+	}
+	public Set<OWLClass> getEquivalentClasses (OWLClassExpression expr){
+		Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(expr);
+	    Set<OWLClass> result;
+	    if (expr.isAnonymous()) {
+	        result = equivalentClasses.getEntities();
+	    }
+	    else {
+	        result = equivalentClasses.getEntitiesMinus(expr.asOWLClass());
+	    }
+	    return result;
+	}
+	
+	public Set<OWLClass> getDirectSuperClasses (OWLClassExpression expr){		
+		 return (reasoner.getSuperClasses(expr, true)).getFlattened();
+	}
+	
+	public Set<OWLClass> getAncestors (OWLClassExpression expr){		
+		 return (reasoner.getSuperClasses(expr, false)).getFlattened();
+	}
+	
+	public Set<OWLClass> getDirectSubClasses (OWLClassExpression expr){		
+		 return (reasoner.getSubClasses(expr, true)).getFlattened();
+	}
+	
+	public Set<OWLClass> getDescendants (OWLClassExpression expr){		
+		 return (reasoner.getSubClasses(expr, false)).getFlattened();
+	}
+	
 	//	CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.	
 	
 	public void addCLASS_ASSERTIONS(){
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/src/OPPLGalaxy.java
--- a/OPPL/src/OPPLGalaxy.java	Thu Mar 22 14:37:46 2012 +0100
+++ b/OPPL/src/OPPLGalaxy.java	Thu Mar 29 14:49:22 2012 +0200
@@ -24,6 +24,7 @@
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 
 
+
 /**
  * @author Mikel Egaña Aranguren
  *
@@ -81,11 +82,13 @@
 		
 		// Parse the OPPL script
 		ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner); 
-		Logger logger = Logger.getLogger(Tool.class.getName());
+		Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
 //		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
 		ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
 		OPPLParser opplparser = parserFactory.build(errorListener);
 		OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
+		
+		
 			
 		// Execute the script
 		ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/src/OWLQueryGalaxy.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/src/OWLQueryGalaxy.java	Thu Mar 29 14:49:22 2012 +0200
@@ -0,0 +1,119 @@
+package es.upm.fi.dia.oeg.oppl.galaxy;
+
+import java.util.Set;
+
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+public class OWLQueryGalaxy {
+
+	/**
+	 * @param args
+	 * @throws OWLOntologyCreationException 
+	 * @throws ParserException 
+	 */
+	public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
+		// Get the arguments from command-line
+		String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
+		String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
+		
+		String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
+		String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
+		String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
+		
+		// Create the manager
+		GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
+				
+		// Load the main ontology and hope for the imported URIs to be resolvable		
+		galaxyowlapi.loadMainOntology(OWLFilePath);
+				
+		// Set the reasoner
+		
+		// Pellet
+		if(reasoner_type.equals("Pellet")){
+			galaxyowlapi.setReasonerPellet();
+		}
+		// FaCTPlusPlus
+		else if (reasoner_type.equals("FaCTPlusPlus")){
+			galaxyowlapi.setReasonerFaCT();
+		}
+		// HermiT
+		else{
+			galaxyowlapi.setReasonerHermit();
+		}
+
+		// Parse the expression to an OWLexpression
+		OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
+		
+		// Execute query and print results
+		if(Answer_type.equals("Individuals")){
+			Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
+			for(OWLNamedIndividual ind : inds){
+				print_result_entity(ind.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("EquivalentClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("DirectSuperClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("Ancestors")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("DirectSubClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		// Descendants
+		else {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}	
+	}
+	
+	//URI|URIfragment|URIfragment2OBO
+	private static void print_result_entity (IRI iri, String Answer_render){
+		if(Answer_render.equals("URI")){
+			System.out.println(iri);
+		}
+		
+		// Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
+		// done manually
+		else if(Answer_render.equals("URIfragment")){	
+			if(iri.toString().contains("#")){
+				System.out.println(iri.getFragment());
+			}
+			else{
+				String [] iri_tokens = iri.toString().split("/");
+				System.out.println(iri_tokens[iri_tokens.length-1]);
+			}
+		}
+		else{
+			if(iri.toString().contains("#")){
+				System.out.println((iri.getFragment()).replace("_", ":"));
+			}
+			else{
+				String [] iri_tokens = iri.toString().split("/");
+				System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
+			}
+		}
+	}
+}
diff -r d0722148cb59 -r 7e6604a5ee55 OPPL/test-data/ontology/single/OWLQueryGalaxyTest.owl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test-data/ontology/single/OWLQueryGalaxyTest.owl	Thu Mar 29 14:49:22 2012 +0200
@@ -0,0 +1,193 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+    <!ENTITY OWLQueryGalaxyTest2 "http://www.oeg-upm.net/OWLQueryGalaxyTest.owl#" >
+    <!ENTITY OWLQueryGalaxyTest "http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/" >
+]>
+
+
+<rdf:RDF xmlns="http://www.oeg-upm.net/OWLQueryGalaxyTest.owl#"
+     xml:base="http://www.oeg-upm.net/OWLQueryGalaxyTest.owl"
+     xmlns:OWLQueryGalaxyTest2="http://www.oeg-upm.net/OWLQueryGalaxyTest.owl#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:OWLQueryGalaxyTest="http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+    <owl:Ontology rdf:about="http://www.oeg-upm.net/OWLQueryGalaxyTest.owl"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Datatypes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/inv_p -->
+
+    <owl:ObjectProperty rdf:about="&OWLQueryGalaxyTest;inv_p"/>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/p -->
+
+    <owl:ObjectProperty rdf:about="&OWLQueryGalaxyTest;p">
+        <owl:inverseOf rdf:resource="&OWLQueryGalaxyTest;inv_p"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl#GO_0000034 -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest2;GO_0000034">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&OWLQueryGalaxyTest;p"/>
+                <owl:someValuesFrom rdf:resource="&OWLQueryGalaxyTest;d"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/GO_0000033 -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest;GO_0000033">
+        <rdfs:subClassOf rdf:resource="&OWLQueryGalaxyTest2;GO_0000034"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/a -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest;a">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&OWLQueryGalaxyTest;p"/>
+                <owl:someValuesFrom rdf:resource="&OWLQueryGalaxyTest;d"/>
+            </owl:Restriction>
+        </owl:equivalentClass>
+    </owl:Class>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/c -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest;c">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&OWLQueryGalaxyTest;p"/>
+                <owl:allValuesFrom rdf:resource="&OWLQueryGalaxyTest;d"/>
+            </owl:Restriction>
+        </owl:equivalentClass>
+    </owl:Class>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/d -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest;d">
+        <rdfs:subClassOf rdf:resource="&OWLQueryGalaxyTest;f"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/f -->
+
+    <owl:Class rdf:about="&OWLQueryGalaxyTest;f"/>
+    
+
+
+    <!-- http://www.w3.org/2002/07/owl#Thing -->
+
+    <rdf:Description rdf:about="&owl;Thing">
+        <rdfs:comment>p some d: 
+
+equiv a 
+sub b
+desc b,b1, 
+ind aa
+
+inv_p some c
+
+ances d,f
+sup d</rdfs:comment>
+    </rdf:Description>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/aa -->
+
+    <owl:Thing rdf:about="&OWLQueryGalaxyTest;aa">
+        <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <OWLQueryGalaxyTest:p rdf:resource="&OWLQueryGalaxyTest;dd"/>
+    </owl:Thing>
+    
+
+
+    <!-- http://www.oeg-upm.net/OWLQueryGalaxyTest.owl/dd -->
+
+    <owl:NamedIndividual rdf:about="&OWLQueryGalaxyTest;dd">
+        <rdf:type rdf:resource="&OWLQueryGalaxyTest;d"/>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net -->
+