diff --git a/html/tutorial/tutorial1/index.html b/html/tutorial/tutorial1/index.html
index cec3690abe282855a43d52d544ea3adc76ef00e4..8e342b57f887eee643a9d8d99f5e00808acddc15 100644
--- a/html/tutorial/tutorial1/index.html
+++ b/html/tutorial/tutorial1/index.html
@@ -44,14 +44,15 @@ div.logic {
<p style="border-bottom: 2px solid #AAAAAA; border-top: 2px solid
#AAAAAA; padding-top: 15px; padding-bottom: 15px;">
-Here is a small tutorial for the alignment <abbr>API</abbr>. Most of the tutorial is based on command-lines invocations. Of course, it is not the natural way to use this <abbr>API</abbr>: it is made for being <a href="../tutotial3/embbed.html">embedded in some application programme</a> and we are working towards implementing an <a href="server.html">alignment server</a> that can help programmes to use the <abbr>API</abbr> remotely. The complete tutorial is also available as a self-contained <a href="script.sh" title="script for UNIX systems">script.sh</a> or <a href="script.bat" title="script for Windows systems">script.bat</a>.
+Here is a small tutorial for the alignment <abbr>API</abbr>. Most of the tutorial is based on command-lines invocations. Of course, it is not the natural way to use this <abbr>API</abbr>: it is made for being <a href="../tutorial3/embed.html">embedded in some application programme</a> and we are working towards implementing an <a href="server.html">alignment server</a> that can help programmes to use the <abbr>API</abbr> remotely. The complete tutorial is also available as a self-contained <a href="script.sh" title="script for UNIX systems">script.sh</a> or <a href="script.bat" title="script for Windows systems">script.bat</a>.
We make no garantee on the MS-DOS script, it is only here for helping.
</p>
<p>A <a href="server.html">companion tutorial</a> has been designed for the Alignment
Server. It follows, as much as possible, the reasoning of this
tutorial but provides input and output through a web browser.</p>
-<div style="font-size: 75%;">This tutorial has been designed for the Alignment API version
- 2.4 (it has been updated to work with version 4.0).</div>
+<div style="font-size: 75%;">This tutorial has been updated for the Alignment API version
+ 4.0 (versions working with previous versions, starting with 2.4, can be found in their
+ respective html directory).</div>
<h2>Preparation</h2>
@@ -59,7 +60,7 @@ We make no garantee on the MS-DOS script, it is only here for helping.
First you must download the Alignment API and check that it works
as indicated <a href="../index.html">here</a>.</p>
-<p>You can <a href="../align.html">modify the Alignment <abbr>API</abbr> and its implementation</a>. In this tutorial, we will simply learn how to use it.</p>
+<p>You can <a href="../tutorial3/index.html"></a>modify the Alignment <abbr>API</abbr> and its implementation. In this tutorial, we will simply learn how to use it.</p>
<p>You will then go to the directory of this tutorial by doing:</p>
<div class="fragment">
@@ -95,7 +96,7 @@ between two bibliographic ontologies. They can be seen here:</p>
<dd>is an extension of the previous one that contains a number of supplementary concepts. It can be seen here in <a href="../myOnto.owl"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="../myOnto.html"><abbr>HTML</abbr></a>.</dd>
</dl>
-<p>These two ontologies have been used for a few years in the <a href="oaei.ontologymatching.org">Ontology Alignment Evaluation Initiative</a>.</p>
+<p>These two ontologies have been used for a few years in the <a href="http://oaei.ontologymatching.org">Ontology Alignment Evaluation Initiative</a>.</p>
<h2>Matching</h2>
@@ -137,7 +138,7 @@ and opening the <a href="results/equals.html">results/equals.html</a>
in a browser.
</p>
-<p>See the output in <a href="results/equal.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/equal.html"><abbr>HTML</abbr></a>.</p>
+<p>See the output in <a href="results/equal.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/equals.html"><abbr>HTML</abbr></a>.</p>
<p>The result is expressed in the Alignment format. This format, in <abbr>RDF</abbr>/<abbr>XML</abbr>, is made of a header containing "metadata" about the alignment:
</p>
<div class="owl"><pre>
@@ -185,7 +186,7 @@ in a browser.
$ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/levenshtein.rdf
</div>
-<p>See the output in <a href="results/levenshtein.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/levenshtein.html"><abbr>HTML</abbr></a>.</p>
+<p>See the output in <a href="results/levenshtein.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/levenshtein.html"><abbr>HTML</abbr></a> (if rendered as before).</p>
<p>This is achieved by specifying the class of Alignment to be used (through the <tt>-i</tt> switch) and the distance function to be used (<tt>-DstringFunction=levenshteinDistance</tt>).</p>
@@ -208,10 +209,10 @@ $ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.St
a WordNet based distance provided with the <abbr>API</abbr>
implementation by ($WNDIR is the directory where wordnet 3.0 is installed):</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.impl.util.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
+$ java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.util.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
</div>
-<p>See the output in <a href="jwnl.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="jwnl.html"><abbr>HTML</abbr></a>.</p></div>
+<p>See the output in <a href="results/jwnl.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/jwnl.html"><abbr>HTML</abbr></a> (if rendered as before).</p></div>
<h2>Manipulating</h2>
@@ -220,7 +221,7 @@ $ java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.ex
$ java -jar ../../../lib/procalign.jar file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.33 -o results/levenshtein33.rdf
</div>
-<p>See the output in <a href="results/levenshtein33.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/levenshtein33.html"><abbr>HTML</abbr></a>.</p>
+<p>See the output in <a href="results/levenshtein33.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/levenshtein33.html"><abbr>HTML</abbr></a> (if rendered as before).</p>
<p>As expected we have suppressed some of these inaccurate correspondences. But did we also suppressed accurate ones?</p>
<div class="button">
@@ -234,13 +235,13 @@ $ java -jar ../../../lib/procalign.jar file://$CWD/myOnto.owl file://$CWD/edu.mi
$ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -t 0.5 -o results/SMOA5.rdf
</div>
-<p>See the output in <a href="results/SMOA5.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/SMOA5.html"><abbr>HTML</abbr></a>.</p>
+<p>See the output in <a href="results/SMOA5.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/SMOA5.html"><abbr>HTML</abbr></a> (if rendered as before).</p>
<p><b>Other manipulations:</b> It is possible to invert an alignment with the following command:</p>
<div class="fragment">
$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter -i results/SMOA5.rdf -o results/AOMS5.rdf
</div>
-<p>See the output in <a href="results/AOMS5.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/AOMS5.html"><abbr>HTML</abbr></a>. The results is an alignment from the source to the target. Inverting alignment is only the exchange of the order of the elements in the alignment file. This can be useful when you have an alignment of <i>A</i> to <i>B</i>, an alignment from <i>C</i> to <i>B</i> and you want to go from <i>A</i> to <i>C</i>. The solution is then to invert the second alignment and to compose them.</p>
+<p>See the output in <a href="results/AOMS5.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/AOMS5.html"><abbr>HTML</abbr></a> (if rendered as before). The results is an alignment from the source to the target. Inverting alignment is only the exchange of the order of the elements in the alignment file. This can be useful when you have an alignment of <i>A</i> to <i>B</i>, an alignment from <i>C</i> to <i>B</i> and you want to go from <i>A</i> to <i>C</i>. The solution is then to invert the second alignment and to compose them.</p>
<div class="logic"><p><b>More work:</b> There is another switch (<tt>-T</tt>) in Procalign that specifies the way a threshold is applied (hard|perc|prop|best|span) the default being "hard". The curious reader can apply these and see the difference in results. How they work is explained in the Alignment <abbr>API</abbr> documentation.</p></div>
@@ -313,7 +314,7 @@ $ xsltproc results/SMOA5.xsl data.xml > results/data.xml
<h2>Evaluating</h2>
-<p>We will evaluate alignments by comparing them to some reference alignment which is supposed to express what is expected from an alignment of these two ontologies. The reference alignment is <a href="refalign.rdf">refalign.rdf</a> (or <a href="results/refalign.html"><abbr>HTML</abbr></a>).</p>
+<p>We will evaluate alignments by comparing them to some reference alignment which is supposed to express what is expected from an alignment of these two ontologies. The reference alignment is <a href="refalign.rdf">refalign.rdf</a> (or <a href="results/refalign.html"><abbr>HTML</abbr></a>, if rendered as before).</p>
<p>For evaluating we use another class than <tt>Procalign</tt>. It is called <tt>EvalAlign</tt> we should specify this to <tt>java</tt>. By default, it computes precision, recall and associated measures. It can be invoked this way:</p>
<div class="fragment">
@@ -356,19 +357,18 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i
<input type="button" onclick="hide('qu6')" value="Hide result"/>
</div>
<div class="explain" id="qu6"><pre>
-<?xml version='1.0' encoding='utf-8' standalone='yes'?>
<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
xmlns:map='http://www.atl.external.lmco.com/projects/ontology/ResultsOntology.n3#'>
<map:output rdf:about=''>
<map:input1 rdf:resource="http://alignapi.gforge.inria.fr/tutorial/myOnto.owl"/>
<map:input2 rdf:resource="http://alignapi.gforge.inria.fr/tutorial/edu.mit.visus.bibtex.owl"/>
- <map:precision>0.6153846153846154</map:precision>
+ <map:precision>0.6233766233766234</map:precision>
<map:recall>1.0</map:recall>
- <fallout>0.38461538461538464</fallout>
- <map:fMeasure>0.761904761904762</map:fMeasure>
- <map:oMeasure>0.375</map:oMeasure>
- <time>28</time>
- <result>1.625</result>
+ <fallout>0.37662337662337664</fallout>
+ <map:fMeasure>0.768</map:fMeasure>
+ <map:oMeasure>0.39583333333333326</map:oMeasure>
+ <time>47</time>
+ <result>1.6041666666666667</result>
</map:output>
</rdf:RDF>
</pre></div>
@@ -426,15 +426,15 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupEval -r
<td>0.53</td>
<td>0.96</td>
<td>0.69</td>
-<td>0.66</td>
+<td>0.67</td>
<td>0.96</td>
-<td>0.78</td>
+<td>0.79</td>
<td>0.51</td>
<td>1.00</td>
<td>0.68</td>
<td>0.62</td>
<td>1.00</td>
-<td>0.76</td>
+<td>0.77</td>
</tr>
<tr bgcolor="yellow"><td>H-mean</td><td>1.00</td>
<td>1.00</td>
@@ -445,18 +445,20 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupEval -r
<td>0.53</td>
<td>0.96</td>
<td>0.69</td>
-<td>0.66</td>
+<td>0.67</td>
<td>0.96</td>
-<td>0.78</td>
+<td>0.79</td>
<td>0.51</td>
<td>1.00</td>
<td>0.68</td>
<td>0.62</td>
<td>1.00</td>
-<td>0.76</td>
+<td>0.77</td>
</tr>
</tbody></table>
</center>
+<p><small>n/a: result alignment not provided or not readable<br />
+NaN: division per zero, likely due to empty alignment.</small></p>
<!--div class="fragment">
$ java -jar ../../../lib/Procalign.jar file://$CWD/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -DprintMatrix=1 -o /dev/null > matrix.tex
@@ -468,7 +470,7 @@ $ java -jar ../../../lib/Procalign.jar file://$CWD/rdf/edu.umbc.ebiquity.publica
<h2>Further exercises</h2>
-<p>More info: <a href="http://alignapi.gforge.inria.fr">http://alignapi.gforge.inria.fr</a></p>
+<p>More info: <a href="http://alignapi.gforge.inria.fr/tutorial/">http://alignapi.gforge.inria.fr/tutorial/</a></p>
<hr />
<small>
diff --git a/html/tutorial/tutorial1/server.html b/html/tutorial/tutorial1/server.html
index 572f90d763898a532179208824aa7ed30346897e..5a9243536597ee51af7172f17e2d7a84f2b0c66c 100644
--- a/html/tutorial/tutorial1/server.html
+++ b/html/tutorial/tutorial1/server.html
@@ -73,9 +73,9 @@ You can browse in these menus to see what is available.</p>
available on the web at http://alignapi.gforge.inria.fr. They can be seen here:</p>
<dl>
<dt>edu.mit.visus.bibtex.owl</dt>
- <dd>is a relatively faithfull transcription of BibTeX as an ontology. It can be seen here in <a href="edu.mit.visus.bibtex.owl"><abbr title="Ressource Description Framework">RDF</abbr>/<abbr title="eXtansible Markup Language">XML</abbr></a> or <a href="edu.mit.visus.bibtex.html"><abbr>HTML</abbr></a>.</dd>
+ <dd>is a relatively faithfull transcription of BibTeX as an ontology. It can be seen here in <a href="../edu.mit.visus.bibtex.owl"><abbr title="Ressource Description Framework">RDF</abbr>/<abbr title="eXtansible Markup Language">XML</abbr></a> or <a href="../edu.mit.visus.bibtex.html"><abbr>HTML</abbr></a>.</dd>
<dt>myOnto.owl</dt>
- <dd>is an extension of the previous one that contains a number of supplementary concepts. It can be seen here in <a href="myOnto.owl"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="myOnto.html"><abbr>HTML</abbr></a>.</dd>
+ <dd>is an extension of the previous one that contains a number of supplementary concepts. It can be seen here in <a href="../myOnto.owl"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="../myOnto.html"><abbr>HTML</abbr></a>.</dd>
</dl>
<h2>Matching</h2>
diff --git a/html/tutorial/tutorial2/index.html b/html/tutorial/tutorial2/index.html
index be29e235a49cc674ddbc2b33a7e3a2dce6d4c44e..2671572fcb30fb93b03ae8a7a76d858dff868758 100644
--- a/html/tutorial/tutorial2/index.html
+++ b/html/tutorial/tutorial2/index.html
@@ -34,6 +34,10 @@ div.logic {
<h1>Manipulating alignments in Java programs: advanced tutorial on the Alignment <abbr title="Application Programming Interface">API</abbr> and server</h1>
+<p style="background-color: yellow;">
+This tutorial is to be revised (by you can try it anyway and report).
+</p>
+<p>
<dl>
<dt>This version:</dt>
<dd>http://alignapi.gforge.inria.fr/tutorial/tutorial2/</dd>
@@ -41,6 +45,7 @@ div.logic {
<dd><a href="http://exmo.inrialpes.fr/people/euzenat">Jérôme Euzenat</a>, INRIA & LIG
</dd>
</dl>
+</p>
<p style="border-top: 2px solid
#AAAAAA; padding-top: 15px; padding-bottom: 15px;">
@@ -59,8 +64,8 @@ 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>
+A more <a href="../tutorial1/index.html">simple tutorial</a> as well as
+ a small <a href="../tutorial1/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 4.0.</small></p>
<h2>Preparation</h2>
@@ -78,7 +83,7 @@ We have two ontologies, <a href="ontology1.owl">ontology1.owl</a>
and <a href="ontology2.owl">ontology2.owl</a>, under which two sets of
students are described. Unfortunately, the
administration started to record participants with their own ontology
-before recogning that using <a href="http://foaf-project.org">FOAF</a>
+before finding 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>