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Commit 64671892 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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......@@ -64,7 +64,8 @@ related APIs.
Other tutorials are <a href="../index.html">available</a>.</p>
<p style="border-top: 2px solid #AAAAAA;">
<small>This tutorial has been initially designed for the Alignment API 4.0 using Jena, Pellet and IDDL.
It has been reengineered in the Alignment API 4.5 to use Jena, HermiT and IDDL 1.4.</small></p>
It has been reengineered in the Alignment API 4.5 to use Jena, HermiT
1.3.8, IDDL (now DRaon) 1.4 and LogMap 2.</small></p>
<h2>Preparation</h2>
......@@ -124,21 +125,47 @@ This can be achieved:
</ul>
</p>
<p>
Write a program that does try to find an alignment on the alignment
server <a href="http://aserv.inrialpes.fr">http://aserv.inrialpes.fr</a>
and, if none is found, computes one.
</p>
<h3>by finding an alignment from the web/server</h3>
<div class="button">
<input type="button" onclick="show('qu0')" value="Various variables"/>
<input type="button" onclick="show('qu1')" value="Show server searching"/>
<input type="button" onclick="show('qu2')" value="Show local matching"/>
<input type="button" onclick="show('qu3')" value="Show server matching"/>
<input type="button" onclick="hide('qu0');hide('qu1');hide('qu2');hide('qu3');" value="Hide solutions"/>
<input type="button" onclick="show('qu0cli')" value="Command line"/>
<input type="button" onclick="show('qu0java')" value="Java"/>
<!--input type="button" onclick="show('qu0serv')" value="Browser"/-->
<input type="button" onclick="hide('qu0cli');hide('qu0java');hide('qu0serv');" value="Hide solutions"/>
</div>
<div class="explain" id="qu0cli">
<p>After introducing the main variables:</p>
<div class="terminal">
RESTSERV=http://aserv.inrialpes.fr/rest
U1=http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl
U2=http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl
CWD=`pwd`
</div>
<div class="explain" id="qu0">
<p></p>
<div class="terminal">
$ curl -L -H "Accept:application/rdf+xml" ${RESTSERV}'/find?onto1='${U1}'&onto2='${U2}
</div>
resulting in something like:
<div class="result">
&lt;findResponse
xml:base='http://exmo.inrialpes.fr/align/service#'
xmlns='http://exmo.inrialpes.fr/align/service#'>
&lt;id>274&lt;/id>
&lt;sender>http://aserv.inrialpes.fr&lt;/sender>
&lt;alignmentList>
&lt;alid>http://aserv.inrialpes.fr/alid/1417700303045/7849&lt;/alid>
&lt;/alignmentList>
&lt;/findResponse>
</div>
which can always been retrieved in RDF/XML by
<div class="terminal">
$ curl -L -H "Accept:application/rdf+xml" http://aserv.inrialpes.fr/alid/1417700303045/7849
</div>
</div>
<div class="explain" id="qu0java">
<p>After introducing the main variables:</p>
<div class="java">
String RESTServ = "http://aserv.inrialpes.fr/rest/";
String myId = "Test";
Alignment al = null;
URI uri1 = null;
......@@ -152,8 +179,6 @@ try {
uri2 = new URI( u2 );
} catch (URISyntaxException use) { use.printStackTrace(); }
</div>
</div>
<div class="explain" id="qu1">
<p>The programme will invoke the alignment server:</p>
<div class="java">
// (Sol1) Try to find an alignment between two ontologies from the server
......@@ -174,7 +199,34 @@ Alignment alu = aparser.parseString( xmlString );
al = ObjectAlignment.toObjectAlignment((URIAlignment)alu);
</div>
</div>
<div class="explain" id="qu2">
<!--div class="explain" id="qu0serv">
<p>After introducing the main variables:</p>
<div class="java">
</div>
</div-->
<div class="explain" id="qu0cli">
<p>After introducing the main variables:</p>
<div class="java">
</div>
</div>
<h3>by running a matcher locally</h3>
<div class="button">
<input type="button" onclick="show('qu2cli')" value="Command line"/>
<input type="button" onclick="show('qu2java')" value="Java"/>
<!--input type="button" onclick="show('qu2serv')" value="Browser"/-->
<input type="button" onclick="hide('qu2cli');hide('qu2java');hide('qu2serv');" value="Hide solutions"/>
</div>
<div class="explain" id="qu2cli">
<div class="terminal">
$ java -cp $CLASSPATH fr.inrialpes.exmo.align.cli.Procalign -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance -Dnoinst=1 http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl
</div>
or:
<div class="terminal">
$ java -cp $CLASSPATH fr.inrialpes.exmo.align.cli.Procalign -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance -Dnoinst=1 file:ontology1.owl file:ontology2.owl
</div>
</div>
<div class="explain" id="qu2java">
<p>Just create an instance of AlignmentProcess and call it:</p>
<div class="java">
// (Sol2) Match the ontologies with a local algorithm
......@@ -188,7 +240,35 @@ if ( al == null ){ // Unfortunatelly no alignment was available
}
</div>
</div>
<div class="explain" id="qu3"><p>Match on the server:</p>
<!--div class="explain" id="qu2serv">
<p>After introducing the main variables:</p>
<div class="java">
</div-->
</div>
<h3>by running a matcher on the alignment server</h3>
<p>
Write a program that does try to find an alignment on the alignment
server <a href="http://aserv.inrialpes.fr">http://aserv.inrialpes.fr</a>
and, if none is found, computes one.
</p>
<div class="button">
<input type="button" onclick="show('qu3cli')" value="Command line"/>
<input type="button" onclick="show('qu3java')" value="Java"/>
<!--input type="button" onclick="show('qu3serv')" value="Browser"/-->
<input type="button" onclick="hide('qu3cli');hide('qu3java');hide('qu3serv');" value="Hide solutions"/>
</div>
<div class="explain" id="qu3cli">
<p>After introducing the main variables:</p>
<div class="terminal">
$ curl -L -H "Accept:application/rdf+xml" ${RESTSERV}'/match?method=fr.inrialpes.exmo.align.impl.method.StringDistAlignment&stringFunction=smoaDistance&noinst=1&onto1='${U1}'&onto2='${U2}
</div>
returning the URL:
</div>
<div class="explain" id="qu3java">
<p>Match on the server:</p>
<div class="java">
// (Sol3) Match the ontologies on the server
if ( alset.getLength() == 0 ) {
......@@ -196,6 +276,23 @@ if ( alset.getLength() == 0 ) {
String match = getFromURLString( RESTServ+"match?onto1="+u1+"&onto2="+u2+"&method="+method+"&pretty="+myId+"&action=Match", true );
}
</div>
</div>
</div>
<!--div class="explain" id="qu3serv">
<p>After introducing the main variables:</p>
<div class="java">
</div>
</div-->
<div class="explain" id="qu3cli">
<p>After introducing the main variables:</p>
<div class="java">
</div>
</div>
<!--h3>by finding a chain of alignments from the web/server</h3>
<p>Not yet ready</p-->
<p>The remainder is the same as in the first solution.</p>
</div>
<div class="note">
......@@ -211,25 +308,30 @@ if ( alset.getLength() == 0 ) {
</pre>
</div>
<h2>Manipulating data</h2>
<h2>Merge ontologies and test consistency</h2>
<h3>Generating an OWL ontology merging the two ontologies</h3>
<p>
Again, this is either:
<ul>
<li>generating OWL axioms from the alignments and merge the ontologies</li>
<li>transforming data from one ontology to another</li>
</ul>
Generating OWL axioms from the alignments and merge the ontologies can be done with the alignment API support.
</p>
<p>
This can be done with the alignment API support.
</p>
<div class="button">
<input type="button" onclick="show('qu5')" value="Show generating OWL"/>
<!--input type="button" onclick="show('qu6')" value="Show solution 2"/-->
<input type="button" onclick="hide('qu5');hide('qu6');" value="Hide solutions"/>
<input type="button" onclick="show('qu5cli')" value="Command line"/>
<input type="button" onclick="show('qu5java')" value="Java"/>
<!--input type="button" onclick="show('qu5serv')" value="Show solution 2"/-->
<input type="button" onclick="hide('qu5cli');hide('qu5java');hide('qu5serv');" value="Hide solutions"/>
</div>
<div class="explain" id="qu5cli">
<p>Considering that the alignment has been stored in a file:
alignment.rdf, this can be obtained locally:</p>
<div class="terminal">
$ java -cp $CLASSPATH fr.inrialpes.exmo.align.cli.ParserPrinter file:alignment.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor -o result/alignment.owl
</div>
or from the server:
<div class="terminal">
$ curl -L -H "Accept:application/rdf+xml" ${RESTSERV}'/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor&id=http://aserv.inrialpes.fr/alid/1417700303045/7849' > result/alignment.owl
</div>
</div>
<div class="explain" id="qu5">
<div class="explain" id="qu5java">
<p>In fact everything is done in one step:</p>
<div class="java">
// (Sol1) generate a merged ontology between the ontologies (OWLAxioms)
......@@ -240,77 +342,46 @@ al.render(renderer);
writer.flush();
writer.close();
</div>
<p>You can look at the result in <a href="results/myresult.owl">results/myresult.owl</a>.</p>
<p>You can look at the result in <a href="results/alignment.owl">results/alignment.owl</a>.</p>
</div>
<div class="explain" id="qu6"><p>Not ready yet</p>
<pre>
</pre>
</div>
<h2>Generating answers</h2>
<h3>Testing ontology consistency with HermiT</h3>
<p>
This can be done in three ways:
<ul>
<li>using SPARQL</li>
<li>using an OWLReasoner such as HermiT to answer these queries against
the merged ontologies.</li>
<li>using a "distributed" reasoner, in our case IDDL, to answer these
queries against non merged aligned ontologies.</li>
</ul>
</p>
<p>
In case you go for SPARQL please, take care of the inference regime
and observe what are the differences in this case. You can of course
run various queries and start by running them in one of the initial
ontologies instead of the merged one.
</p>
</p>
<div class="button">
<input type="button" onclick="show('qu7')" value="Show SPARQL solution"/>
<input type="button" onclick="show('qu8')" value="Show HermiT solution"/>
<input type="button" onclick="show('qu9')" value="Show IDDL solution"/>
<input type="button" onclick="hide('qu7');hide('qu8');hide('qu9');" value="Hide solutions"/>
<input type="button" onclick="show('qu8cli')" value="Command line with HermiT"/>
<input type="button" onclick="show('qu8java')" value="Java with HermiT"/>
<input type="button" onclick="show('qu9java')" value="Java with Draon"/>
<!--input type="button" onclick="show('qu8serv')" value="Browser"/-->
<input type="button" onclick="hide('qu8cli');hide('qu8java');hide('qu9java');" value="Hide solutions"/>
</div>
<div class="explain" id="qu8cli">
<p>Considering that the merged ontologies in a file: results/alignment.owl,
and that you have <a href="http://hermit-reasoner.com/">downloaded HermiT</a> (the Command line version of
hermit requires gnu getopt which is not shipped anymore with the
Alignment API):</p>
<!--div class="terminal">
$ java -jar HermiT.jar -l result/alignment.owl -k
http://www.w3.org/2002/07/owl#Thing is satisfiable.
</div>
another option is:-->
<div class="terminal">
$ java -jar HermiT.jar results/alignment.owl -U
</div>
<div class="explain" id="qu7">
<p>Prepare the system:</p>
<div class="java">
// (Sol1) Use SPARQL to answer queries (at the data level)
InputStream in = new FileInputStream( merged );
Model model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF,null);
model.read( in, "file:"+merged.getPath() );
in.close();
</div>
<p>Query (please play by changing the query)</p>
<div class="java">
// Create a new query
String queryString =
"PREFIX foaf: <http://xmlns.com/foaf/0.1/> " +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
"PREFIX aa: <http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#> " +
"SELECT ?fn ?ln ?t ?s " +
"WHERE {" +
" ?student rdf:type aa:Estudiante . " +
" ?student aa:firstname ?fn. " +
" ?student aa:lastname ?ln. " +
"OPTIONAL { ?student aa:affiliation ?t . } " +
"OPTIONAL { ?student aa:supervisor ?s . } " +
" }";
Query query = QueryFactory.create(queryString);
</div>
<p>Evaluation:</p>
<div class="java">
// Execute the query and obtain results
QueryExecution qe = QueryExecutionFactory.create(query, model);
ResultSet results = qe.execSelect();
// Output query results
ResultSetFormatter.out(System.out, results, query);
<p>which displays</p>
<div class="result">
Exception in thread "main" org.semanticweb.owlapi.reasoner.InconsistentOntologyException: Inconsistent ontology
at org.semanticweb.HermiT.Reasoner.throwInconsistentOntologyExceptionIfNecessary(Unknown Source)
at org.semanticweb.HermiT.Reasoner.checkPreConditions(Unknown Source)
at org.semanticweb.HermiT.Reasoner.isSatisfiable(Unknown Source)
at org.semanticweb.HermiT.cli.CommandLine$SatisfiabilityAction.run(Unknown Source)
at org.semanticweb.HermiT.cli.CommandLine.main(Unknown Source)
</div>
</div>
<div class="explain" id="qu8">
<div class="explain" id="qu8java">
<p>Create Reasoner instance and load the merged ontologies:</p>
<div class="java">
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
......@@ -318,16 +389,129 @@ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology( IRI.create( "file:"+merged.getPath() ) );
OWLReasoner reasoner = new Reasoner( ontology );
</div>
<p>Get the instances of "Estudiantes":</p>
<p>Test consistency:</p>
<div class="java">
// get the instances of a class
OWLClass estud = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante" ) );
OWLClass person = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Person" ) );
OWLClass student = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student" ) );
Set&lt;OWLNamedIndividual> instances = reasoner.getInstances( estud, false ).getFlattened();
System.err.println("OWLReasoner(Merged): There are "+instances.size()+" students ("+clname(estud)+")");
// Test consistency
if ( reasoner.isConsistent() ) {
System.out.println( " *** The aligned ontologies are consistent" );
} else {
System.out.println( " *** The aligned ontologies are inconsistent" );
return;
}
</div>
<p>It is even possible to test the satisfiability of classes:</p>
<div class="java">
// Test coherence
for ( OWLClass cl : ontology.getClassesInSignature( true ) ) {
if ( !reasoner.isSatisfiable( cl ) ) {
System.out.println( cl+" is incoherent" );
}
}
</div>
</div>
<div class="explain" id="qu9java">
<p>Load the two ontologies and the alignment in the IDDL reasoner:</p>
<div class="java">
ArrayList<Alignment> allist = new ArrayList<Alignment>();
allist.add( al );
IDDLReasoner dreasoner = new IDDLReasoner( allist, Semantics.DL );
</div>
<p>Test consistency and check if a particular correspondence is a consequence:</p>
<div class="java">
if ( dreasoner.isConsistent() ) {
System.out.println( "IDDL: the alignment network is consistent");
} else {
System.out.println( "IDDL: the alignment network is inconsistent");
}
</div>
</div>
<h3>Repairing an alignment with LogMap repair</h3>
<div class="button">
<input type="button" onclick="show('qu10cli')" value="Command line"/>
<!--input type="button" onclick="show('qu10java')" value="Java"/-->
<input type="button" onclick="hide('qu10cli');" value="Hide solutions"/>
</div>
<div class="explain" id="qu10cli">
<p>Assuming
that <a href="https://code.google.com/p/logmap-matcher/">LogMap has
been downloaded</a> (it takes directly the Alignment format as input):
<div class="terminal">
$ java -jar logmap2_standalone.jar DEBUGGER http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl RDF $CWD/alignment.rdf $CWD/results false false
</div>
this displays the following output:
<div class="result">
Loading ontologies...
IRI: http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl
IRI: http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl
...Done
Read RDF Align mapping objects: 1
Num original mappings: 1
Num repaired mappings: 1
TOTAL REPAIR TIME (s): 0.164
</div>
obviously it had nothing to do since the aligned ontologies are consistent.
</div>
<!--h3>Repairing an alignment with Alcomo</h3>
<div class="button">
<input type="button" onclick="show('qu11cli')" value="Command line"/>
<input type="button" onclick="show('qu11java')" value="Java"/>
<input type="button" onclick="hide('qu11cli');" value="Hide solutions"/>
</div>
<div class="explain" id="qu11cli">
<p>Assuming that <a href="http://web.informatik.uni-mannheim.de/alcomo/">Alcomo has been downloaded</a> as well
<div class="terminal">
$
</div>
</div-->
<h3>Testing subsumption</h3>
<p>
It is now possible to check that the newly generated alignment is
consistent. Hence we can check some entailment results.
</p>
<div class="button">
<input type="button" onclick="show('qu11cli')" value="Command line with HermiT"/>
<input type="button" onclick="show('qu11java')" value="Java with HermiT"/>
<input type="button" onclick="show('qu11iddljava')" value="Java with DRaon"/>
<!--input type="button" onclick="show('qu11serv')" value="Browser"/-->
<input type="button" onclick="hide('qu11cli');hide('qu11java');hide('qu11iddljava');" value="Hide solutions"/>
</div>
<div class="explain" id="qu11cli">
<p>Considering that the merged ontologies in a file: result/alignment.owl,
and that you have uploaded HermiT (the Command line version of
hermit requires gnu getopt which is not shipped anymore with the
Alignment API):</p>
<div class="terminal">
$ java -jar HermiT.jar results/alignment.owl -s http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante -e http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante
</div>
<p>which displays</p>
<div class="result">
All sub-classes of 'http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante':
owl:Nothing
Classes equivalent to '&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante>':
&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante>
&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student>
</div>
<p>Some subsumption tests:</p>
and
<div class="terminal">
$ java -jar HermiT.jar results/alignment.owl -s http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student -e http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student
</div>
<p>which displays</p>
<div class="result">
All sub-classes of 'http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student':
owl:Nothing
Classes equivalent to '&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student>':
&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante>
&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student>
</div>
</div>
<div class="explain" id="qu11java">
<p>Create Reasoner instance and load the merged ontologies as before
and perform some subsumption tests:</p>
<div class="java">
testOWLReasonerSubClass( manager, reasoner, estud, person );
testOWLReasonerSubClass( manager, reasoner, estud, student );
......@@ -347,23 +531,17 @@ public void testOWLReasonerSubClass( OWLOntologyManager manager, OWLReasoner rea
}
}
</div>
The answer should be:
<div class="result">
OWLReasoner(Merged): Estudiante is not necessarily subclass of Person
OWLReasoner(Merged): Estudiante is subclass of Student
</div>
<div class="explain" id="qu9">
<p>Load the two ontologies and the alignment in the IDDL reasoner:</p>
<div class="java">
ArrayList<Alignment> allist = new ArrayList<Alignment>();
allist.add( al );
IDDLReasoner dreasoner = new IDDLReasoner( allist, Semantics.DL );
</div>
<p>Test consistency and check if a particular correspondence is a consequence:</p>
<div class="explain" id="qu11iddljava">
<p>Check if a particular correspondence is a consequence:</p>
<div class="java">
if ( dreasoner.isConsistent() ) {
System.out.println( "IDDL: the alignment network is consistent");
testIDDLSubClass( dreasoner, uri1, uri2, estud, person );
testIDDLSubClass( dreasoner, uri1, uri2, estud, student );
} else {
System.out.println( "IDDL: the alignment network is inconsistent");
}
testIDDLSubClass( dreasoner, uri1, uri2, estud, person );
testIDDLSubClass( dreasoner, uri1, uri2, estud, student );
</div>
<p>Such that:</p>
<div class="java">
......@@ -381,9 +559,135 @@ public void testOWLReasonerSubClass( OWLOntologyManager manager, OWLReasoner rea
}
}
</div>
the result should be:
<div class="result">
IDDL: Estudiante <= Person is not entailed
IDDL: Estudiante <= Student is entailed
</div>
The results for these execution are, for SPARQL:
<pre>
</div>
<h2>SPARQL querying with an alignment</h2>
<p>Our final goal is to get that list of students.
For that purpose, several strategies may be adopted:
<ul>
<li><a href="inst">Using a reasonner for retrieving all instances of the
aligned classes;</a></li>
<li><a href="transf">Using a SPARQL query against one data set and
transforming the query to apply it to the other dataset;</a></li>
<li><a href="merged">Using this same query against the merged data sets;</a></li>
<li><a href="construct">Generating a SPARQL CONSTRUCT query from the alignment
to merge the instances of both data sets.</a></li>
</ul>
Let explore them.
</p>
<h3><a name="inst"></a>Instance reasoning</h3>
<div class="button">
<input type="button" onclick="show('qu13java')" value="Java"/>
<!--input type="button" onclick="show('qu14serv')" value="Browser"/-->
<input type="button" onclick="hide('qu13java')" value="Hide solution"/>
</div>
<div class="explain" id="qu13java">
<p>Starting from where we were with the HermiT reasonner, it is
possible to retrive the instances of "Estudiantes" and to
manipulate them:</p>
<div class="java">
// get the instances of a class
OWLClass estud = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#Estudiante" ) );
OWLClass person = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Person" ) );
OWLClass student = manager.getOWLDataFactory().getOWLClass( IRI.create( "http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#Student" ) );
Set&lt;OWLNamedIndividual> instances = reasoner.getInstances( estud, false ).getFlattened();
System.err.println("OWLReasoner(Merged): There are "+instances.size()+" students ("+clname(estud)+")");
</div>
This should output:
<div class="result">
OWLReasoner(Merged): There are 47 students (Estudiante)
</div>
</div>
<h3><a name="transf"></a>Transforming queries</h3>
<p>The following solutions use the query in the file <a href="query.sparql">query.sparql</a>.</p>
<div class="button">
<input type="button" onclick="show('qu14cli')" value="Command line"/>
<input type="button" onclick="show('qu14java')" value="Java"/>
<!--input type="button" onclick="show('qu14serv')" value="Browser"/-->
<input type="button" onclick="hide('qu14cli');hide('qu14java');hide('qu14serv');" value="Hide solutions"/>
</div>
<div class="explain" id="qu14cli">
The query can be transformed on command line through:
<div class="terminal">
$ java -cp $CLASSPATH fr.inrialpes.exmo.align.cli.TransformQuery -a file:alignment.rdf -q query.sparql -Donto2=http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#
</div>
The result will be:
<div class="result">
PREFIX onto2: &lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#>
PREFIX aa: &lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#>
PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/>
SELECT ?fn ?ln ?t ?s
WHERE {
?student rdf:type onto2:Student .
?student onto2:first-name ?fn.
?student onto2:name ?ln.
OPTIONAL { ?student onto2:institution ?t . }
OPTIONAL { ?student onto2:phd-advisor ?s . }
}
</div>
</div>
<div class="explain" id="qu14java">
<p>In fact everything is done in one step:</p>
<div class="java">
Not ready yet... USE MY TRANSFORM + USE THE EVALUATION AGAINST A DATA SET.
</div>
</div>
<h3><a name="merged"></a>Querying with the merged ontology</h3>
<p>
In case you go for SPARQL please, take care of the inference regime
and observe what are the differences in this case. You can of course
run various queries and start by running them in one of the initial
ontologies instead of the merged one.
</p>
<div class="button">
<!--input type="button" onclick="show('qu7cli')" value="Command line"/-->
<input type="button" onclick="show('qu7java')" value="Java"/>
<!--input type="button" onclick="show('qu7serv')" value="Browser"/-->
<input type="button" onclick="hide('qu7java')" value="Hide solutions"/>
</div>
<div class="explain" id="qu7java">
<p>Load the merged ontology under Jena:</p>
<div class="java">
// (Sol1) Use SPARQL to answer queries (at the data level)
InputStream in = new FileInputStream( merged );
Model model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF,null);
model.read( in, "file:"+merged.getPath() );
in.close();
</div>
<p>Read the query (please play by changing the query)</p>
<div class="java">
// Create a new query
<!--String queryString = readFile( "query.sparql", Charset.defaultCharset() );
create(queryString);-->
Query query = QueryFactory.read( "file:query.sparql" );
</div>
<p>Evaluation:</p>
<div class="java">
// Execute the query and obtain results
QueryExecution qe = QueryExecutionFactory.create(query, model);
ResultSet results = qe.execSelect();
// Output query results
ResultSetFormatter.out(System.out, results, query);
</div>
The results for this evaluation is:
<div class="result">
---------------------------------------------------------------------------------------
| fn | ln | t | s |
=======================================================================================
......@@ -391,20 +695,122 @@ The results for these execution are, for SPARQL:
| "Chet" | "Baker" | "University Pie XXIII" | |
| "McCoy" | "Tyner" | "University of Soupaloignon" | "Dr Nanni Girasole" |
...
</pre>
for OWLReasoner:
<pre>
OWLReasoner(Merged): There are 47 students (Estudiante)
OWLReasoner(Merged): Estudiante is not necessarily subclass of Person
OWLReasoner(Merged): Estudiante is subclass of Student
</pre>
and for IDDL:
<pre>
IDDL: the alignment network is consistent
IDDL: Estudiante <= Person is not entailed
IDDL: Estudiante <= Student is entailed
</pre>
</div>
</div>
<h3><a name="construct"></a>Generating SPARQL constructs</h3>
<p>
A SPARQL construct query may be use for extracting data expressed
in one ontology and generate this data with respect to the other
ontology.
It is possible to generate such constructs from
<div class="button">
<input type="button" onclick="show('qu15cli')" value="Command line"/>
<!--input type="button" onclick="show('qu15java')" value="Java"/-->
<!--input type="button" onclick="show('qu15serv')" value="Browser"/-->
<input type="button" onclick="hide('qu15cli')" value="Hide solutions"/>
</div>
<div class="explain" id="qu15cli">
<div class="terminal">
$ java -cp $CLASSPATH fr.inrialpes.exmo.align.cli.ParserPrinter file:alignment.rdf -r fr.inrialpes.exmo.align.impl.renderer.SPARQLConstructRendererVisitor
</div>
which generates a set of queries containing at least this:
<div class="result">
PREFIX ns1:&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology2.owl#>
PREFIX ns0:&lt;http://alignapi.gforge.inria.fr/tutorial/tutorial4/ontology1.owl#>
PREFIX rdf:&lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {
?s rdf:type ns0:Estudiante .
}
WHERE {
?s rdf:type ns1:Student .
}
CONSTRUCT {
?s ns0:supervisor ?o .
}
WHERE {
?s ns1:phd-advisor ?o .
}
[...]
CONSTRUCT {
?s rdf:type ns0:Tutor .
}
WHERE {
?s rdf:type ns1:Professor .
}
[...]
CONSTRUCT {
?s ns0:lastname ?o .
}
WHERE {
?s ns1:name ?o .
}
[...]
CONSTRUCT {
?s ns0:year ?o .
}
WHERE {
?s ns1:year-in-phd ?o .
}
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {
?s ns0:country ?o .
}
WHERE {
?s ns1:country-of-study ?o .
}
CONSTRUCT {
?s ns0:gender ?o .
}
WHERE {
?s ns1:gender ?o .
}
CONSTRUCT {
?s ns0:firstname ?o .
}
WHERE {
?s ns1:first-name ?o .
}
CONSTRUCT {
?s ns0:city ?o .
}
WHERE {
?s ns1:city-of-study ?o .
}
CONSTRUCT {
?s ns0:topic ?o .
}
WHERE {
?s ns1:topics-of-interest ?o .
}
CONSTRUCT {
?s ns0:affiliation ?o .
}
WHERE {
?s ns1:institution ?o .
}
</div>
These queries may be applied to the entries of ontology2.owl and
generates triples using ontology1.
</div>
<h2>Full solution</h2>
<p>Do you want to see a possible solution?</p>
......
html/tutorial/tutorial4/ontology1.owl
+ 8
− 3
View file @ 64671892
......@@ -39,6 +39,12 @@
<rdfs:label xml:lang="es">Professor</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="TutorEstudiante">
<rdfs:subClassOf rdf:resource="#Estudiante" />
<rdfs:subClassOf rdf:resource="#Tutor" />
<rdfs:label xml:lang="es">Professor</rdfs:label>
</owl:Class>
<owl:DatatypeProperty rdf:ID="lastname">
<rdfs:domain rdf:resource="#Participante" />
<rdfs:range rdf:resource="&xsd;string" />
......@@ -304,8 +310,7 @@
<supervisor>Prof. Pierpaolo Polenta</supervisor>
</Estudiante>
<Estudiante rdf:about="#Zorn">
<rdf:type rdf:resource="#Tutor" />
<TutorEstudiante rdf:about="#Zorn">
<lastname>Zorn</lastname>
<firstname>John</firstname>
<gender>Male</gender>
......@@ -315,7 +320,7 @@
<year>1</year>
<topic>Complex Event Processing</topic>
<supervisor>Prof. Pierpaolo Polenta</supervisor>
</Estudiante>
</TutorEstudiante>
<Estudiante rdf:about="#Tyner">
<lastname>Tyner</lastname>
......
html/tutorial/tutorial4/ontology2.owl
+ 1
− 1
View file @ 64671892
......@@ -31,7 +31,7 @@
<rdfs:label xml:lang="en">Student</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="Professor">
<owl:Class rdf:ID="Teacher">
<rdfs:subClassOf rdf:resource="http://xmlns.com/foaf/0.1/Person" />
<owl:disjointWith rdf:resource="#Student" />
<rdfs:label xml:lang="en">Staff</rdfs:label>
......
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