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<title>Alignment API: Release notes</title>
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<center><h1>Alignment API: release notes</h1></center>
<p style="font-size: 80%;"><span style="font-weight: bold;">Release numbers:</span> major release numbers are for majors
redesign that will modify the API and may lead you to
change your code; minor release numbers bring bug fixes and new
functionnalities but should not require change in existing code.</p>
The next major release, release 5, is under design progressively under
version 4. Here are
the main ruptures that will appear:
<ul compact="1">
<li>The use of Java 1.5 parametrization facilities for refining the
API: Hence we will
define <tt>Alignment<Ontology,Ontology,Relation,Confidence></tt>. This
will provide the opportunity to define everyone owns relation (and
generalise the use of relation algebras). (api/impl)</li>
</ul>
Other less radical changes include:
<ul compact="1">
<li>Implementation of <tt>Relation</tt> and <tt>Confidence</tt> interfaces </li>
</ul>
The development of 4 versions continues.
<li>Provide several URIs for the same alignment (serv)</li>
<li>Implement database store for EDOAL (serv)</li>
<li>Implementation of a provenance metadata tag (serv/impl)</li>
<li>Complete tutorial4 (doc).</li>
<li>Implement metadata edition (serv)</li>
<li>Add simple "harder" test generator (gen)</li>
<li>Add simple "hidden" test generator (gen)</li>
<li>Add a <tt>dependsOn</tt> alignment property (api)</li>
<li>Consolidate alignment based on <tt>dependsOn</tt> (loop checking, cell ingestion) (impl)</li>
<li>Use the OWLReasoner interface and HermiT for adding inference to Ontowrap (ontowrap)</li>
<li>Integrate tests from generator (test)</li>
<li>Integrate some basic reasoning (impl).</li>
<li>Genericize evaluators in <tt>GraphEvaluator</tt> and <tt>GenPlot</tt> (eval)</li>
Jérôme Euzenat
committed
<li>Replace <tt>DistanceAlignment</tt> and <tt>Similarity</tt> with a version more in line with <a href="http://ontosim.gforge.inria.fr">OntoSim</a> (impl)</tt>
<li>Implement transformations in EDOAL (edoal)</li>
<li>Implement linkkeys in EDOAL (edoal)</li>
<li>Improve HTML interface layout and usability (serv)</li>
<li>Implement correspondence selection (serv)</li>
<li>Automatically switch to correct <tt>ontowrap</tt> implementation in parsers (parser)</li>
<li>Render alignments as module descriptions (impl)</li>
<li>Implement extensive evaluation framework (impl)</li>
<li>Matcher plugin for OpenII? (util)</li>
<!-- NOTE FOR VERSION 5
The default type of StringDistAlignment should be reverted to "**"
with a warning:
-->
<!--h2>Version 4.9 (1xxx): ??/??/201X - Al pesto</h2-->
<!--h2>Version 4.8 (1xxx): ??/??/201x - Antsine</h2-->
<!--h2>Version 4.7 (19xx): ??/0?/2014 - Letraset</h2-->
<p><ul compact="1">
<li><span style="color: red;">Deprecated</span> <tt>BasicAlignment.removeAlignCell()</tt>, use <tt>remCell()</tt> instead (impl)</tt>
<li><span style="color: red;">Moved</span> <tt>QueryMediator</tt>, from <tt>service</tt> to <tt>queryprocessor</tt> (impl)</tt>
<li>Fixed a bug in <tt>QueryMediator</tt> which doubled '#' (serv)</li>
<li>Fixed a few mistakes in <tt>SilkRendererVisitor</tt> (impl)</li>
<li>Fixed several bugs in <tt>GraphPatternRendererVisitor</tt> (impl)</li>
<li>Implemented <tt>translateMessage()</tt> and <tt>rewriteQuery()</tt> in <tt>BasicAlignment</tt> (impl)</li>
Jérôme Euzenat
committed
<li>Reorganised AlignmentServices into transport (HTTP) and service (HTML/Web service) (serv)</li>
<li>Enabled query translation in interface (serv)</li>
<li>Added JSON interface for server (serv)</li>
<li>Added a command-line utility for query translation (cli)</li>
<li>Added a guard forbiding to create a <tt>BasicCell</tt> with null objects (impl)</li>
<li>Added httpcore library necessary for tutorial4 (tutorial/lib)</li>
<li>Added extensions to <tt>BasicOntologyNetwork</tt> (impl)</li>
<li>Added read/write to <tt>BasicOntologyNetwork</tt> (impl)</li>
<li>Added algebraic manipulation of <tt>BasicOntologyNetwork</tt> (impl)</li>
<li>Added storage support for networks of ontologies (serv)</li>
<li>Genericised storage <tt>Cache</tt> and implemented <tt>VolatilCache</tt> which contains a full Cache implementation without storage (serv)</li>
</ul></p>
<h2>Version 4.6 (1875): 22/01/2014 - Da lec'h all</h2>
<li>Fixed a bug in <tt>EDOALAlignment.init()</tt> which would prohibit rendering (edoal)</li>
<li>Fixed a bug in <tt>OWLAxiomsRendererVisitor</tt>, <tt>SWRLRendererVisitor</tt>, <tt>SEKTMappingRendererVisitor</tt>, <tt>COWLMappingRendererVisitor</tt> <tt>SPARQLConstructRendererVisitor</tt>, and <tt>SPARQLSelectRendererVisitor</tt> which sometimes rendered alignments empty (impl)</li>
<li>All logging and signaling is now through slf4j (impl/serv)</li>
<li>Replaced getopt by <span style="color: green">commons cli 1.2</span> as command line interpreter (lib/cli)</li>
<li>Completed <tt>SWRLRendererVisitor</tt> to fill equivalence and subsumption statements (impl)</li>
<li>Declared Alignment server as an OSGi service (serv)</li>
<li>Made EDOAL vocabulary dereferenceable (edoal)</li>
<li>Fixed the build.xml file for using slf4j in microalign (android)</li>
<li>Fixed several bugs in <tt>WeightedPREvaluator</tt>, now two versions (impl)</li>
<li>Fixed display bugs in <tt>GroupEval</tt> and <tt>WGroupEval</tt> (cli)</li>
<li>Cancelled test <tt>EDOALTest.anotherRoundTripTest()</tt> because would try to load a WSMO ontology (test)</li>
<li>Changed <tt>-o</tt> option in <tt>GroupAlign</tt> to be homogeneous (cli)</li>
<li>Updated tutorial2 with deprecated <tt>BasicParameters</tt> (tutorial)</li>
<li>Added complete command line option tests in <tt>tests/clitest.sh</tt> (cli)</li>
<li>Upgraded to <span style="color: green">SLF4J 1.7.5</span> (lib)</li>
<li>Upgraded to <span style="color: green">xercesImpl 2.11.0</span> (lib)</li>
<li>Upgraded to <span style="color: green">Lucene 4.6.0</span> (lib)</li>
<li>Upgraded to <span style="color: green">OntoSim 2.4</span> (lib)</li>
<li>Upgraded to <span style="color: green">mysql 5.1.28</span> and <span style="color: green">postgres 9.3-1100</span> (lib)</li>
<li>Upgraded to <span style="color: green">Jena 2.9.0</span> (lib)</li>
<li>Upgraded to <span style="color: green">OWL API 3.4.8</span> (lib)</li>
<li>Upgraded to <span style="color: green">HermiT 1.3.8</span> (lib)</li>
<li>Added several EDOAL-SPARQL renderers (impl)</li>
<li>Added <tt>ontowrap</tt> support in database store (serv)</li>
<li>Made Alignment URIs independent from URL prefix (serv)</li>
<li>Added alignment selection per ontologies in list alignment interface (serv)</li>
<li>Added relation sensitiveness to evaluators (impl)</li>
<li>Added generation of local <a href="maven.html">maven repository</a> in build.xml</li>
<li>Implemented transactions in database store (serv)</li>
<li>Modified evaluators needing <tt>ObjectAlignment</tt> to convert them on the fly (impl)</li>
Jérôme Euzenat
committed
<li>Modified renderers needing <tt>ObjectAlignment</tt> to convert them on the fly (impl)</li>
<li>Evaluators report better errors on the server (serv)</li>
<li>Fixed a bug in <tt>WeightedPREvaluator</tt> (can be more than 1.) (impl)</li>
<li>Fixed strong bug in the implementation of relaxed precision and recall (impl)</li>
<li>Fixed a (non manifested) bug in cache management (serv)</li>
<li>Fixed a bug in displaying evaluation tables (cli)</li>
<li>Fixed a bug with subsumption statements in <tt>OWLAxiomsRendererVisitor</tt> (impl)</li>
<li>Simplified and rewritten <tt>SemPRecEvaluator</tt> (impl)</li>
<li>Fixed all issues but IDDL in <a href="tutorial/tutorial4/index.html">tutorial4</a> (impl)</li>
<li>Fixed display bug in <tt>HTMLMetadataRenderer</tt> (impl)</li>
<li>Upgraded to <span style="color: green">IDDL 1.5</span> (lib)</li>
<li>Upgraded to <span style="color: green">OWL API 3.4.2</span> (lib)</li>
<li>Upgraded to <span style="color: green">SLF4J 1.7.2</span>; suppressed slf4j-log4j (lib)</li>
<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
<li>Replaced Commons-Logging and Log4j by jcl-over-slf4j and log4j-over-slf4j (lib)</li>
<a name="4.4"></a><h2>Version 4.4 (1754): 17/07/2012 - Casa Cirilo</h2>
<li><span style="color: red;">Deprecated</span> <tt>BasicParameters</tt>,
use <tt>java.lang.Properties</tt> instead; <tt>BasicParameters</tt>
is not used anymore in the API (impl)</tt>
<li><tt>BasicAlignment.getXNamespaces()</tt> returns <tt>Properties</tt> (impl)</li>
<li>Simplified visitor patterns (impl/edoal/renderer)</li>
<li><span style="color: red;">Use</span> edoal prefix instead of xsd for comparators (edoal)</li>
Jérôme Euzenat
committed
<li>Integrated <tt>owl:propertyChain</tt> in OWL rendering (edoal)</li>
<li>Upgraded to <span style="color: green">SKOS API 2</span> and
<span style="color: green">OntoSim 2.3</span> (lib)</li>
<li>Added <tt>JSONRendererVisitor</tt> (impl)</li>
<li>Added <tt>corresp</tt> primitive (serv)</li>
<li>Added <tt>EDOALAlignment.toEDOALAlignment()</tt> (edoal)</li>
<li>Simplified <tt>TestGen</tt> options (cli)</li>
<li>Fixed server initialisation error with new log4j (serv)</li>
<li>Fixed a float parsing bug in <tt>XMLParser</tt> (parser)</li>
<li>Fixed a display error in <tt>DiffEvaluator</tt> (impl)</li>
<li>Corrected bug with <tt>owl:inverseOf</tt> in OWL rendering (edoal)</li>
<li>All documentation has now been revised in html and is not in the (outdated) manuals (html)</li>
<li>Replaced version.txt and license.txt by pom.xml (lib)</li>
<li>Added minimal pom.xml for generated jar files (lib)</li>
<a name="4.3"></a><h2>Version 4.3 (1690): 22/02/2012 - Zimt</h2>
<p><span style="color: red;">BEWARE:</span> All command-line utilities
are now found in the <span style="color: red;">cli</span> package
instead of <b>util</b>.<br />
<span style="color: red;">BEWARE:</span> The server will not work
in this version; use more recent version instead.</p>
<p><ul compact="1">
<li>Created new "Command line interface" directory (util/cli)</li>
<li>Full reengineering of the test generator (gen)</li>
Jérôme Euzenat
committed
<li>Improved visitors by implementing a reflective visitor (impl)</li>
<li>Implemented <tt>extractss</tt> for ** alignments in <tt>DistanceAlignment</tt> (impl)</li>
<li>Changed default type of <tt>StringDistAlignment</tt> to "?*" for
preserving the previous behaviour (impl)</li>
<li>Added level lines in the triangle display of <tt>GroupEval</tt> (cli)</li>
<li>Implemented LaTeX output in <tt>GroupEval</tt> (cli)</li>
<li>Added <tt>BasicAlignment.deleteAllCells()</tt> (impl)</li>
Jérôme Euzenat
committed
<li>Added a guard in <tt>loadOntology</tt> for OWLAPI 3.0, in case the
ontology has no URI (ontowrap)</li>
<li>Suppressed the guard for applying the Hungarian algorithm to
equisimilarity situations (impl)</li>
Jérôme Euzenat
committed
<li>Slightly modified the parser so that it accepts Alignment URI with
or without # (parser)</li>
<li>Added better error checking in <tt>toObjectAlignment</tt> (impl)</li>
<li>Upgraded to <span style="color: green">Jena 2.7</span>,
<span style="color: green">Xerces 2.10</span>,
<span style="color: green">log4j 1.2.16</span>,
<span style="color: green">slf4j 1.6.4</span> (lib)</li>
<li>Fixed a bug on <tt>DistanceAlignment</tt> 1:1 extraction when the
second ontology is larger than the first one (impl)</li>
Jérôme Euzenat
committed
<li>Fixed a bug in the EDOAL parser and printer for taking into
account the <tt>edoal:type</tt> within <tt>edoal:Literal</tt> (edoal)</li>
<li>Used more systematically <tt>finally</tt></li>
<a name="4.2"></a><h2>Version 4.2 (1618): 31/05/2011 - Tring</h2>
<p><ul compact="1">
<li>Added minimal API implementation for embedded devices (android)</li>
<li>Added type checking to EDOAL parser (parser)</li>
<li>Added <tt>WeightedPRecEvaluator</tt> weighting confidences (eval)</li>
<li>Added <tt>toURIAlignment</tt> and <tt>toEDOALAlignment</tt> for <tt>EDOALAlignment</tt> (edoal)</li>
<li>Added matching test generator facility (gen)</li>
<li>Added autoselecting <tt>BasicOntology.load()</tt> (ontowrap)</li>
<li>Reengineered <tt>OntologyNetworkWeakener</tt> and added further weakening methods (gen)</li>
<!--li>Added <tt>SEALSAlignment</tt> for SEALS evaluation (impl)</li-->
<li>Added a few statistical primitives to BasicAlignment (impl)</li>
<li>Suppressed <tt>EDOALRelation</tt>: EDOAL uses <tt>BasicRelation</tt> (edoal)</li>
<li>EDOAL default printout now uses pretty relations, i.e., <, >, =, % (edoal)</li>
<li>Modified server answers so that namespaces are well placed in REST (serv)</li>
<li>Changed order of display to precision/F-measure/recall (util)</li>
<li><span style="color: red;">Suppressed</span> incorrect computation of fallout (eval)</li>
<li>Corrected NaN derived measures when precision is 0. (eval)</li>
<li>Set precision to 1. when alignments are empty (eval)</li>
<li>Upgraded to <span style="color: green">OntoSim 2.2</span> (lib)</li>
<li>Minor display changes in HTML display (serv)</li>
<li>Suppressed <tt>PreAlignment</tt> (impl)</li>
</ul></p>
<a name="4.1"></a><h2>Version 4.1 (1534): 13/10/2010 - Napjakmandu</h2>
<li>Integration of skoslite (home made SKOS API) (ontowrap)</li>
<li>Integration of SKOS API (ontowrap)</li>
<li>Extended ontowrap so that all methods can raise exceptions (ontowrap)</li>
<li>Added method <tt>getEntityAnnotationsL</tt> (ontowrap)</li>
<li><tt>DistanceAligment</tt> can now deal indifferently with similarity or distances (impl)</li>
<li>Implemented fully relaxed precision and recall (impl)</li>
<li>Implemented FMeasure/threshold plotting <tt>ThresholdGraphEvaluator</tt> (eval)</li>
<li>Completed implementation of relaxed precision and recall (eval)</li>
<li>Added Wu-Palmer and gloss overlap similarity over WordNet to <tt>JWNLAlignment</tt> (impl)</li>
<li>Added <tt>InstanceBasedMatrixMeasure</tt> for instance based alignments (impl)</li>
<li>Added a <tt>getResult()</tt> method to <tt>Evaluator</tt> (api)</li>
<li>Added a <tt>DiffAlign( al1, al2 )</tt> evaluator (impl)</li>
<li>Added an <tt>aggr.ConsensusAggregator</tt> for merging several alignments (impl)</li>
<li>Implemented online evaluation and diff (serv)</li>
<li>Added the possibility to drop a number of correspondences in <tt>ONetworkWeakener</tt> (util)</li>
<li>Added a google chart API display of plots <tt>GenPlot -t html</tt> (util)</li>
<li><tt>edoal:or</tt>, <tt>edoal:and</tt> and <tt>edoal:compose</tt> can be empty (edoal)</li>
<li>Added universal (<tt>all</tt>) and existantial (<tt>exists</tt>) quantification of domains in edoal (edoal)</li>
<li>Implement full OWL rendering of EDOAL (impl)</li>
<li>Upgraded to <span style="color: green">Pellet 2.1</span> (but Pellet is not anymore distributed <a href="lib.html">due to license restrictions</a>)</li>
<li>Upgraded to <span style="color: green">OntoSim 2.1</span> (lib)</li>
<li>Added <a href="tutorial/tutorial4/index.html">tutorial 4</a> Pellet action (tutorial)</li>
<li>Added <a href="tutorial/tutorial5/index.html">tutorial 5</a> about exposing matchers as web services (tutorial)</li>
<li>Fixed several problems with loading twice the same ontology in the OWL API (ontowrap)</li>
<li>Corrected an error in matching when a alignment existed without method extension (serv)</li>
<li>Improved RDF Rendering layout (impl)</li>
<a name="4.0"></a><h2>Version 4.0 (1415): 31/03/2010 - Rouquine carmélite</h2>
<p>The Alignment API is now compiled in Java 1.6 (older versions should still be able to run it). All <a href="lib.html">imported libraries</a> have been upgraded to their current versions. Only the upgrade from <span style="color: green">Jena 2.5 to 2.6</span> required a minor change (due to parameterised declarations: the API still works with 2.5 but needs 2.6 to compile).
Jérôme Euzenat
committed
</p>
<p>This is still a major release, so see the <a href="up3to4.html">(small) instructions</a> if you need to upgrade your codebase.
<p>
<ul compact="1">
<li>Integration and reengineering of OMWG alignments as the new <a href="edoal.html">EDOAL language</a> (edoal)</li>
<li>Separated the Alignment API from <a href="http://ontosim.gforge.inria.fr">OntoSim</a> (impl/ling)</li>
Jérôme Euzenat
committed
<li><span style="color: red;">Replacement</span> of <tt>Parameters</tt> by Java <tt>Properties</tt> (api/impl)</li>
<li>Reintegrated <tt>JWNLAlignment</tt> in implementation (procalign)</li>
<li>Separated <tt>ontowrap</tt> (previously <tt>onto</tt>) as a distinct library (ontowrap)</li>
<li>Migrated to <span style="color: green">OWL API 3</span> as the default Ontology implementation (ontowrap)</li>
<li>Lifted OWL API 3 as <tt>HeavyLoadedOntology</tt> (ontowrap)</li>
<li>Added cache management to <tt>JENAOntology</tt> (ontowrap)</li>
<li>Addition of advanced tutorial and <a href="tutorial">reengineered tutorials</a> (doc)</li>
<li>Implemented semantic precision and recall (impl)</li>
<li>Implemented ROC curve computing and reimplemented the plotting
structure. Now they are based on harmonic means instead of average. (eval)</li>
<li>Fully implemented <tt>find</tt> to interface (serv)</li>
<li>Completely modified the web service interface so that SOAP and
REST are fully aligned. This is
now <a href="rest.html#version4">documented</a> (serv)</li>
<li>Added a <tt>listevaluators</tt> primitive to the service interface (serv)</li>
<li>Added computation of MAP (Mean Average Precision) in <tt>PRGraphEvaluator</tt> (impl).</li>
<li>Added pretty-printing of names in server (serv)</li>
<li>Added provenance tracking in server (serv)</li>
<li>Added initialisation through initial alignment
in <tt>MatrixMeasure</tt> (impl)</li>
<li>Added a parameter to the <tt>OWLAxiomsRendererVisitor</tt> so that it could render
heterogeneous axioms, like Class sameAs Property (impl).</li>
<li>Upgraded NeOn plug-in to work with <span style="color: green">NeOn toolkit 2.3.0</span> (plugin)</li>
<li>Rewritten NeOn Alignment plug-in interface so that it works on more platforms (plugin)</li>
<li>Added documentation for the NeOn Alignment plug-in (plugin)</li>
<li>Suppressed <tt>OWLAPICell</tt> and <tt>OWLAPIAlignment</tt>
<li>Changed the signature of <tt></tt> from <tt>Enumeration</tt>
to <tt>Collection<Alignment></tt> (serv)</tt>
<li>Reorganised the lib directory hierarchically (build)</li>
<li>Corrected missing <tt>hashCode()</tt> (bug #9680) (impl)</li>
<li>Corrected a bug when the server is launched without -S
(serv)</li>
<li>Fixed error message in server (#8502: org.apache.xml.resolver.readers.CatalogReader: deprecated) by upgrading resolver.jar (serv)</li>
<li>Corrected a bug in <tt>HTMLRendererVisitor</tt> that made the
display of alignments, especially stored, to break (serv)</li>
<li>Corrected the README.TXT of examples/wservice (serv)</li>
<li>Corrected a bug in retrieving alignments from ontologies when the
<li>Corrected a bug in triming, which left one item too much (impl)</li>
<li>Corrected a bug when <tt>StringDistAlignment</tt> fails to raise
<li>Corrected a problem due to parser reentrance which led two
alignment parsed by the same parser to go into the same alignment (parser)</li>
<li>Corrected a bug introduced in 3.6 which prevented from storing the
"stored" date of alignments (serv)</li>
<li>Corrected a bug in the "find" primitive of service (serv)</li>
<li>Corrected a bug that prevented proper search of <tt>aserv.wsdl</tt> file in all imported jars (serv)</li>
Jérôme Euzenat
committed
<li>Corrected a bug in tests that did not force to clean-up the state
after <tt>OntoTest</tt> (test)</li>
<li>Corrected a (commented) error in the <tt>wine.xml</tt> OMWG
example (edoal)</li>
<!--li>Suppressed the capability to export alignments in WSML (edoal)</li-->
<a name="3.6"></a><h2>Version 3.6 (988): 27/05/2009 - Sabai sabai</h2>
<p><span style="color: red;">BEWARE:</span>
Java WordNet Library (JWNL) has been upgraded to version 1.4.1rc2 (from 1.3rc3). This is included in the lib directory.
Hence, it is necessary to use WordNet-3.0 (the jwnl part will not work
anymore with 2.0).
If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
library by the older one and this will work. However, using WordNet
with the Alignment API is not compulsory.
<li><tt>tokenize</tt> has been moved from <tt>JWNLDistances</tt> to <tt>StringDistances</tt> (ling)</li>
<li>Added REST interface to the HTML interface (serv)</li>
<li>Addition of the notion of <tt>OntologyNetwork</tt> made of a set of
ontologies and alignments within the API (api/impl/test).</li>
<li>Added new gap based (hardgap and propgap) methods in <tt>BasicAlignment.cut()</tt> (impl)</li>
<li>Added new methods (Cosynonymy, Wu-Palmer) in JWNLDistances (ling)</li>
<li>Added tests for ling and set noling as default in build (test)</li>
<li>Added the possibility for <tt>OWLAxiomsRendererVisitor</tt> to output relations between individuals (renderer)</li>
<li>Added JDBC drivers for Postgress and improved mySQL code for genericity (serv)</li>
<li>Improved renderers with more metadata (renderer)</li>
<li>Completed individual alignment and extraction in <tt>DistanceAlignment</tt> (impl)</li>
<li>Completed matrix printing in <tt>MatrixMeasure</tt> (impl)</li>
<li><tt>ConcatenatedIterator</tt> is now parameterised and iterable (impl)</li>
<li>Corrected a bug in <tt>XMLMetadataRendererVisitor</tt> (renderer)</li>
<li>Corrected a bug in <tt>RDFRendererVisitor</tt> that output rdf:ID="" (renderer)</li>
<li>Corrected a bug in <tt>OWLAxiomsRendererVisitor</tt> for generating disjointWith statements (renderer)</li>
<li>Corrected a (rare) bug in server which was not able to recognise URIs (serv)</li>
<li>Corrected a bug in <tt>BasicAlignment.cut("best")</tt> (impl)</li>
<li>Prevented <tt>OWLAxiomsRenderer</tt> from returning equivalence
between Data and Object properties and, in general, heterogeneous equivalences (impl)</li>
<li>Cleaned up the wservice example (examples)</li>
<a name="3.5"></a><h2>Version 3.5 (886): 21/10/2008 - La granja</h2>
<li><span style="color: red;">Deprecated</span> <tt>Alignment.init(onto,onto,cache)</tt>
in favour of <tt>Alignment.init(onto,onto)</tt>, see below (api)</tt>
<li>NeOn plug-in compatible with <span style="color: green">NeOn toolkit 1.2</span> (plugin)</li>
<li><tt>OntologyCache</tt> is now local to each <tt>OntologyFactory</tt>, it does not need to be manipulated from outside (onto)</li>
<li>Implemented <tt>owlapi10</tt> as <tt>HeavyLoadedAlignment</tt> (ontowrap)</li>
<li>Completed the integration of Jena ontologies (ontowrap)</li>
<li>Implemented basic algebraic operations (impl)</li>
<li>Added diff algebraic operation (api)</li>
<li>Reengineered parameter passing for web service interface (serv)</li>
<li>Updated <tt>SKOSRendererVisitor</tt> to work with 2008 version of
SKOS, old version can be obtained by parameter <tt>pre2008</tt> (impl)</li>
<li>Corrected an error preventing DistanceAlignment to consider individuals (impl)</li>
<li>Corrected an error transmitting the DBMS coordinates on the web (serv)</li>
<li>Corrected a bug in <tt>SKOSRendererVisitor</tt> and <tt>XSLTRendererVisitor</tt> (impl)</li>
<li>Started to put copyright notices to INRIA instead of INRIA Rhône-Alpes (misc)</li>
<li>Used Java 1.5 print Formatter instead of our printFormat (impl)</li>
<li>Unit tests for onto and owlapi10 (ontowrap)</li>
<a name="3.4"></a><h2>Version 3.4 (815): 31/08/2008 - Barbare</h2>
<li>Implemented WSAlignment connecting to remote web service for
<li><span style="color: red;">Deprecated</span> <tt>Cell.getObjectXAsURI()</tt>
in favour of <tt>Cell.getObjectXAsURI(Alignment al)</tt> (api)</tt>
<li>Upgraded NeOn plug-in for working with <span style="color: green">NeOn toolkit 1.1</span> (plugin)</li>
<li>Implemented OWL API 2 support [not shipped] (ontowrap)</li>
<li>Added <tt>init( Parameters )</tt> arguments to visitors (api)</tt>
<li>Implemented <tt>embedded</tt> parameter allowing to avoid ?xml
declaration when embedded (renderer)</li>
<li>Added <tt>derivedFrom</tt> standard annotation and implemented it (impl)</li>
<li>Added <tt>method</tt> annotation for <tt>clone()</tt>
and <tt>inverse()</tt> (impl)</li>
<li>Added <tt>initAlignment(URIAlignment)</tt> to parser (parser)</li>
<li>Added <tt>parse(InputStream)</tt> to parser (parser)</li>
<li>Parser now ignore SOAP envelops (parser)</li>
<li>Implemented a better recovery in case of database connection loss (serv)</li>
<li>Implemented cache flushing functions (serv)</li>
<li>Provided better return forms in <tt>HTMLAServManager</tt> (serv)</li>
<li>Catched <tt>init()</tt> errors in server (serv)</li>
<li>Reorganised HTML interface (serv)</li>
<li>Added indentation and namespaces in the Web service interface (serv)</li>
<li>Implemented <a href="http://www.webcontent.fr">WebContent</a> plug-in (plugin)</li>
<li>Improved NeOn plug-in documentation (html)</li>
<li>Increased the size of relation id to 25 char (serv)</li>
<li>Corrected <tt>MyAlign</tt> example which was not adapted to the
new onto structure (examples)</li>
<li>Corrected tutorial so that it works with new code (tutorial)</li>
<li>Corrected an error of the <tt>Cell.inverse()</tt> method (impl)</li>
<li>Corrected an error in storing alignments (serv)</li>
<li>Corrected an error in the MANIFEST of the NeOn plug in (plugin)</li>
<li>Corrected an error that prevented the server to work on Windows (serv)</li>
<a name="3.3"></a><h2>Version 3.3 (710): 24/04/2008 - O sole mio</h2>
<p><ul compact="1">
<li>Suppressed language dependent (OWLAPI) alignments (impl)</li>
<li><a href="up2to3.html" style="color:red;">Deprecated</a>
<tt>OWLAPIAlignment</tt> to be replaced by <tt>ObjectAlignment</tt></li>
<li>Reimplemented the whole API in function of the onto package (impl)</li>
<li>Added an abstract ontology package allowing to change API (ontowrap)</li>
<li>Added Jena 2.5 ontology plug-in (ontowrap)</li>
<li>Made <tt>Alignment</tt> iterable<Cell> (api/impl)</li>
<li>Improved NeOn plug-in and upgraded to <span style="color: green">
NeOn toolkit 1.0</span> (plugin)</li>
<li>Corrected a bug in Web service when the content was XML (serv)</li>
<li>Corrected a bug when loading an alignment with id (serv)</li>
<li>Corrected a bug in AlignmentParser that overlooked formalism URI (parser)</li>
<li>Passed to Java 1.5 generics [incl. API modif] (dev/api)</li>
<li>Added first unit tests (TestNG) (dev)</li>
<li>Passed all code through lint (dev)</li>
<li>Corrected link to documentation (doc)</li>
</ul></p>
<a name="3.2"></a><h2>Version 3.2 (666): 29/02/2008 - Blejsko jezero</h2>
<li>Connection to Oyster directory (serv)</li>
<li>Added the opportunity to run matchers asynchronously (serv)</li>
<li>Made sure that http server is launched when wsdl option is chosen
<li>Moved NeOn toolkit plugin in the plugins/neon (plugin)</li>
<li>Cleaned-up working NeOn plug-in for NeOn toolkit (plugin)</li>
<li>Introduced abstract directories (serv)</li>
<li>Improved the WordNet interface by introducing version. 3.0 is default (ling)</li>
<li>Reinstated the possibility to use the old namespace in the parser (parser)</li>
<li>Corrected a bug that prevented to store alignments in Web service
interface (serv)</li>
<li>Passed command line parameters to <tt>align()</tt> (serv)</li>
<li>Created an Annotation class for storing static strings (impl)</li>
<li>Enriched Ontology objects (impl)</li>
<li>Progressed in the implementation of alignment composition (impl)</li>
<li>MANIFEST generation in buildfile (distrib)</li>
<li>Improved version number management</li>
<li>Javadoc generation flawless in buildfile (distrib)</li>
<li>Revised reference manual (doc)</li>
<a name="3.1"></a><h2>Version 3.1 (614): 05/02/2008 - Klippekort</h2>
<p><span style="color: red;">BEWARE:</span>
For better conforming with RDF practice, we have
<ul compact="1">
<li>Changed the Alignment namespace by adding a '#' at its end (format).</li>
<li>Modified the extension mechanism so that getExtension and
setExtension take a namespace URI as first argument (api).</li>
<li>Modified the service database extension format for recording this
</ul></p>
<p>
Other improvements include:
<ul compact="1">
<li>Implement level 2OMWG alignments by using OMWG Mapping API (impl/omwg)</li>
<li>Integrated first <a href="http://www.neon-project.org">NeOn</a> toolkit plugin (plugin)</li>
<li>Added a <tt>parseString( String )</tt> method
in <tt>AlignmentParser</tt> (parser)</li>
<li>Implemented parsing of relations named by class name (parser)</li>
<li>Added more ontology information in format, changed the
implementation of ontology descriptions (format/parser/impl)</li>
<li>Modified the Alignement namespace by adding a '#'(format)</li>
<li>Separated namespace from pName in extension keys</li>
<li>Added Web Service Alignment server profile (serv)</li>
<li>Multithreaded matching in Services (serv)</li>
<li>Got rid of the property file for wordnet (ling)</li>
<li>In Server/FIPA, suppressed generated files on <tt>close()</tt> (serv)</li>
<li>Suppressed all printouts (Jade or Jetty logging) (serv)</li>
<li>Added file logging option (serv)</li>
<li>Added the inverse operation (serv)</li>
<li>Completely rewritten autodetection of renderers and methods in server (serv)</li>
<li>Modified interface of embedded methods</li>
<li>Added guarantee that results displayed by <tt>GroupEval</tt> be sorted
(thanks Vassilis Spiliopoulos) (util)</li>
<li>Added namespace support in BasicAlignment (impl)</li>
<li>Forced trailing slash in HTML menu URLs (serv)</li>
<li>Added fetching alignments from URIs (serv)</li>
<li>Changed for Jetty as an embedded HTTP server (serv)</li>
<li>Implemented alignment upload (serv)</li>
<li>Corrected an error on "force"-ing alignment in Server/HTML (was
<li>Corrected a bug concerning extension namespaces (impl)</li>
<li>Corrected a bug in the DistanceAlignment Hungarian method
extraction (impl)</li>
<li>Corrected bugs in relation writing/parsing (parser)</li>
<li>Corrected a bug in <tt>SubsDistanceAlignment</tt> when URI have no
fragments (method)</li>
<li>Improved web pages (reorganisation) (html)</li>
<li>Transferred the TODOs to gforge (html)</li>
<li>Updated tutorial sh and bat scripts, thanks to Angel Lopez Cima
(tutorial)</li>
<li>Added a server-based tutorial (tutorial)</li>
<a name="3.0"></a><h2>Version 3.0 (436): 25/02/2007 - Hyderabad</h2>
<p><span style="color: red;">BEWARE:</span>
The main modification in this version is more independence from the
OWL API which is not anymore compulsory. Consequently, the existing
implementation of matching methods with Alignment API should undergo
some modifications: <a href="up2to3.html">Here is how to do</a>
(this document has been updated to help migrating directly to
version 3.3 if necessary).</p>
<p>The Alignment API is now compiled in Java 1.5 (older versions
should still be able to run it).</p>
<li>Separated <tt>BasicAlignment</tt>
from <tt>OWLAPIAlignment</tt></li>
<li>Implemented <tt>URIAlignment</tt></li>
<li><tt>AlignmentParser</tt> returns an <tt>URIAlignment</tt>, for
obtaining an <tt>OWLAPIAlignment</tt>,
use <tt>OWLAPIAlignment.toOWLAPIAlignemnent(URIAlignment)</tt>.</li>
<li>Introduced an abstract notion of <tt>OntologyCache</tt> object in
place of the previous <tt>Hashtable</tt> (this is independent from
the OWL API)</li>
<li>Based all implemented methods on <tt>OWLAPIAlignment</tt></li>
<li>Implemented all renderer methods for <tt>URIAlignments</tt> (but
those requiring <tt>OWLAPIAlignment</tt>)</li>
<li>Adapted all util functions to the relevant methods</li>
<li>Added autodetection of renderers and methods in server</li>
<li>Added menu of available alignments when possibles</li>
<li>Added cut method in server</li>
<li>Revised server database structure, implemented automatic creation
of the database</li>
<li>Protected database insertion with safe-quoting function</li>
<li>Suppressed all useless import and imprecise catch</li>
<li>Suppressed "localhost" from local URL in README, tutorial and
documentation</li>
<li>Reorganised the root directory (renamed samples into examples,
deleted rdf and aligns);</li>
<li>Redefined the example suite in README.TXT;</li>
<li><tt>PRecEvaluator</tt> now counts as false in
precision and recall, cells which previously were not acounted
because they raised an exception. This is because, alignments are
judged based on URI and not OWLAPI entities anymore.</li>
<a name="2.5"></a><h2>Version 2.5 (375): 30/12/2006 - Thalia</h2>
<li>Added Alignment server</li>
<li>Added HTML Alignment server profile</li>
<li>Added new output of algorithms strength in OAEI (GroupOutput)</li>
<li>Suppressed outdated "tutorial" from repository (see html/tutorial)</li>
<li>Corrected Cell id rendering/parse in RDF/XML (rdf:about)</li>
<li>Improved Precision/recall graph rendering in LaTeX</li>
<li>Improved Weighted harmonic means computation in GroupEval</li>
<a name="2.4"></a><h2>Version 2.4 (302): 10/07/2006 - Cercedilla noches</h2>
<p><ul compact="1">
<li>Added a <a href="tutorial">tutorial</a> in the html pages.</li>
<li>Integrated first implementation of HTTP Alignment Server</li>
<li>Slightly changed GroupAlign for accomodating "DOS-based" C:</li>
<li>Made Alignment an extension of Cloneable</li>
<li>Put more conformity to the actual practice of DTD</li>
<li>Corrected output format of some evaluators</li>
<li>Corrected XSLTRenderer for working with RDF/XML output</li>
<li>Corrected ParserPrinter so that inverse() be recorded</li>
<li>Suppressed a printout in MatrixMeasure</li>
</ul></p>
<a name="2.3"></a><h2>Version 2.3 (271): 15/06/2006 - OAEI-2006 ready</h2>
<li>Added <tt>HTMLRendererVisitor</tt></li>
<li><tt>ProcAlign</tt> and <tt>GroupAlign</tt> automatically store "time" tag;</li>
<li><tt>StringDistAlignment</tt> and <tt>RDFRenderer</tt> protect the instances without URIs;</li>
<li><tt>GroupAlign</tt> default matcher becomes <tt>StringDistAlignment</tt>.</li>
<a name="2.2"></a><h2>Version 2.2 (263): 05/06/2006 - Onyeari's version a.k.a. may GForge be with you</h2>
<p>Upgraded to <span style="color: green">OWL-API 06-04-12 (1.4.3)</span><br />
<span style="color: red;"></span> No problem encountered.
</p>
<p>New version featuring:
<ul compact="1">
<li>Moved sources to gforge.inria.fr</li>
<li>Moved web site to alignapi.gforge.inria.fr</li>
<li>Updated documentation to reflect new source location</li>
<li>Revisited the release target of the build file for svn compatibility</li>
<li>Added service directory, alignsvc.jar and QueryMediator class</li>
<li>Reengineered StringDistances (only return normalized values) and
StringDistNameAlignment (replaces all the others). This fully
implement individual alignment;</li>
<li>Added similarity matrix printer (-DprintMatrix=1)</li>
<li>Added Hamming, N-gramms, Needleman-Wunch distance, Jaro and
Jaro-Winckler measures on strings</li>
<li>Added -r option for changing reference name in GroupEval</li>
<li>Corrected bug in SymMeanEvaluator</li>
<li>Corrected cut behavior (did not cut the last item, best did not work)</li>
<li>GenPlot generates directly gnuplot output and LaTeX/PGF inclusion.</li>
<a name="2.1"></a><h2>Version 2.1: 17/02/2006 - pre GForge</h2>
<p>New version featuring:
<ul compact="1">
<li>Fixed SEKT renderer problem;</li>
<li>Further fixed ingest and addAlignCell methods that were not 1-1
ready;</li>
<li>Fixed unicity problem in cell sets;</li>
<li>Reintroduced hash indexing by objects in BasicAlignment;</li>
<li>Added PRExtEvaluator implementing Ehrig/Euzenat extended precision
and recall;</li>
<li>Added CERTH string comparison method;</li>
<li>Added SKOSRendererVisitor;</li>
<li>Corrected OWL/RDF mistakes in some example files;</li>
<li>Corrected mistakes in align.owl and align.rdfs (thanks to Antoine Isaac);</li>
<a name="2.0"></a><h2>Version 2: 1/10/2005 - Raphael's version a.k.a. AC385 version</h2>
<p><span style="color: red;">BEWARE:</span> <tt>Alignment</tt> methods <tt>getAlignCell1</tt>, <tt>getAlignCell2</tt>, <tt>getAlignedObject1</tt>, <tt>getAlignedObject2</tt>, <tt>getStrength1</tt>, <tt>getStrength2</tt>, <tt>getRelation1</tt>
Jérôme Euzenat
committed
and <tt>getRelation2</tt> deprecated (implementation is still
provided however).
</p>
<li>Fixed all implementation that assume 1-1 alignments;</li>
<li>Deprecated accessor from the Alignment to the cell of an object;</li>
<li>Implemented the deprecated with a compile-time tag;</li>
<li>Implemented the Hungarian method for maximal pairing in building 1-1 alignments;</li>
<li>Added equals() method to Cell and Relation;</li>
<li>Added Precision-recall graph generators (GenPlot,PRGraphEvaluator);</li>
<li>Computation of aggregated precision and recall rather than average (GroupEval);</li>
<li>Added options for avoiding the alignment on some namespaces;</li>
<li>Added timing in Procalign and Groupalign;</li>
<li>Added extension mechnism for alignments (any extra-annotation stored).</li>
<a name="1.4"></a><h2>Version 1.4: 04/07/2005 - OAEI 2005 facilities</h2>
<p>New version featuring:
<ul compact="1">
<li>Many new parameters on GroupAlign (target/source/prefix) for
accomodating new test sets</li>
<li>Added freeing of ontology from memory between tests in GroupAlign</li>
</ul></p>
<a name="1.3"></a><h2>Version 1.3: 15/06/2005 - Ready for OAEI 2005</h2>
<p>Upgraded to <span style="color: green">OWL-API 05-03-21 (1.4.2)</span><br />
<span style="color: red;">BEWARE:</span> if you experience problems
recompiling after upgrading to this version of the OWL-API, this is
because it requires and additional method:
<tt>owlFullConstruct(int code, String message, Object o)</tt> in the
<tt>OWLRDFErrorHandler</tt> (see Procalign.java for the fix).
</p>
<p>Compatible with <span style="color: green">Java 1.5</span></p>
<li>Full implementation of parameters (reader included)</li>
<li>Separated the API from its implementation (align/procalign)</li>
<li>Separated the WordNet from the implementation (alignwn)</li>
<li>Corrected XML header of some examples (necessary for Java 1.5)</li>
<li>Fixed usability of Wordnet (on Mac OS X)</li>
<li>Added a (necessary) SubsumedRelation!</li>
<li>Added a sample embedding of main functions</li>
<li>Added three replicas of align(A,p) -> align(), align(A) and align(p)</li>
<li>Added SEKTMapping renderer</li>
<li>Added method and semantics tags to format</li>
<li>Added -p parameter for reading parameter file on most util classes</li>
<li>Added alignment method name output in the output format</li>
<li>Implemented GroupAlign allowing to batch-align several ontologies</li>
<li>Started reengineering matrix-based distance alignments</li>
<a name="1.2"></a><h2>Version 1.2: 23/11/2004 - ISWC suggestions and improvements</h2>
<p>New version featuring:
<ul compact="1">
<li>Added multiple cut implementation (hard/perc/prop/best...)</li>
<li>Added COWL renderer</li>
<li>Added warning about the need of log4j and getopts</li>
<li>Forced the RDFRenderer to generate UTF-8 (the parser does only accept UTF-8 in element names). All renderers take PrintWriters as arguments.</li>
<li>Fully implemented the parser and the printer so that onto tags contains file info and uri tags contain URI info.</li>
</ul></p>
<a name="1.1"></a><h2>Version 1.1: 5/11/2004 - Lessons from EON</h2>
<li>Fixed the format output and parsing to true RDF</li>
<li>Implemented GroupEval</li>
<li>Added WordNet method</li>
<li>Fixed two bugs in methods ()</li>
<li>Divided impl directory into method/rendered...</li>
<li>Implemented the inverse method</li>
<li>Added RDFS Format</li>
<li>Added an "id" to each cell (in API, Renderer and Parser);</li>
<li>Provided an XSLT stylesheet for alignments;</li>
<a name="1.01"></a><h2>April 19th, 2004</h2>
<p>New version featuring:
<ul compact="1">
<li>Corrected the problem of putting directly distances into strength
({get/set}Measure{1/2} are now called Strength,
new class DistanceAlignment which takes care of converting distances into strength);</li>
<li>Implemented effectively SymMeanEvaluator with a dispatch per elements;</li>
<li>Added correct 1:1 tags to all implemented OWL alignments</li>
<li>Used Object in API: no OWL in the format (all API methods which
returned OWL... now returns Objects, dynamic typecheckking of the
basic methods: maybe not the best idea)</li>
<li>Implemented parameters (align() and eval() take an additionnal
Parameters parameter, new Parameters interface and
BasicParameters class);</li>
<li>Corrected the visitor for the Renderer (now robust to subclassing);</li>
<li>Built a renderer for RDF and use it
(suppression of the write method in Cell and Alignment,
Procalign uses the same code for rendering);</li>
<li>Added a StringDistance class providing substring and editstriung distances;</li>
<li>Reviewed all catch with a printStackTraces (parser still unsatisfactory);</li>
<li>Cleaned-up traces;</li>
<li>Provided a full-fledged example illustrated with a paper;</li>
<li>Corrected StrucSubsDistNameAlignment;</li>
<li>Changed name: Evaluator.evaluate() --> Evaluator.eval();</li>
</ul>
<a name="1.0"></a><h2>Version 1.0: 4/4/2004 - First complete version</h2>
<p>This uses the 090304 (1.2.0) version of the <span style="color: green">OWL API</span>.</p>
<p>New version featuring:
<ul compact="1">
<li>Added the Evaluator interface and implementation (PRecEvaluator
and SymMeanEvaluator).</li>
<li>Added Exceptions</li>
<li>Added Renderer as visitors</li>
<li>Added a simple structural algorithm (StrucSubsDistNameAlignment).</li>
<li>Added a number of alignment based on substring distance;</li>
<li>Various improvements.</li>
</ul>
</p>
<a name="0.2"></a><h2>January 2004</h2>
<p>Put under CVS at Sophia-Antipolis</p>
<p>New version featuring:
<ul compact="1">
<li>Added a number of alignment implementations (EditDistAlignment);</li>
</ul>
</p>
<a name="0.1"></a><h2>Version 0.1: 12/12/2003 - First release</h2>
<center>http://alignapi.gforge.inria.fr/relnotes.html</center>
<hr />
$Id$
</small>
</address>
</body>
</html>