diff --git a/html/align.html b/html/align.html
index ca1e63375570f067308050371540ef42c0a4accc..1ba82ff2047d87bd41afa5c133fc91c7ae0ab508 100644
--- a/html/align.html
+++ b/html/align.html
@@ -1,81 +1,31 @@
<html>
<head>
-<title>The alignment API in Java</title>
+<title>Alignment API: Quick start</title>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
-<h1 class="titre">The alignment API in Java</h1>
-
-<p>We have developed an alignment toolkit for OWL by:
-<ul compact="1">
-<li>Extending the OWL-API towards <a href="format.html">alignment</a>;</li>
-<li>Providing an implementation of the Alignment API;</li>
-<li>Implementing further alignment methods;</li>
-</ul></p>
+<h1 class="titre">Quick start with the Alignment API in Java</h1>
<p>An extensive presentation of the alignment API can be
- found <a href="align.pdf">here</a>. We also have
- a <a href="tutorial">tutorial</a> on using it.</p>
+ found at <a href="http://gforge.inria.fr/docman/?group_id=117">http://gforge.inria.fr/docman/?group_id=117</a>. We also have
+ an on-line <a href="tutorial">tutorial</a> on using it.</p>
+
+<h2>Fetching the Alignment API and starting</h2>
-<h2>Getting the Alignment API</h2>
+<h3>Requirements</h3>
+
+<p><b>For using</b> you will need <a href="http://java.sun.com">Java
+ runtime environment</a> (tested in 1.5). All other necessary
+ libraries are available in the archive (see the list of <a href="lib.html">libraries</a>).</p>
<h3>Fetching the ZIP'ed version</h3>
<p>The simplest way to use alignapi is to get the last release
zipfile from the site <a href="http://gforge.inria.fr/frs/?group_id=117">http://gforge.inria.fr/frs/?group_id=117</a>. It contains all the sources, compiled
-library, OWL API library.</p>
-
-<h3>Anonymous Subversion</h3>
-
-<p>The very last version of alignapi can be fetched from the subversion
- source tree that can be found at:
-<a href="http://gforge.inria.fr/scm/?group_id=117">http://gforge.inria.fr/scm/?group_id=117</a>
-</p>
-<p>From there you have two options:
-<dl compact="1">
-<dt>Getting the last nightly build</dt>
-<dd>This will provide you with the source but no opportunity to
- smoothly upgrade it.</dd>
-<dt>Checking out (anonymously) the repository</dt>
-<dd>Can be achieved by just doing the following:
-<!-- $ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft login
-<ENTER return when asked for the password>
-$ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft checkout
-alignapi-->
-<div class="fragment"><pre>
-$ svn checkout svn://scm.gforge.inria.fr/svn/alignapi/trunk/
-</pre></div>
-... and you are done.</dd>
-</dl>
-Note that you may have to fetch separately the <a href="owlapi.html">OWL-API</a>.</p>
-
-<h3>Subversion account</h3>
-
-<p>If you have improved alignapi and want this to be included in the
- source base or if you want to seriously work on improving the
- software, please contact
- Jerome . Euzenat (À) inrialpes . fr.</p>
-
-<p>We can either commit your ponctual changes or give you commit
- rights to the repository (for that purpose, you will have to first
- register by <a href="http://gforge.inria.fr">http://gforge.inria.fr</a>.</p>
-
-<p>Once provided with a password you will be able to check out from and
- commit in our repository through:
-<div class="fragment"><pre>
-<!--
-$ export CVS_RSH=`which ssh`
-$ cvs -d :ext:<loginname>@cvs-sop.inria.fr:/CVS/exmosoft --
- --checkout alignapi
--->
-$ svn checkout svn+ssh://username@scm.gforge.inria.fr/svn/alignapi/trunk
-</pre></div>
-(If you are not familliar with subversion, it is worth looking at the
-documentation. If you are familiar with CVS, the move is straightforward.)
-</p>
+library, required libraries.</p>
<h3>Running</h3>
@@ -92,114 +42,137 @@ options are:
--debug[=n] -d [n] Report debug info at level n
--help -h Print this message
</pre></div>
-More details are available below.
-</p>
-
-<h3>Release notes</h3>
-<p>They are provided <a href="relnotes.html">here</a>.</p>
+Congratutalations, you are done. We
+advise you to learn more by using the <a href="tutorial">tutorial</a>
+and the documentation.</p>
-<h3>Documentation</h3>
-<p>The documentation can be found on <a href="http://gforge.inria.fr/docman/?group_id=117">http://gforge.inria.fr/docman/?group_id=117</a>.</p>
+<p>Details below are for developing with the Alignment API.</p>
-<h2>Installation</h2>
+<h3>Bug reports</h3>
-<p>"Installing" is really straightforward.</p>
-
-<h3>Files</h3>
+<h2>Package content</h2>
<p>Whatever your mode of getting ontolign you will get an alignapi
directory containing the following subdirectories:
<ul compact="1">
- <li>src: source classes;</li>
- <li>rdf: some examples to be tested;</li>
- <li>results: some result alignments and evaluations;</li>
+ <li>README.TXT this file</li>
+ <li>README.AServ instructions for setting up an Alignment Server</li>
+ <li>LICENSE.TXT the terms under which the software is licensed to you.</li>
+ <li>build.xml: ant file to compile and generate jar-files.</li>
<li>dtd: the align.dtd and align.owl alignment specification;</li>
- <li>lib: jar-files (in the zip-file the owl-api libraries are included);</li>
+ <li>lib: contains align.jar, alignwn.jar, procalign.jar, alignsvc.jar
+ and other necessary jarfiles;</li>
<li>html: a few html presentation files</li>
<li>html/tutorial: a tutorial on using the API</li>
- <li>build.xml: ant file to compile and generate jar-files.</li>
<li>distrib: contains a few files for building the distribution</li>
<li>classes: the compiled classes (in the zip file, the classes are
included)</li>
- <li>samples: </li>
+ <li>examples: some examples of use of the API and the Server.</li>
<li>javadoc: generated javadoc (in the zip file the doc are
pregenerated);</li>
+ <li>src: source classes:
+ <ul compact="1">
+ <li>org.semanticweb.owl.align: the API
+ <li>fr.inrialpes.exmo.align.impl: basic implementation</li>
+ <li>fr.inrialpes.exmo.align.util: utility wrapper functions</li>
+ <li>fr.inrialpes.exmo.align.ling: WordNet-based implementation</li>
+ <li>fr.inrialpes.exmo.align.service: Alignment Service</li>
+</ul></li>
</ul>
</p>
-<h3>Requirements</h3>
+<h2>Developing with the Alignement API</h2>
-<p><b>For using</b> you will need <a href="http://java.sun.com">Java
- runtime environment</a> (tested in 1.4.1) and the <a href="owlapi.html">OWL-API binary distribution</a> (this is
- included in the above zip file).<br/>
-Note that OWL-API needs log4j and getopt packages, but these are
- included in the binary distribution of the OWL API.
-</p>
+<h3>Requirements</h3>
<p><b>For extending</b> you will need Java compiler (tested in <a href="http://java.sun.com">Java
- standard edition</a> 1.4.1) and the <a href="owlapi.html">OWL-API binary distribution</a> (this is included in the
- above zip file).
+ standard edition</a> 1.5). Other libraries are included. It is also very usefull to have <a ref="http://ant.apache.org">Ant</a>.</p>
-<p><b>For developing</b> (compiling) you will need Java compiler
- (tested in <a href="http://java.sun.com">Java standard edition</a> 1.4.1) and the <a href="owlapi.html">OWL-API binary distribution</a> (which is
- included in the SVN repository). It is also very usefull to
- have <a ref="http://ant.apache.org">Ant</a>.</p>
+<h3>Compilation and use</h3>
-<h3>Required libraries (jar)</h3>
-
-<p>Using the api (align.jar) requires:
-<ul compact="1">
-<li>OWL-API (api.jar)</li>
-</ul></p>
-<p>Using its implementation (procalign.jar) requires in addition:
-<ul compact="1">
-<li>the implementation of the OWL-API (impl.jar, io.jar, rdfparser.jar,
-rdfapi.jar),</li>
-<li>GNU parameter management (getopt.jar),</li>
-<li>(log4j.jar).</li>
-</ul></p>
-<p>Using the <a href="alignwn.html">Wordnet example</a> requires, in
-addition:
-<ul compact="1">
-<li>commons-logging.jar</li>
-<li>The Java WordNet Library (jwnl.jar).</li>
-</ul></p>
-
-<h3>Assembling</h3>
-
-<p>A good way of setting your environment (from the SVN archive) for
- developing is to unzip the OWL-API binary distribution and put the
- files in the alignapi directories:
+<p>Generating the jar-files corresponding to the Alignment API can
+ be achieved by launching:
<div class="fragment"><pre>
-$ unzip owlapi-bin-03-10-15.zip
-$ mv owl/lib/* lib
$ ant jar
-$ mv owl/javadoc/* javadoc
-$ ant javadoc
-$ rm -rf owl
</pre></div>
-</p>
+This recompiles the necessary files.</p>
-<h2>Compilation and use</h2>
+<p>Only compiling the necessary files is obtained by:
+<div class="fragment"><pre>
+$ ant compile
+</pre></div></p>
-<p>Generating the lib/procalign.jar file (and the other libraries) can
- be done by launching:
+<p>Recompiling all files is achieved by:
<div class="fragment"><pre>
-$ ant jar
+$ ant compileall
</pre></div></p>
-<h2>Using the API</h2>
+<h3>Typical development with the API</h3>
+
+<p>We can distinguish four types of developments in the API:
+<ul>
+<li>Developing the API: modifying the code of the API for adding
+ functions or fixing bugs;</li>
+<li>Extending the API: creating new instances of the API interface
+ (new alignment methods, new renderers, new server plug-ins, etc.);</li>
+<li>Embedding the API: creating an application using the API which
+ directly embedded the API libraries and invoke them;</li>
+<li>Using the API as a server: creating an application using the API
+ which communicates loosely with an instance of Alignment Server.</li>
+</ul></p>
+
+<p>In theory, only the first aspect requires recompiling and modifying
+ the Alignment API code. However, it may be useful for others (for
+ instance for debugging).</p>
+
+<!--h3>Anonymous Subversion</h3>
+
+<p>The very last version of alignapi can be fetched from the subversion
+ source tree that can be found at:
+<a href="http://gforge.inria.fr/scm/?group_id=117">http://gforge.inria.fr/scm/?group_id=117</a>
+</p>
+<p>From there you have two options:
+<dl compact="1">
+<dt>Getting the last nightly build</dt>
+<dd>This will provide you with the source but no opportunity to
+ smoothly upgrade it.</dd>
+<dt>Checking out (anonymously) the repository</dt>
+<dd>Can be achieved by just doing the following:-->
+<!-- $ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft login
+<ENTER return when asked for the password>
+$ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft checkout
+alignapi-->
+<!--div class="fragment"><pre>
+$ svn checkout svn://scm.gforge.inria.fr/svn/alignapi/trunk/
+</pre></div>
+... and you are done.</dd>
+</dl>
+Note that you may have to fetch separately the <a href="owlapi.html">OWL-API</a>.</p>
-<p>A <a href="tutorial">tutorial</a> presents how to use the Alignment
- API</p>
+<h3>Subversion account</h3>
-<p>An extensive presentation of the alignment API can be found
-in the documentation section. It documents use and extension of the API.</p>
+<p>If you have improved alignapi and want this to be included in the
+ source base or if you want to seriously work on improving the
+ software, please contact
+ Jerome . Euzenat (À) inrialpes . fr.</p>
-<h2>License</h2>
+<p>We can either commit your ponctual changes or give you commit
+ rights to the repository (for that purpose, you will have to first
+ register by <a href="http://gforge.inria.fr">http://gforge.inria.fr</a>.</p>
-<p>The alignment API and its implementation is distributed under the
- GNU <a href="../distrib/LICENSE.TXT">Lesser General Public License</a>.</p>
+<p>Once provided with a password you will be able to check out from and
+ commit in our repository through:
+<div class="fragment"><pre-->
+<!--
+$ export CVS_RSH=`which ssh`
+$ cvs -d :ext:<loginname>@cvs-sop.inria.fr:/CVS/exmosoft --
+ --checkout alignapi
+-->
+<!--$ svn checkout svn+ssh://username@scm.gforge.inria.fr/svn/alignapi/trunk
+</pre></div>
+(If you are not familliar with subversion, it is worth looking at the
+documentation. If you are familiar with CVS, the move is straightforward.)
+</p-->
<h2>The alignment API</h2>
<p>The OWL-API is extended with the
@@ -244,7 +217,7 @@ in the documentation section. It documents use and extension of the API.</p>
distance on class names. It thus have to build a matrix of distance
and to choose the alignment from the distance. It can be called by:
<div class="fragment"><pre>
-$ java -jar lib/procalign.jar file://localhost$CWD/rdf/onto1.owl file://localhost$CWD/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
+$ java -jar lib/procalign.jar file://$CWD/rdf/onto1.owl file://$CWD/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
</pre></div>
which returns:
<div class="code"><pre>
@@ -256,8 +229,8 @@ which returns:
<xml>yes</xml>
<level>0</level>
<type>11</type>
- <onto1>file://localhost$CWD/rdf/onto1.owl</onto1>
- <onto2>file://localhost$CWD/rdf/onto2.owl</onto2>
+ <onto1>file://$CWD/rdf/onto1.owl</onto1>
+ <onto2>file://$CWD/rdf/onto2.owl</onto2>
<map>
<Cell>
<entity1 rdf:resource='http://www.example.org/ontology1#reviewedarticle'/>
diff --git a/html/alignwn.html b/html/alignwn.html
index 8d9b76e6bc939b21fe8c6d673d2f1c9e8d912eb8..358c0839d8b248890c9e39a57b4d176ba8ab2ef0 100644
--- a/html/alignwn.html
+++ b/html/alignwn.html
@@ -48,14 +48,14 @@ the path of this dict directory:
<p>This usually can be obtained by:
<pre>
$ setenv CWD `pwd`
-$ java -jar lib/procalign.jar file://localhost$CWD/rdf/edu.umbc.ebiquity.publication.owl file://localhost$CWD/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.ling.JWNLAlignmentTest -o aligns/JWNL.owl
+$ 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.ling.JWNLAlignmentTest -o aligns/JWNL.owl
</pre>
<address>
<small>
<hr />
-<center>http://co4.inrialpes.fr/align/alignwn.html</center>
+<center>http://alignapi.gforge.inria.fr/alignwn.html</center>
<hr />
$Id$
</small>
diff --git a/html/aserv.html b/html/aserv.html
new file mode 100644
index 0000000000000000000000000000000000000000..5a0f601b3ad3ed9075e4736e6455b597bcf89cd6
--- /dev/null
+++ b/html/aserv.html
@@ -0,0 +1,100 @@
+<html>
+<head>
+<title>Alignment API: Server</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<h1 class="titre">Setting up an Alignment Server</h1>
+
+<p>An extensive presentation of the alignment API can be
+ found at <a href="http://gforge.inria.fr/docman/?group_id=117">http://gforge.inria.fr/docman/?group_id=117</a>. We also have
+ an on-line <a href="tutorial">tutorial</a> on using it.</p>
+
+<h2>Requirements</h2>
+
+<p>Using the alignment server requires an SQL database server.
+We see here, how to use mysql (http://dev.mysql.com/doc/refman).</p>
+
+<h2>Creating the MySQL database</h2>
+
+<div class="fragment"><pre>
+$ sudo /usr/local/mysql/bin/mysqld_safe --user=mysql &
+$ /usr/local/mysql/bin/mysqladmin -u root password <mysqlpassword>
+$ /usr/local/mysql/bin/mysqladmin -u root -h localhost password <mysqlpassword>
+$ /usr/local/mysql/bin/mysql -u root -p<mysqlpassword>
+sql> CREATE DATABASE AServDB;
+sql> GRANT ALL PRIVILEGES ON AServDB.* TO adminAServ@localhost IDENTIFIED BY 'aaa345';
+sql> quit
+</pre></div>
+<p>
+Of course, you are advised to use different user, password and
+database name. This can be achieved either:
+<ul>
+<li>by changing values of DBMSBASE, DBMSUSER and DBMSPASS in AlignmentServer and recompiling;</li>
+<li>by passing parameters dbmsbase, dbmsuser and dbmspass to
+ AlignmentServer.</li>
+</ul>
+</p>
+
+<p>Sample backup of the server content:
+<div class="fragment"><pre>
+$ /usr/local/mysql/bin/mysqldump -u adminAServ -paaa345 AServDB > toto.sql
+</pre></div>
+And restoring:
+<div class="fragment"><pre>
+$ /usr/local/mysql/bin/mysql -u adminAServ -paaa345 AServDB
+sql> source toto.sql;
+</pre></div>
+</p>
+
+<h2>Launching the Alignment server</h2>
+
+<p>The next time it is sufficient that mysql is running... (with the database loaded)
+
+<div class="fragment"><pre>
+$ sudo /usr/local/mysql/bin/mysqld_safe --user=mysql &
+</pre></div>
+
+<div class="fragment"><pre>
+$ java -jar lib/alignsvc.jar -H
+</pre></div>
+
+The alignment server is then available through HTTP with:
+
+ http://localhost:8089/html/
+</p>
+
+<h2>Ports used by the Alignment Server (by default)</h2>
+
+<p>The alignment server is a communicating system that communicates through
+TCP sockets which are bound to ports on your machines. We provide here the
+list of default ports and options to change them as well as the necessity
+for the firewalls to open these ports:
+
+<center>
+<table>
+<th><td>default</td><td>option</td><td>open?</td></th>
+<tr><td>HTTP</td><td>8089</td><td>-H</td><td>Y</td></tr>
+<tr><td>Jade</td><td>8888</td><td>-A</td></tr>
+<tr><td>//</td><td>1099</td><td></td><td>? (RMI)</td></tr>
+<tr><td></td><td>7778</td><td></td><td>Y (MTP HTTP)</td></tr>
+<tr><td>WSDL</td><td>7777</td><td>-W</td></tr>
+<tr><td>JXTA</td><td>6666</td><td>-P</td></tr>
+<tr><td>MySQL</td><td>3306</td><td>--dbmsport</td><td>N (if on the same machine)</td></tr>
+</table>
+</center>
+</p>
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/aserv.html</center>
+<hr />
+$Id$
+</small>
+</address>
+</body>
+</html>
diff --git a/html/credits.html b/html/credits.html
new file mode 100644
index 0000000000000000000000000000000000000000..d10428c2226fcccb067db8924c4f1f7b14abc026
--- /dev/null
+++ b/html/credits.html
@@ -0,0 +1,95 @@
+<html>
+<head>
+<title>Alignment API: Credits</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<center><h1>Alignment API: Credits</h1></center>
+
+<h2>Contributors</h2>
+
+<p>Below is the name of individual whose work has contributed to the
+ Alignment API. This can be either because they directly worked on
+ the project or because the released some code that has been
+ integrated within the project.</p>
+
+<dl>
+<dt><a href="http://exmo.inrialpes.fr/people/euzenat">Jérôme Euzenat</a></dt><dd>is the main architect and
+ developer of the Alignment API and Server.</dd>
+<dt><a href="">Petko Valtchev</a></dt><dd>was instrumental in fixing many
+ different parts of the code when working on other projects.</dd>
+<dt><a href="">Jérôme Pierson</a></dt><dd>initially developed the
+ WordNet interface and the agent profile for the Alignment Server</dd>
+<dt><a href="">Seunkeun Lee</a></dt><dd>developped the low-level
+ storage layer and the web service profile for the Alignment Server</dd>
+<dt><a href="">Raphaël Troncy</a></dt><dd>fixed the basic
+ implementation of BasicAlignment for n:m alignments.</dd>
+<dt><a href="">Arun Sharma</a></dt><dd>Developed the queryinterface</dd>
+<dt><a href="">Giorgos Stoilos and Georges Stamou</a></dt><dd>offered the code of their "SMOA" paper
+ similarity</dd>
+<dt><a href="">Sean Bechhofer</a> and
+<a href="">Raphael Voltz</a></dt><dd>provided some code snippets for
+ using the OWL API</dd>
+<dt><a href="">Jarno Elonen</a></dt><dd>developped a small footprint HTTP server
+ that is embedded in the Alignment Server</dd>
+<dt><a href="">Konstantinos A. Nedas</a></dt><dd>implemented the Hungarian method which is
+ embedded in the Alignment API implementation.</dd>
+<dt><a href="">an anonymous person</a></dt><dd>developped the Levensthein
+ distance implementation that is used in the Alignement API
+ implementation.</dd>
+</dl>
+
+<h2>Copyright owners</h2>
+
+<p>
+Copyright (C) 2003-2007 INRIA Rhône-Alpes (most of the code)<br />
+Copyright (C) 2004-2005 Université de Montréal (parts of the impl/ and
+ling/ directories)<br />
+Copyright (C) 2005 CNR Pisa. (parts of BasicAlignment)<br />
+Copyright (C) 2003 The University of Manchester (parts of the util/ directory)<br />
+Copyright (C) 2003 The University of Karlsruhe (parts of the util/ directory)<br />
+Copyright (C) 2005 Konstantinos A. Nedas (HungarianAlgorithm).<br />
+Copyright (C) 2006 CERT. (ISub class in org.ivml.alimo)<br />
+Copyright (C) 2006 Seungkeun Lee. (server database access in service/)<br />
+Copyright (C) 2001, 2005-2006 Jarno Elonen. (parts of HTTPAServProfile)<br />
+Copyright (C) 2006-2007 Orange R&D (parts of JADEFIPAAServProfile)<br />
+</p>
+
+<h2>Acknowledgements</h2>
+
+<p>Other people participated in the developement of the Alignment API
+ by providing bug reports, feature requests and patches:
+Mathieu d'Aquin,
+Mark Ingram,
+Antoine Isaac,
+Kotis Kostas,
+Sabine Mass;mann,
+Vassilis Spiliopoulos,
+Anna Zhdanova
+</p>
+
+<h2>Enablers</h2>
+
+<p>See the list of <a href="lib.html">Embedded libraries</a> for the
+ enabling technologies the Alignment API gladly relies on.</p>
+
+<h2>Sponsors</h2>
+
+<dl>
+<dt><a href="http://knowledgeweb.semanticweb.org">Knowledge web</a></dt><dd></dd>
+<dt><a href="http://www.neon-project.org">NeOn</a></dt><dd></dd>
+<dt><a href="http://www.webcontent.fr">WebContent</a></dt><dd></dd>
+</dl>
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/credits.html</center>
+<hr />
+$Id$
+</small>
+</body>
+</html>
diff --git a/html/eval.html b/html/eval.html
index d5088a574ced15524b95413d7c7afa28e5815220..718ff9f111da52480c37fe97f96f30c845a7ef69 100644
--- a/html/eval.html
+++ b/html/eval.html
@@ -35,7 +35,7 @@ options are:
</pre>
or ($CWD is the current directory)
<pre>
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign file://localhost$CWD/result/align1.owl file://localhost$CWD/result/align2.owl
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign file://$CWD/result/align1.owl file://$CWD/result/align2.owl
</pre>
</p>
@@ -49,9 +49,16 @@ $ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign file://local
class.</p>
<p>The <tt>BasicEvaluator</tt> has the good taste of defining the storage
sructures for alignment, but that is all.</p>
-<p>The <tt>PRecEvaluator</tt> class extends
- the <tt>BasicEvaluator</tt> by computing a very basic
- Precision/Recall rate.</p>
+<p>The <tt>BasicEvaluator</tt> has been extended so as to provide
+ different evaluation:
+<dl>
+<dt><tt>PRecEvaluator</tt></dt><dd>computes
+ Precision/Recall rates as well as derived measures.</dd>
+<dt><tt>ExtPRecEvaluator</tt></dt><dd>provide the relaxed precision
+ and recall as defined in a paper by Ehrig and Euzenat in 2005.</dd>
+<dt><tt></tt></dt><dd></dd>
+</dl>
+</p>
</p>
<address>
diff --git a/html/format.html b/html/format.html
index 6bf0eb46d327cb54d5f0a62372a44e4da16d2e06..80a615f37c0161b286c20126863906cfdd10db0e 100644
--- a/html/format.html
+++ b/html/format.html
@@ -9,7 +9,7 @@
<h1 class="titre">A format for ontology alignment</h1>
-<p>A format for expressing ontology alignment is provided here. Its
+<p>The Alignment API use a general Alignment format. Its
goal is to be able to express an alignment in a consensual
format. It can then be manipulated by various tools which will use
it as imput for further alignment methods, transform it into axioms
@@ -72,22 +72,18 @@
its implementation). Currently, the relation is expressed as a string.</p>
<h2>JAVA implementation</h2>
-<p>There is a <a href="align.html">JAVA API</a>, extending the <a href="owlapi.html">OWL API</a> implementing this
- format.</p>
-<p>We have implemented this API and provided tools for:
+<p>The Alignment API implements this format. In particular it provides tools for:
<ul compact="1">
<li>Outputing the RDF/XML format from the API;</li>
<li>Parsing the RDF/XML format into the API;</li>
<li>Processing alignment methods on ontologies and generating the
alignment Cells.</li>
</ul></p>
-<p>This API and its implementation could fairly easily be adapted to
- other representation languages than OWL.</p>
<p>There is a small stand-alone program that parses an alignment and
displays it ($CWD is the directory where you are):
-<pre>
-$ java -jar lib/procalign file://localhost$$CWD/rdf/onto1.owl file://localhost$CWD/rdf/onto2.owl
+<div class="fragment"><pre>
+$ java -jar lib/procalign file://$CWD/rdf/onto1.owl file://$CWD/rdf/onto2.owl
<?xml version='1.0' encoding='utf-8' standalone='no'?>
<!DOCTYPE rdf:RDF SYSTEM "align.dtd">
@@ -97,8 +93,8 @@ $ java -jar lib/procalign file://localhost$$CWD/rdf/onto1.owl file://localhost$C
<Alignment>
<xml>yes</xml>
<type>11</type>
- <onto1>file://localhost$CWD/rdf/onto1.owl</onto1>
- <onto2>file://localhost$CWD/rdf/onto2.owl</onto2>
+ <onto1>file://$CWD/rdf/onto1.owl</onto1>
+ <onto2>file://$CWD/rdf/onto2.owl</onto2>
<map>
<Cell>
<entity1 rdf:resource='http://www.example.org/ontology1#journalarticle'/>
@@ -109,7 +105,7 @@ $ java -jar lib/procalign file://localhost$$CWD/rdf/onto1.owl file://localhost$C
</map>
</Alignment>
</rdf:RDF>
-</pre>
+</pre></div>
</p>
<address>
diff --git a/html/impl.html b/html/impl.html
new file mode 100644
index 0000000000000000000000000000000000000000..6cb29e758408d0ade49696bf722e8078644f0d14
--- /dev/null
+++ b/html/impl.html
@@ -0,0 +1,63 @@
+<html>
+<head>
+<title>Alignment API: Systems</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<center><h1>Alignment API: System using the Alignment API</h1></center>
+
+<h2>Systems embarking the alignment API</h2>
+
+<p>These systems can use any implementation of the API and integrate
+ many more matching algorithms.</p>
+
+Alignment Server
+Anna's stuff
+<dt><a href="http://align.deri.org">[<font color="red">OWL Ontology Aligner</font>]</a></dt>
+<dd>A server built around the API for processing, editing and
+ rendering alignments (University of Innsbruck).</dd>
+Adrian's stuff when the merge is completed
+<dt><a href="http://VisOn.gforge.inria.fr">[<font color="red">VisOn</font>]</a></dt>
+<dd>The VisOn ontology visualizer now works with any implementation of
+ the API. It provides the opportunity to load and display
+ ontologies, load, run, display and compare alignment algorithms.</dd>
+</dl></p>
+
+
+<h2>Systems implementing the Alignment API</h2>
+
+<p>These systems offer the interface of the API and can take place in
+ any system using the API.</p>
+
+<h2>Systems extending the alignment API</h2>
+
+<p>These systems usually implement some matching algorithm on top of
+ the API implementation (and benefit from all implemented
+ services).</p>
+
+OLA
+<dt><a href="http://ola.gforge.inria.fr">[<font color="red">The OLA algorithm</font>]</a></dt>
+<dd>A matching algorithm for OWL-Lite that measures distance between
+ all ontology components and perform an iterative fixpoint search
+ (University of Montréal and INRIA Rhône-Alpes).</dd>
+
+oMap
+OMWG Expressive alignment format
+
+<h2>Systems outputing the alignment API</h2>
+
+FOAM
+CMS
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/impl.html</center>
+<hr />
+$Id: relnotes.html 406 2007-02-10 20:47:39Z euzenat $
+</small>
+</body>
+</html>
diff --git a/html/index.html b/html/index.html
index a78cc741ddd29f93892b74e96b56289d6e4683e9..551eca1f230d8d4dc7212247796710e1fc5bc046 100644
--- a/html/index.html
+++ b/html/index.html
@@ -7,65 +7,110 @@
</head>
<body>
-<h1 class="titre">Alignment API and implementation</h1>
+[<a href="http://gforge.inria.fr/frs/?group_id=117">Download</a>]
+[<a href="align.html">Install & use</a>]
+[<a href="tutorial/">Tutorial</a>]
+[<a
+ href="http://gforge.inria.fr/docman/view.php/117/251/align.pdf">Documentation</a>]
+[<a href="relnotes.html">Release notes</a>]
+[<a href="http://gforge.inria.fr/scm/?group_id=117">SVN access</a>]
+[<a href="aserv.html">Server</a>]
+
+<h1 class="titre">Alignment API and Alignment Server</h1>
+
+<p>The alignment API is an API and implementation for expressing and
+ sharing ontology alignments.</p>
+
+<p>Using ontologies is the priviledged way to achieve interoperability
+ among heterogeneous systems within the Semantic web. However, as the
+ ontologies underlying two systems are not necessarily compatible,
+ they may in turn need to be reconcilied.
+ Ontology reconciliation requires most of the time to find the
+ correspondences between entities (e.g., classes, objects,
+ properties) occuring in the ontologies. We call a set of such
+ correspondences an alignment.<!--/p-->
+
+<!--p-->We have designed a format for expressing alignments in a uniform
+ way. The goal of this format is to be able to share on the web the
+ available alignments. The format is expressed in <small>RDF</small>,
+ so it is freely extensible<!--, and has been defined by a <small>DTD</small> (for <small>RDF/XML</small>), an <small>OWL</small> ontology and an
+ <small>RDF</small> Schema. Aligned entities are
+ identified by their <small>URI</small>s-->.</p>
+
+<p>The Alignment API itself is a <i>Java</i> description of tools for accessing the common format. It defines four main interfaces (Alignment, Cell, Relation and Evaluator) and proposes the following services:
+<ul compact="1">
+<li>Storing, finding, and sharing alignments;</li>
+<li>Piping alignment algorithms (improving an existing alignment);</li>
+<li>Manipulating (thresholding and hardening);</li>
+<li>Generating processing output (transformations, axioms, rules);</li>
+<li>Comparing alignments.</li>
+</ul>
+</p>
+
+<!-- ******************************************************** -->
<p>Here is the new alignment API and implementation homepage. It is
hosted by gforge.inria.fr which helps the developement process (by
integrating theses pages within the SVN repository for instance).</p>
-<p>We proposed an alignment format and API which is presented
- technically below. A general overview can be found <a href="http://gforge.inria.fr/docman/view.php/117/251/align.pdf">here</a>.</p>
<h2>Main resources</h2>
-<p>
-<dl compact="1">
-<dt><a href="format.html">Alignment format</a>
-<a href="http://gforge.inria.fr/docman/view.php/117/251/align.pdf">[<font color="red">Download PDF</font>]</a></dt>
-</dt>
-<dd>The alignment format in RDF/XML.</dd>
-<dt><a href="align.html">Alignment API</a>
-[<a
- href="http://gforge.inria.fr/frs/?group_id=117"><font
- color="red">Download page</font></a> + <a href="relnotes.html"><font
- color="red">Release notes</font></a>]</dt>
-<dd>
-An alignment API in Java and implementation on top of the OWL
-API.</dd>
-<dt><a href="tutorial">A tutorial</a></dt><dd>on how to use the Alignment API implementation</dd>
-<dt><a href="alignwn.html">Using the API with wordnet</a>
-[Included with the API zip file]</dt>
-<dd>Demonstrate how to use wordnet within the API</dd>
-<dt><a href="owlapi.html">OWL-API</a> [Included with the API zip file]</dt>
-<dd>Starting quickly with OWL-API.</dd>
-<!--dt><a href="data.html">Ontologies</a></dt>
-<dd>Some data for aligning.</dd>
-<dt><a href="eval.html">Evaluators</a></dt>
-<dd>Evaluating alignments from the format.</dd-->
-<dt><a href="http://VisOn.gforge.inria.fr">[<font color="red">VisOn</font>]</a></dt>
-<dd>The VisOn ontology visualizer now works with any implementation of
- the API. It provides the opportunity to load and display
- ontologies, load, run, display and compare alignment algorithms.</dd>
+<p><dl>
+<dt><a href="http://gforge.inria.fr/frs/?group_id=117">Download page</a></dt>
+<dd>Official releases.</dd>
+<dt><a href="align.html">Install & use</a></dt>
+<dd>Quick start with the API.</dd>
+<dt><a href="aserv.html">Alignment Server</a></dt>
+<dd>Installing a server that will generate and store alignments</dd>
+<dt><a href="tutorial/">Tutorial</a></dt>
+<dd>Walk through the Alignment API features</dd>
+<dt><a href="http://gforge.inria.fr/docman/view.php/117/251/align.pdf">Documentation</a></dt>
+<dd>Supposed to be a reference manual, but outdated. It could be
+ useful anyway.</dd>
+</dl>
+</p>
+
+<h2>Additional resources</h2>
+
+<p><dl>
+<dt><a href="relnotes.html">Release notes</a></dt>
+<dd></dd>
+<dt><a href="http://gforge.inria.fr/scm/?group_id=117">SVN access</a></dt>
+<dd></dd>
+<dt><a href="lib.html">Included libraries</a></dt>
+<dd></dd>
+<dt><a href="license.html">License</a></dt>
+<dd></dd>
+<dt><a href="credits.html">Credits</a></dt>
+<dd></dd>
+<!--dt><a href="impl.html">Systems using the API</a></dt>
+<dd></dd-->
+<!--dt><a href="other.html">Other extensions</a></dt>
+<dd></dd-->
+</dl></p>
+
+<h2>Technical information</h2>
+<p><dl>
+<dt><a href="alignwn.html">Wordnet extension</a></dt>
+<dd>How to use wordnet within the API</dd>
+<dt><a href="owlapi.html">OWL API extension</a></dt>
+<dd>Starting quickly with OWL-API (Outdated notes about the OWL API and its integration in the Alignment API).</dd>
+<dt><a href="format.html">Alignment format</a></dt>
+<dd>Presentation of the alignment format in RDF/XML.</dd>
+<dt><a href="labels.html">Registered annotations</a></dt>
+<dd>List of extension labels that are declared (and should not be
+ used by others)</dd>
+<dt><a href="eval.html">Eval</a></dt>
+<dd>Using the API for evaluating alignments.</dd>
</dl></p>
-<h2>Related resources</h2>
-<p><dl compact="1">
-<dt><a href="http://ola.gforge.inria.fr">[<font color="red">The OLA algorithm</font>]</a></dt>
-<dd>A matching algorithm for OWL-Lite that measures distance between
- all ontology components and perform an iterative fixpoint search
- (University of Montréal and INRIA Rhône-Alpes).</dd>
-<dt><a href="http://align.deri.org">[<font color="red">OWL Ontology Aligner</font>]</a></dt>
-<dd>A server built around the API for processing, editing and
- rendering alignments (University of Innsbruck).</dd>
-<dt><a
- href="http://oaei.ontologymatching.org">[<font
- color="red">Ontology Alignment Evaluation Initiative</font>]</a></dt>
-<dd>Benchmarks for evaluating ontology matchers and benchmarking
- campaigns (since 2004).</dd>
-<dt><a
- href="http://.ontologymatching.org">[<font
- color="red">ontologymatching.org</font>]</a></dt>
+<h2>External resources</h2>
+<p><dl>
+<dt><a href="http://oaei.ontologymatching.org">OAEI</a></dt>
+<dd>The Ontology Alignment Evaluation Initiative: Benchmarks for evaluating ontology matchers and benchmarking campaigns (since 2004).</dd>
+<dt><a href="http://www.ontologymatching.org">ontologymatching.org</a></dt>
<dd>The central resource for ontology matching and alignment information.</dd>
-</dl>
-</p>
+</dl></p>
+
<address>
<small>
diff --git a/html/labels.html b/html/labels.html
new file mode 100644
index 0000000000000000000000000000000000000000..23d637d01207e897b1e158da7c6d9f311c31315d
--- /dev/null
+++ b/html/labels.html
@@ -0,0 +1,97 @@
+<html>
+<head>
+<title>Alignment API: Annotation labels</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<center><h1>Alignment API: Declared annotation labels</h1></center>
+
+<p>The Alignment API provides the opportunity for applications to
+ attach additional information to the alignments and the
+ correspondences (Cell). This extension mechanism is also used
+ internally by the API for testing new techniques. We try to do our
+ best for honouring these extensions: they are rendered and parsed in
+ RDF/XML, they are stored in the Alignment Server database.</p>
+<p>In order to avoid conflicting use of the extension labels, it is
+ strongly advised to package them in a particular XML namespace and
+ to register them by us. Here is the list of currently known
+ extension labels.</p>
+
+<h2>Standard API tags</h2>
+
+<dl>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:xml</dd>
+<dd>BOOLEAN telling if the file can be read as XML</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:level</dd>
+<dd>STRING </dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:type</dd>
+<dd>STRING identifying the type of alignment (1:1, 1:*, ?:+...)</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:uri1</dd>
+<dd>URI the uri of the first ontology</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:uri2</dd>
+<dd>URI the uri of the second ontology</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:onto1</dd>
+<dd>URL the location of the first ontology</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:onto2</dd>
+<dd>URL the location of the second ontology</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:semantics</dd>
+<dd>STRING the intended interpretation of a correspondence</dd>
+</dl>
+
+<h2>Standard API extensions</h2>
+
+<dl>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:id</dd>
+<dd>URI identifying the alignment</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:method</dd>
+<dd>CLASSNAME of the generating matching method</dd>
+<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment:time</dd>
+<dd>DURATION of the matching process</dd>
+</dl>
+
+<h2>Alignment server extensions</h2>
+
+<dl>
+<dt>http://exmo.inrialpes.fr/align/service:cached</dt>
+<dd>TIMESTAMP of the last time the alignment was read</dd>
+<dt>http://exmo.inrialpes.fr/align/service:stored</dt>
+<dd>TIMESTAMP of the time the alignment was stored in database</dd>
+<dt>http://exmo.inrialpes.fr/align/service:ouri1</dt>
+<dd>URI of the first ontology (temporary store)</dd>
+<dt>http://exmo.inrialpes.fr/align/service:ouri2</dt>
+<dd>URI of the second ontology (temporary store)</dd>
+</dl>
+
+<h2>Argumentation extensions</h2>
+
+<dl>
+<dt>http://ac.liv.ac.uk/just:reason</dt>
+<dd>STRING denoting an argument for the correspondence to be valid or invalid</dd>
+<dt>http://ac.liv.ac.uk/just:type</dt>
+<dd>STRING denoting the type of method used for supporting a
+ correspondence (this is a value in value argumentation framework)</dd>
+<dt>http://ac.liv.ac.uk/just:support</dt>
+<dd>BOOLEAN denoting if the argument is in favour or against</dd>
+<!--dt>http://ac.liv.ac.uk/just:type</dt>
+<dd>STRING denoting the type of method used for supporting a correspondence</dd-->
+</dl>
+
+<h2>OMV Metadata</h2>
+
+<!--dl>
+<dt>xxxx:type</dt>
+<dd>STRING denoting the type of method used for supporting a correspondence</dd>
+</dl-->
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/labels.html</center>
+<hr />
+$Id$
+</small>
+</body>
+</html>
diff --git a/html/lib.html b/html/lib.html
new file mode 100644
index 0000000000000000000000000000000000000000..923cdc1d4305f53c0aa3a54f8555820f0a8161e3
--- /dev/null
+++ b/html/lib.html
@@ -0,0 +1,108 @@
+<html>
+<head>
+<title>Alignment API: Libraries</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<h1 class="titre">Alignment API: Libraries shipped with the package (release 3.0)</h1>
+
+<p>The Alignment API uses a number of external libraries. These libraries
+are shipped (in the lib directory) with the Alignment API. We provide
+here the list of these libraries together with the reason why they may
+be necessary within the API and some other information.</p>
+
+<h2>Required for the API implementation (procalign)</h2>
+
+<dl>
+<dt><a href="http://www.urbanophile.com/arenn/hacking/download.html">Gnu getopt</a>: getopt.jar [BSD/GPL]</dt>
+<dd>Gnu library for parsing command line arguments. Required
+ everywhere (included by OWL-API).</dd>
+<dt><a href="http://logging.apache.org/log4j">Apache Log4J</a>:
+ log4j.jar [Apache]</dt>
+<dd>Required by OWL-API -- maybe used by procalign.</dd>
+<!--dt><a href=""></a>: xerces.jar xml-apis.jar</dt>
+<dd>Certainly not required anymore...</dd-->
+</dl>
+
+<h3>Required for the OWL-API part</h3>
+
+<dl>
+<dt><a href="http://owl.man.ac.uk/api.shtml">OWL API</a> 1.4.3:
+ rdfapi.jar rdfparser.jar api.jar impl.jar io.jar [LGPL]</dt>
+<dd>Provide parsing and API to OWL entities. Used by
+ OWLAPIAlignments. api.jar is required for compiling, the others are
+ necessary for executing parts of the Alignment API which need the
+ OWL API.</dd>
+</dl>
+
+<h3>Required for the WSMO part</h3>
+
+<dl>
+<dt><a href="http://www.sourceforge.net/projects/mediation">WSMO Mapping API</a> 1.4.3:
+ mappingapi.jar mappingparser.jar mappingexported.jar [LGPL]</dt>
+<dd>Provide the implementation of an expressive alignment format which
+ is the basis for level 2OMWG alignments.</dd>
+</dl>
+
+<h2>Required for the WordNet addition</h2>
+
+<dl>
+<dt><a href="http://jwordnet.sourceforge.net/">JWordNet (JWNL)</a>
+ 1.3: jwnl.jar [BSD]</dt>
+<dd>This also requires WordNet to be installed in the computer.</dd>
+<dt><a href="http://jakarta.apache.org/commons/logging/">Jakarta
+ Commons Logging</a>: commons-logging.jar [Apache]</dt>
+<dd>Necessary for alignwn.</dd>
+</dl>
+
+<h2>Required for the Alignment Server</h2>
+
+<dl>
+<dt><a
+ href="http://dev.mysql.com/downloads/connector/j/3.0.html">MySQL
+ JDBC Connectors</a> 5.0.3: mysql-connector-java-5.0.3-bin.jar [GPL]</dt>
+<dd>This also requires MySQL to be installed. Required for alignsvc.</dd>
+</dl>
+
+<h3>Required for the Agent/JADE part</h3>
+
+<dl>
+<dt><a href="http://jade.tilab.com/">Java Agent Development
+ Environment (JADE)</a> 3.3: jade.jar http.jar iiop.jar [LGPL]</dt>
+<dd>Required by alignsvc (Agent version).</dd>
+</dl>
+
+<h3>Required for the Web service part</h3>
+
+<dl>
+</dl>
+
+<h3>Required for the P2P/JXTA part</h3>
+
+<dl>
+</dl>
+
+<dl>
+<dd></dd>
+<dt><a href=""></a> </dt>
+<dd></dd>
+</dl>
+
+<!--
+commons-fileupload-1.1.1.jar
+jakarta-httpcore-4.0-alpha3.jar
+jakarta-httpcore-nio-4.0-alpha3.jar
+-->
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/lib.html</center>
+<hr />
+$Id$
+</small>
+</body>
+</html>
diff --git a/html/license.html b/html/license.html
new file mode 100644
index 0000000000000000000000000000000000000000..7190875422676f35b3a0126b235d362a2d5115da
--- /dev/null
+++ b/html/license.html
@@ -0,0 +1,504 @@
+<html>
+<head>
+<title>License</title>
+<!--style type="text/css">@import url(style.css);</style-->
+<link rel="stylesheet" type="text/css" href="base.css" />
+<link rel="stylesheet" type="text/css" href="style.css" />
+</head>
+<body bgcolor="#ffffff">
+
+<h1 class="titre">Licensing terms</h1>
+
+<p>Rights on the distributed software can be found on
+ the <a href="credits.html">credit page</a>.</p>
+
+<p>The alignment API and its implementation is distributed under the
+ GNU <a href="../distrib/LICENSE.TXT">Lesser General Public
+ License</a>.</p>
+
+<p>Other terms may be granted on demand.</p>
+
+<pre>
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+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
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+--------------------------------------------------------------------------
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
+code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
+introduced by others.
+
+ Finally, software patents pose a constant threat to the existence of
+any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that
+any patent license obtained for a version of the library must be
+consistent with the full freedom of use specified in this license.
+
+ Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License. This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License. We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+ When a program is linked with a library, whether statically or using
+a shared library, the combination of the two is legally speaking a
+combined work, a derivative of the original library. The ordinary
+General Public License therefore permits such linking only if the
+entire combination fits its criteria of freedom. The Lesser General
+Public License permits more lax criteria for linking other code with
+the library.
+
+ We call this license the "Lesser" General Public License because it
+does Less to protect the user's freedom than the ordinary General
+Public License. It also provides other free software developers Less
+of an advantage over competing non-free programs. These disadvantages
+are the reason we use the ordinary General Public License for many
+libraries. However, the Lesser license provides advantages in certain
+special circumstances.
+
+ For example, on rare occasions, there may be a special need to
+encourage the widest possible use of a certain library, so that it becomes
+a de-facto standard. To achieve this, non-free programs must be
+allowed to use the library. A more frequent case is that a free
+library does the same job as widely used non-free libraries. In this
+case, there is little to gain by limiting the free library to free
+software only, so we use the Lesser General Public License.
+
+ In other cases, permission to use a particular library in non-free
+programs enables a greater number of people to use a large body of
+free software. For example, permission to use the GNU C Library in
+non-free programs enables many more people to use the whole GNU
+operating system, as well as its variant, the GNU/Linux operating
+system.
+
+ Although the Lesser General Public License is Less protective of the
+users' freedom, it does ensure that the user of a program that is
+linked with the Library has the freedom and the wherewithal to run
+that program using a modified version of the Library.
+
+ The precise terms and conditions for copying, distribution and
+modification follow. Pay close attention to the difference between a
+"work based on the library" and a "work that uses the library". The
+former contains code derived from the library, whereas the latter must
+be combined with the library in order to run.
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License Agreement applies to any software library or other
+program which contains a notice placed by the copyright holder or
+other authorized party saying it may be distributed under the terms of
+this Lesser General Public License (also called "this License").
+Each licensee is addressed as "you".
+
+ A "library" means a collection of software functions and/or data
+prepared so as to be conveniently linked with application programs
+(which use some of those functions and data) to form executables.
+
+ The "Library", below, refers to any such software library or work
+which has been distributed under these terms. A "work based on the
+Library" means either the Library or any derivative work under
+copyright law: that is to say, a work containing the Library or a
+portion of it, either verbatim or with modifications and/or translated
+straightforwardly into another language. (Hereinafter, translation is
+included without limitation in the term "modification".)
+
+ "Source code" for a work means the preferred form of the work for
+making modifications to it. For a library, complete source code means
+all the source code for all modules it contains, plus any associated
+interface definition files, plus the scripts used to control compilation
+and installation of the library.
+
+ Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running a program using the Library is not restricted, and output from
+such a program is covered only if its contents constitute a work based
+on the Library (independent of the use of the Library in a tool for
+writing it). Whether that is true depends on what the Library does
+and what the program that uses the Library does.
+
+ 1. You may copy and distribute verbatim copies of the Library's
+complete source code as you receive it, in any medium, provided that
+you conspicuously and appropriately publish on each copy an
+appropriate copyright notice and disclaimer of warranty; keep intact
+all the notices that refer to this License and to the absence of any
+warranty; and distribute a copy of this License along with the
+Library.
+
+ You may charge a fee for the physical act of transferring a copy,
+and you may at your option offer warranty protection in exchange for a
+fee.
+
+ 2. You may modify your copy or copies of the Library or any portion
+of it, thus forming a work based on the Library, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) The modified work must itself be a software library.
+
+ b) You must cause the files modified to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ c) You must cause the whole of the work to be licensed at no
+ charge to all third parties under the terms of this License.
+
+ d) If a facility in the modified Library refers to a function or a
+ table of data to be supplied by an application program that uses
+ the facility, other than as an argument passed when the facility
+ is invoked, then you must make a good faith effort to ensure that,
+ in the event an application does not supply such function or
+ table, the facility still operates, and performs whatever part of
+ its purpose remains meaningful.
+
+ (For example, a function in a library to compute square roots has
+ a purpose that is entirely well-defined independent of the
+ application. Therefore, Subsection 2d requires that any
+ application-supplied function or table used by this function must
+ be optional: if the application does not supply it, the square
+ root function must still compute square roots.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Library,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Library, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote
+it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Library.
+
+In addition, mere aggregation of another work not based on the Library
+with the Library (or with a work based on the Library) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may opt to apply the terms of the ordinary GNU General Public
+License instead of this License to a given copy of the Library. To do
+this, you must alter all the notices that refer to this License, so
+that they refer to the ordinary GNU General Public License, version 2,
+instead of to this License. (If a newer version than version 2 of the
+ordinary GNU General Public License has appeared, then you can specify
+that version instead if you wish.) Do not make any other change in
+these notices.
+
+ Once this change is made in a given copy, it is irreversible for
+that copy, so the ordinary GNU General Public License applies to all
+subsequent copies and derivative works made from that copy.
+
+ This option is useful when you wish to copy part of the code of
+the Library into a program that is not a library.
+
+ 4. You may copy and distribute the Library (or a portion or
+derivative of it, under Section 2) in object code or executable form
+under the terms of Sections 1 and 2 above provided that you accompany
+it with the complete corresponding machine-readable source code, which
+must be distributed under the terms of Sections 1 and 2 above on a
+medium customarily used for software interchange.
+
+ If distribution of object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the
+source code from the same place satisfies the requirement to
+distribute the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 5. A program that contains no derivative of any portion of the
+Library, but is designed to work with the Library by being compiled or
+linked with it, is called a "work that uses the Library". Such a
+work, in isolation, is not a derivative work of the Library, and
+therefore falls outside the scope of this License.
+
+ However, linking a "work that uses the Library" with the Library
+creates an executable that is a derivative of the Library (because it
+contains portions of the Library), rather than a "work that uses the
+library". The executable is therefore covered by this License.
+Section 6 states terms for distribution of such executables.
+
+ When a "work that uses the Library" uses material from a header file
+that is part of the Library, the object code for the work may be a
+derivative work of the Library even though the source code is not.
+Whether this is true is especially significant if the work can be
+linked without the Library, or if the work is itself a library. The
+threshold for this to be true is not precisely defined by law.
+
+ If such an object file uses only numerical parameters, data
+structure layouts and accessors, and small macros and small inline
+functions (ten lines or less in length), then the use of the object
+file is unrestricted, regardless of whether it is legally a derivative
+work. (Executables containing this object code plus portions of the
+Library will still fall under Section 6.)
+
+ Otherwise, if the work is a derivative of the Library, you may
+distribute the object code for the work under the terms of Section 6.
+Any executables containing that work also fall under Section 6,
+whether or not they are linked directly with the Library itself.
+
+ 6. As an exception to the Sections above, you may also combine or
+link a "work that uses the Library" with the Library to produce a
+work containing portions of the Library, and distribute that work
+under terms of your choice, provided that the terms permit
+modification of the work for the customer's own use and reverse
+engineering for debugging such modifications.
+
+ You must give prominent notice with each copy of the work that the
+Library is used in it and that the Library and its use are covered by
+this License. You must supply a copy of this License. If the work
+during execution displays copyright notices, you must include the
+copyright notice for the Library among them, as well as a reference
+directing the user to the copy of this License. Also, you must do one
+of these things:
+
+ a) Accompany the work with the complete corresponding
+ machine-readable source code for the Library including whatever
+ changes were used in the work (which must be distributed under
+ Sections 1 and 2 above); and, if the work is an executable linked
+ with the Library, with the complete machine-readable "work that
+ uses the Library", as object code and/or source code, so that the
+ user can modify the Library and then relink to produce a modified
+ executable containing the modified Library. (It is understood
+ that the user who changes the contents of definitions files in the
+ Library will not necessarily be able to recompile the application
+ to use the modified definitions.)
+
+ b) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (1) uses at run time a
+ copy of the library already present on the user's computer system,
+ rather than copying library functions into the executable, and (2)
+ will operate properly with a modified version of the library, if
+ the user installs one, as long as the modified version is
+ interface-compatible with the version that the work was made with.
+
+ c) Accompany the work with a written offer, valid for at
+ least three years, to give the same user the materials
+ specified in Subsection 6a, above, for a charge no more
+ than the cost of performing this distribution.
+
+ d) If distribution of the work is made by offering access to copy
+ from a designated place, offer equivalent access to copy the above
+ specified materials from the same place.
+
+ e) Verify that the user has already received a copy of these
+ materials or that you have already sent this user a copy.
+
+ For an executable, the required form of the "work that uses the
+Library" must include any data and utility programs needed for
+reproducing the executable from it. However, as a special exception,
+the materials to be distributed need not include anything that is
+normally distributed (in either source or binary form) with the major
+components (compiler, kernel, and so on) of the operating system on
+which the executable runs, unless that component itself accompanies
+the executable.
+
+ It may happen that this requirement contradicts the license
+restrictions of other proprietary libraries that do not normally
+accompany the operating system. Such a contradiction means you cannot
+use both them and the Library together in an executable that you
+distribute.
+
+ 7. You may place library facilities that are a work based on the
+Library side-by-side in a single library together with other library
+facilities not covered by this License, and distribute such a combined
+library, provided that the separate distribution of the work based on
+the Library and of the other library facilities is otherwise
+permitted, and provided that you do these two things:
+
+ a) Accompany the combined library with a copy of the same work
+ based on the Library, uncombined with any other library
+ facilities. This must be distributed under the terms of the
+ Sections above.
+
+ b) Give prominent notice with the combined library of the fact
+ that part of it is a work based on the Library, and explaining
+ where to find the accompanying uncombined form of the same work.
+
+ 8. You may not copy, modify, sublicense, link with, or distribute
+the Library except as expressly provided under this License. Any
+attempt otherwise to copy, modify, sublicense, link with, or
+distribute the Library is void, and will automatically terminate your
+rights under this License. However, parties who have received copies,
+or rights, from you under this License will not have their licenses
+terminated so long as such parties remain in full compliance.
+
+ 9. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Library or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Library (or any work based on the
+Library), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Library or works based on it.
+
+ 10. Each time you redistribute the Library (or any work based on the
+Library), the recipient automatically receives a license from the
+original licensor to copy, distribute, link with or modify the Library
+subject to these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties with
+this License.
+
+ 11. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Library at all. For example, if a patent
+license would not permit royalty-free redistribution of the Library by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Library.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply,
+and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Library under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded. In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+ 13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+specifies a version number of this License which applies to it and
+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
+the Free Software Foundation. If the Library does not specify a
+license version number, you may choose any version ever published by
+the Free Software Foundation.
+
+ 14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
+write to the author to ask for permission. For software which is
+copyrighted by the Free Software Foundation, write to the Free
+Software Foundation; we sometimes make exceptions for this. Our
+decision will be guided by the two goals of preserving the free status
+of all derivatives of our free software and of promoting the sharing
+and reuse of software generally.
+
+ NO WARRANTY
+
+ 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
+OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
+KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+
+</pre>
+
+<address>
+<small>
+<hr />
+<center>http://alignapi.gforge.inria.fr/license.html</center>
+<hr />
+$Id$
+</small>
+</address>
+</body>
+</html>
diff --git a/html/owlapi.html b/html/owlapi.html
index 0ca862a58d46de3d2b088c07e79d0f4aa477eedd..3e0a50a31515db76ac611007deffde10f02b15d5 100644
--- a/html/owlapi.html
+++ b/html/owlapi.html
@@ -116,7 +116,7 @@ given as argument and generates an output which can be:
</p>
<p>For instance:
<pre>
-$ ./processor -a file://localhost/<yourpath>/owl/resources/transitive2.owl
+$ ./processor -a file://<yourpath>/owl/resources/transitive2.owl
[Namespaces:
rdf = http://www.w3.org/1999/02/22-rdf-syntax-ns#
xsd = http://www.w3.org/2001/XMLSchema#
@@ -135,7 +135,7 @@ Ontology(
</pre>
or
<pre>
-$ ./processor --renderer=org.semanticweb.owl.io.owl_rdf.Renderer file://localhost/<yourpath>/owl/resources/transitive2.owl
+$ ./processor --renderer=org.semanticweb.owl.io.owl_rdf.Renderer file://<yourpath>/owl/resources/transitive2.owl
<?Xml version="1.0"?>
<!DOCTYPE owl [
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
@@ -150,7 +150,7 @@ $ ./processor --renderer=org.semanticweb.owl.io.owl_rdf.Renderer file://localhos
xmlns:a ="http://www.example.org/ontology#"
>
<!-- Need to support further ontology metadata, import still missing -->
- <owl:Ontology rdf:about="file://localhost/Volumes/Skratsh/JAVA/owlapi/owl/resources/transitive2.owl" />
+ <owl:Ontology rdf:about="file:///Volumes/Skratsh/JAVA/owlapi/owl/resources/transitive2.owl" />
<owl:ObjectProperty rdf:about="http://www.example.org/ontology#p">
<rdf:type rdf:resource="&owl;TransitiveProperty" />
<rdf:type rdf:resource="&owl;FunctionalProperty" />
diff --git a/html/relnotes.html b/html/relnotes.html
index 57e572cb1b0c067779da139413c76f8d34a6833a..f3dd5f6e80f1d245d546ce8d6890bd565909ffcd 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -18,8 +18,7 @@
<p><ul compact="1">
<li>Adding Web Service Alignment server profile</li>
-<li>Implement level 2OML alignments (version 3);</li>
-<li>Improving web pages</li>
+<li>Implement level 2OMWG alignments (version 3);</li>
<li>Completing the reference manual</li>
</ul></p>
@@ -34,8 +33,15 @@
<li>In Server/FIPA, suppressed generated files on close()</li>
<li>In Server/FIPA, suppressed printout</li>
<li>Completely rewritten autodetection of renderers and methods in server</li>
-<li>Corrected an error on "force"-ing alignment in Server/HTML (was inverted)</li>
+<li>Modified interface of embedded methods</li>
+<li>Added guarantee that results displayed by GroupEval be sorted
+ (thanks Vassilis Spiliopoulos)</li>
+<li>Added namespace support in BasicAlignment</li>
+<li>Corrected an error on "force"-ing alignment in Server/HTML (was
+ inverted)</li>
+<li>Corrected a bug concerning extension namespaces</li>
<li>Corrected bugs in relation writing/parsing</li>
+<li>Improved web pages (reorganisation)</li>
<li>Transferred the TODOs to gforge</li>
</ul></p>