From 04aa601b0d46bb07cae7c68bc944a3ff32949859 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Tue, 7 Jul 2009 10:47:21 +0000
Subject: [PATCH] - full tutorial nearly ready
---
html/tutorial2/index.html | 225 +++++++++++++++++++++++++-------------
1 file changed, 151 insertions(+), 74 deletions(-)
diff --git a/html/tutorial2/index.html b/html/tutorial2/index.html
index 68d04d41..7da5f389 100644
--- a/html/tutorial2/index.html
+++ b/html/tutorial2/index.html
@@ -51,31 +51,51 @@ This tutorial will learn you to:
<ul>
<li>communicate the alignment server
through its REST web service API,</li>
-<li>manipulate the Alignments with the Alignment API in Java,</li>
-<li>perform OWL reasoning on alignmed ontologies and compose
+<li>manipulate alignments with the Alignment API in Java,</li>
+<li>perform OWL reasoning on aligned ontologies and compose
alignments.</li>
</ul>
This time, the tutorial is based on Java programming and using various
related APIs.
</p>
<p>
-
A more <a href="../tutorial/index.html">simple tutorial</a> as well as
a small <a href="../tutorial/server.html">server tutorial</a> are also available.</p>
-<p style="border-top: 2px solid #AAAAAA;"><small>This tutorial has been designed for the Alignment API version 3.6.</small></p>
+<p style="border-top: 2px solid #AAAAAA;"><small>This tutorial has been designed for the Alignment API version 4.0.</small></p>
<h2>Preparation</h2>
-<p>See the <a href="../tutorial/index.html">simple tutorial preparation part</a>.</p>
+<p>
+See the <a href="../tutorial/index.html">simple tutorial
+preparation part</a>.
+</p>
+<p>
+Looking at the last section of this tutorial can help to manipulate
+the Alignment API constructs alone. In the present tutorial, we will
+interface the Alignment API with other components:
+<ul>
+<li>The Alignment server as a web service;</li>
+<li>A SPARQL reasoner (<a href=""></a>ARQ) using <a href=""></a>Jena;</li>
+<li>An OWL reasoner (<a href=""></a>Pellet) using OWL API.</li>
+</ul>
+</p>
<h2>Data</h2>
<p>
-We have two ontologies, to be found on the web, under which two half of the summerschool participants are described.
+We have two ontologies, <a href="ontology1.owl">ontology1.owl</a>
+and <a href="ontology2.owl">ontology2.owl</a>, under which two half of
+the summerschool participants are described. Unfortunately, the
+organiser started to record participants with their own ontology
+before recogning that using <a href="http://foaf-project.org">FOAF</a>
+would be a better idea. We now end up with two incomplete lists of
+participants.
</p>
<p>
-The goal is to have a unified view of these participants.
-.</p>
+The goal is to have a unified view of these participants. For that
+purpose, we will match the two ontologies and reason with the result
+in order to
+</p>
<p>For that purpose, you have to develop a program in Java. This
programme can be compiled by:
@@ -84,9 +104,13 @@ $ javac -classpath ../../lib/align.jar:../../lib/procalign.jar:../../lib/jena/je
</div>
and run by:
<div class="fragment">
-$ java -classpath .:../../lib/align.jar:../../lib/procalign.jar:../../lib/jena/jena.jar:../../lib/jena/arq.jar:../../lib/iddl/iddl.jar:../../lib/pellet/pellet.jar MyApp
+$ java -classpath .:../../lib/align.jar:../../lib/procalign.jar:../../lib/jena/jena.jar:../../lib/jena/arq.jar:../../lib/iddl/iddl.jar:../../lib/pellet/pellet.jar:../../lib/ontosim/ontosim.jar:../../lib/log4j/commons-logging.jar:../../lib/log4j/log4j.jar:../../lib/xerces/xercesImpl.jar:../../lib/jena/iri.jar:../../lib/jena/icu4j_3_4.jar:../../lib/jena/concurrent.jar MyApp
</div>
-
+The long list of jar is boring, but at list it is explicit and you
+should be safe with this one.
+<p>
+</p>
+You can start with the empty template <a href="Skeleton.java">Skeleton.java</a>.
</p>
<h2>Matching ontologies</h2>
@@ -94,8 +118,9 @@ $ java -classpath .:../../lib/align.jar:../../lib/procalign.jar:../../lib/jena/j
<p>
This can be achieved:
<ul>
-<li>by running programs either locally or from the alignment server</li>
<li>by finding an alignment from the web/server</li>
+<li>by running a matcher locally</li>
+<li>by running a matcher on the alignment server</li>
<li>by finding a chain of alignments from the web/server</li>
</ul>
</p>
@@ -103,84 +128,88 @@ This can be achieved:
<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, compute one and store it on the server.
+and, if none is found, computes one.
</p>
-
-
-<p>A skeleton of program using the Alignment <abbr>API</abbr> is <a href="Skeleton.java">Skeleton.java</a>. It can be compiled by invoking:</p>
-
-
<div class="button">
+ <input type="button" onclick="show('qu0')" value="Various variables"/>
<input type="button" onclick="show('qu1')" value="Show solution 1"/>
<input type="button" onclick="show('qu2')" value="Show solution 2"/>
<input type="button" onclick="show('qu3')" value="Show solution 3"/>
<input type="button" onclick="hide('qu1');hide('qu2');hide('qu3');" value="Hide solutions"/>
</div>
-<div class="explain" id="qu1"><p>After introducing the main variables:</p>
+<div class="explain" id="qu0">
+<p>After introducing the main variables:</p>
<pre>
- URI onto1 = null;
- URI onto2 = null;
String myId = "JETest";
- String u1 = "http://alignapi.gforge.inria.fr/tutorial/edu.mit.visus.bibtex.owl";
- String u2 = "http://alignapi.gforge.inria.fr/tutorial/myOnto.owl";
+ Alignment al = null;
+ URI uri1 = null;
+ URI uri2 = null;
+ //String u1 = "http://alignapi.gforge.inria.fr/tutorial2/ontology1.owl";
+ //String u2 = "http://alignapi.gforge.inria.fr/tutorial2/ontology2.owl";
+ String u1 = "file:ontology1.owl";
+ String u2 = "file:ontology2.owl";
String method = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
- // Parameters params = new BasicParameters();
+ String tempOntoFileName = "/tmp/myresult.owl";
+ Parameters params = new BasicParameters();
+ try {
+ uri1 = new URI( u1 );
+ uri2 = new URI( u2 );
+ } catch (URISyntaxException use) { use.printStackTrace(); }
</pre>
-<p>The programme will invoke the alignment server and parse the result:</p>
+</div>
+<div class="explain" id="qu1">
+<p>The programme will invoke the alignment server:</p>
<pre>
- // ***** First exercise: matching *****
- // Try to find an alignment between two ontologies from the server
- String match = getFromURLString( RESTServ+"find?onto1="+u1+"&onto2="+u2, true );
+ // (Sol1) Try to find an alignment between two ontologies from the server
+ // ask for it
+ String found = getFromURLString( RESTServ+"find?onto1="+u1+"&onto2="+u2, false );
+</pre>
+<p>Retrieve the alignment itself:</p>
+<pre>
+ // retrieve it
+ // If there exists alignments, ask for the first one
+ NodeList alset = extractFromResult( found, "//findResponse/alignmentList/alid[1]/text()", false );
+</pre>
+<p>And parse it:</p>
+<pre>
+ // parse it as an alignment
+ // (better passing to the SAXHandler)
+ AlignmentParser aparser = new AlignmentParser(0);
+ Alignment alu = aparser.parseString( xmlString );
+ al = ObjectAlignment.toObjectAlignment((URIAlignment)alu);
</pre>
</div>
-<div class="explain" id="qu2"><p>This programs use a local simple matching
- algorithm (StringDistAlignment) for obtaining an alignment:</p>
+<div class="explain" id="qu2"><p>:</p>
<pre>
-
-
-
-
-// Threshold at various thresholds
-// Evaluate them against the references
-// and choose the one with the best F-Measure
-AlignmentParser aparser = new AlignmentParser(0);
-Alignment reference = aparser.parse( "file://"+(new File ( "refalign.rdf" ) . getAbsolutePath()) );
-Evaluator evaluator = new PRecEvaluator( reference, a1 );
-
-double best = 0.;
-Alignment result = null;
-for ( int i = 0; i <= 10 ; i = i+2 ){
- a1.cut( ((double)i)/10 );
- evaluator.eval( new BasicParameters() );
- System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure());
- if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
- result = (BasicAlignment)((BasicAlignment)a1).clone();
- best = ((PRecEvaluator)evaluator).getFmeasure();
+ // (Sol2) Match the ontologies with a local algorithm
+ if ( al == null ){ // Unfortunatelly no alignment was available
+ AlignmentProcess ap = new StringDistAlignment();
+ ap.init( uri1, uri2 );
+ params.setParameter("stringFunction","smoaDistance");
+ ap.align( (Alignment)null, params );
+ al = ap;
}
-}
-
-// Displays it as SWRL Rules
-PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( System.out, "UTF-8" )), true);
-AlignmentVisitor renderer = new SWRLRendererVisitor(writer);
-result.render(renderer);
-writer.flush();
-writer.close();
-</pre></div>
-<div class="explain" id="qu3"><p>The main piece of code in Skeleton.java is replaced by:</p>
+</pre>
+</div>
+<div class="explain" id="qu3"><p>Match on the server:</p>
<pre>
+ // (Sol3) Match the ontologies on the server
+ if ( alset.getLength() == 0 ) {
+ // call for matching
+ String match = getFromURLString( RESTServ+"match?onto1="+u1+"&onto2="+u2+"&method="+method+"&pretty="+myId+"&action=Match&force=true", true );
+ }
</pre>
+<p>The remainder is the same as in the first solution.</p>
</div>
<div class="logic">
-<p><b>More work:</b> You can also have the matching algorithms run on
- the server instead of localy.</p>
+<p><b>More work:</b> You can also store localy computed alignments on
+ the alignment server.</p>
</div>
<div class="button">
<input type="button" onclick="show('qu4')" value="Show solution"/>
<input type="button" onclick="hide('qu4');" value="Hide solution"/>
</div>
-<div class="explain" id="qu4"><p>The main piece of code in Skeleton.java is replaced by:</p>
+<div class="explain" id="qu4"><p>Not ready yet (but not difficult)</p>
<pre>
</pre>
</div>
@@ -193,52 +222,100 @@ Again, this is either:
<li>generating OWL axioms from the alignments and merge the ontologies</li>
<li>transforming data from one ontology to another</li>
</ul>
-This can be done with the alignment API support.
</p>
<p>
-Show how it can be done in both cases:
+This can be done with the alignment API support.
</p>
+
<div class="button">
<input type="button" onclick="show('qu5')" value="Show solution 1"/>
<input type="button" onclick="show('qu6')" value="Show solution 2"/>
<input type="button" onclick="hide('qu5');hide('qu6');" value="Hide solutions"/>
</div>
-<div class="explain" id="qu5"><p>The main piece of code in Skeleton.java is replaced by:</p>
+<div class="explain" id="qu5">
+<p>In fact everything is done in one step:</p>
<pre>
+ // (Sol1) generate a merged ontology between the ontologies (OWLAxioms)
+ File merged = new File( tempOntoFileName );
+ PrintWriter writer = new PrintWriter ( new FileWriter( merged, false ), true );
+ AlignmentVisitor renderer = new OWLAxiomsRendererVisitor(writer);
+ al.render(renderer);
+ writer.flush();
+ writer.close();
</pre>
+<p>You can look at the result in myresult.owl</p>
</div>
-<div class="explain" id="qu6"><p>The main piece of code in Skeleton.java is replaced by:</p>
+<div class="explain" id="qu6"><p>Not ready yet</p>
<pre>
</pre>
</div>
-
<h2>Generate the answers</h2>
<p>
This can be done in two ways:
<ul>
-<li>using SPARQL but I think that I already</li>
+<li>using SPARQL</li>
<li>using Pellet or something to answer these queries.</li>
</ul>
-Indeed, I will go for the second one (too bad because the first one is nice).
+</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 runing 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 solution 1"/>
<input type="button" onclick="show('qu8')" value="Show solution 2"/>
<input type="button" onclick="hide('qu7');hide('qu8');" value="Hide solutions"/>
</div>
-<div class="explain" id="qu7"><p>The main piece of code in Skeleton.java is replaced by:</p>
+<div class="explain" id="qu7">
+<p>Prepare the system:</p>
+<pre>
+ // (Sol1) Use SPARQL to answer queries (at the data level)
+ InputStream in = new FileInputStream( merged );
+ //OntModelSpec.OWL_MEM_RDFS_INF or no arguments to see the difference...
+ Model model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF,null);
+ model.read(in,"file:///tmp/myresult.owl");
+ in.close();
+</pre>
+<p>Query (please play by chaging the query)</p>
<pre>
+ // 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/tutorial2/ontology1.owl#> " +
+ "SELECT ?fn ?ln ?t " +
+ "WHERE {" +
+ " ?student rdf:type aa:Person . " +
+ " ?student aa:firstname ?fn. " +
+ " ?student aa:lastname ?ln. " +
+ " ?student aa:topic ?t . " +
+ " }";
+</pre>
+<p>Evaluation:</p>
+<pre>
+ Query query = QueryFactory.create(queryString);
+
+ // 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);
</pre>
</div>
-<div class="explain" id="qu8"><p>The main piece of code in Skeleton.java is replaced by:</p>
+<div class="explain" id="qu8"><p>Not yet available</p>
<pre>
</pre>
</div>
+<h2>Full solution</h2>
+
<p>Do you want to see a possible solution?</p>
-
<p>A full working solution is <a href="MyApp.java">MyApp.java</a>.</p>
--
GitLab