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<title>A format for ontology alignment</title>
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<p style="background-color: yellow;">A more expressive format is offered as <a href="edoal.html">EDOAL</a>.</p>
<h1 class="titre">A format for ontology alignment</h1>
<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 input for further alignment methods, transform it into axioms
or transformations or compare different alignments.</p>
<p>This is a first format that could be extended for accomodating
further needs. The Alignment API offers the <a href="edoal.html">Expressive and
Declarative Ontology Alignment Language (EDOAL)</a> for more
elaborate uses.</p>
<p>We describe below its source descriptions, its specifications and
some implementations.</p>
<p>
The Alignment format was initially described as an XML format. It was
given a DTD. It has since been transformed into an RDF format and
given a corresponding OWL ontology. These are currently obsolete due
to the introduction of the EDOAL format.
</p>
<!--p>There are two specifications of the format:
The Alignment format has been given an OWL ontology and a DTD for validating it in RDF/XML.
It can be manipulated through the Alignment API which is presented below.
<dt><a href="align.owl">OWL Ontology</a></dt>
<dd>An OWL description of the format which can then be described in
RDF. This is the reference description of the format.</dd>
<dt><a href="align.dtd">DTD</a></dt>
<dd>A DTD for expressing the same format in RDF/XML. It is useful for
tools which wants to have a more fixed format than RDF.</dd>
</dl>
<p>The namespace used by these formats is <tt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment#</tt>.</p>
<h2>Format description</h2>
<h3><tt>Alignment</tt> element</h3>
<p>The <tt>Alignment</tt> element describes a particular alignment. Its
attributes are the following:
<dl compact="1">
<dt>xml</dt><dd>(value: "yes"/"no") indicates if the alignment can be
read as an XML file compliant with the DTD;</dd>
<dt>level</dt><dd>(values: "0", "1", "2EDOAL") the level of
alignment, characterising its type;</dd>
"11"/"1?"/"1+"/"1*"/"?1"/"??"/"?+"/"?*"/"+1"/"+?"/"++"/"+*"/"*1"/"*?"/"?+"/"**";
default "11") the type or arity of alignment. Usual notations are 1:1, 1:m, n:1 or n:m. We prefer to note if the mapping is injective, surjective and total or partial on both side.
We then end up with more alignment arities (noted with, 1 for injective and total, ? for injective, + for total and * for none and each sign concerning one mapping and its converse);</dd>
<dt>onto1</dt><dd>(value: Ontology) the first aligned ontology;</dd>
<dt>onto2</dt><dd>(value: Ontology) the second aligned ontology;</dd>
<dt>map</dt><dd>(value: Cell) a correspondance between
<?xml version='1.0' encoding='utf-8' standalone='no'?>
<rdf:RDF xmlns='http://knowledgeweb.semanticweb.org/heterogeneity/alignment#'
xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
xmlns:xsd='http://www.w3.org/2001/XMLSchema#'
xmlns:align='http://knowledgeweb.semanticweb.org/heterogeneity/alignment#'>
<level>0</level>
<type>**</type>
<align:method>fr.inrialpes.exmo.align.impl.method.StringDistAlignment</align:method>
<align:time>7</align:time>
<onto1>... </onto1>
<onto2>... </onto2>
...
</Alignment>
</rdf:RDF>
</div>
<h3><tt>Ontology</tt> element</h3>
<p>
Ontology elements provide information concerning the matched
ontologies. It contains three attributes:
<dl>
<dt>rdf:about</dt><dd>contains the URI identifying the ontology;</dd>
<dt>location</dt><dd>contains the URL corresponding to a location
where the ontology may be found;</dd>
<dt>formalism</dt><dd>describes the language in which the ontology is
expressed through its name and URI.</dd>
</dl>
</p>
<div class="align">
<Ontology rdf:about="http://www.example.org/ontology2">
<location>file:examples/rdf/onto2.owl</location>
<formalism>
<Formalism align:name="OWL1.0" align:uri="http://www.w3.org/2002/07/owl#"/>
</formalism>
</Ontology>
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</div>
<p>
A lighter form of the <tt>onto1</tt> and <tt>onto2</tt> values is
still correctly parsed but its use is discouraged.
</p>
<h3><tt>Cell</tt> element</h3>
<p>
In first approximation, an alignment is a set of pairs of entities
from each ontology. Each such pair, called a correspondence, is
identified by the Cell element in alignments. A cell has the following attributes:
<dl compact="1">
<dt>rdf:about</dt><dd>(value: URI; optional) an identifier for the cell;</dd>
<dt>entity1</dt><dd>(value: URI or edoal:Expression) the first aligned ontology entity;</dd>
<dt>entity2</dt><dd>(value: URI or edoal:Expression) the second
aligned ontology entity;</dd>
<dt>relation</dt><dd>(value: String; default: =; see below) the
relation holding between the two entities. It is not restricted to
the equivalence relation, but can be more sophisticated (see below);</dd>
<dt>measure</dt><dd>(value: float between 0. and 1., default: 1.) the confidence
that the relation holds between the first and
the second entity. Since many matching methods compute a strength
of the relation between entities, this strength can be provided as
a normalised measure. The measure should belong to an ordered set <i>M</i> including a maximum
element ⊤ and a minimum element ⊥. Currently, we restrict
this value to be a float value between 0. and 1.. If found useful,
this could be generalised into any lattice domain.</dd>
</dl></p>
denotes the confidence held in this correspondence.
<div class="align">
<map>
<Cell>
<entity1 rdf:resource='http://www.example.org/ontology1#reviewedarticle'/>
<entity2 rdf:resource='http://www.example.org/ontology2#journalarticle'/>
<relation>fr.inrialpes.exmo.align.impl.rel.EquivRelation</relation>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>0.4666666666666667</measure>
</Cell>
</map>
<Cell rdf:about="#veryImportantCell">
<entity1 rdf:resource='http://www.example.org/ontology1#journalarticle'/>
<entity2 rdf:resource='http://www.example.org/ontology2#journalarticle'/>
<relation>=</relation>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
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</div>
<h3><tt>Relation</tt> element</h3>
<p>The relation element only contains the name identifying a relation
between ontology entities. This relation may be given:
<ul>
<li>through a symbol: > (subsumes), < (is subsumed),
= (equivalent), % (incompatible), HasInstance, InstanceOf.</li>
<li>through a fully qualified classname of the relation
implementation. If this class is available
under the Java environment, then the relation will be an instance
of this class.</li>
</ul>
<p>
Hence,
<div class="align">
<relation>=</relation>
</div>
is equivalent to:
<div class="align">
<relation>fr.inrialpes.exmo.align.impl.rel.EquivRelation</relation>
</div>
</p>
<h2>Metadata (extensions)</h2>
<p>
So far, alignments contain information about:
<ul>
<li>the kind of alignment it is (1:1 or n:m for instance);</li>
<li>the algorithm that provided it (or if it has been provided by hand);</li>
<li>the language level used in the alignment (level 0 for the first example, level 2Horn for the second one);</li>
<li>the confidence value in each correspondence.</li>
</ul>
</p>
<p>
The format as implemented here supports extensions both on
Alignments and on Cells. Extensions are additional string-valued
qualified attributes added to cell and alignments. They will be
preserved through the implementation. This extensions allows for
adding metadata in the alignment.
</p>
<p>
These attributes must belong to a different namespace than the
Alignment format namespace. Otherwise, errors will be raised.
</p>
<p>
Other valuable information that may be added to the alignment format are:
<ul>
<li>the parameters passed to the generating algorithm;</li>
<li>the properties satisfied by the correspondences (and their proof if necessary);</li>
<li>the certificate from an issuing source;</li>
<li>the limitations of the use of the alignment;</li>
<li>the arguments in favour or against a correspondence, etc.</li>
</ul>
</p>
<p>
Many standard extensions have already been defined and are
<a href="labels.html">documented</a>.
</p>
<h2>Levels</h2>
<p>
In order to be able to evolve, the Alignment format is provided on
several levels, which depend on more elaborate alignment definitions.
So, far here are the identified levels:
<dl>
<dt>0</dt><dd>is reserved to alignments in which matched entities
are identified by URIs. This corresponds to the alignment
presented here.</dd>
<dt>1</dt><dd>was intended to alignments in which correspondences
match sets of entities identified by URIs. This has never been
used.</dd>
<dt>2</dt><dd>is used for more structured entities that may be
represented in RDF/XML. It is necessary to further identify the
structure of entities, hence advised to use a qualified level
name such as 2EDOAL. <a href="edoal.html">EDOAL</a> mandates
level 2 alignments.</dd>
</dl>
</p>
<h2>JAVA implementation</h2>
<p>
The <a href="index.html">Alignment API</a> implements this format.
In particular it provides tools for:
<ul compact="1">
<li>Outputing the RDF/XML format from the API, through
the <tt>RDFRendererVisitor</tt> renderer;</li>
<li>Parsing the RDF/XML format into the API, through
the <tt>AlignmentParser</tt> parser.</li>
</ul>
</p>
<p>
The <tt>AlignmentParser</tt> is itself made of an <tt>XMLParser</tt>
based on SAX and an <tt>RDFParser</tt> based on Jena. They are tried
in a row starting from the <tt>XMLParser</tt>.
</p>
<p>There is a <a href="cli.html">command</a> that parses an alignment and
displays it ($CWD is the directory where you are):
<div class="terminal">
$ java -jar lib/procalign file://$CWD/rdf/onto1.owl file://$CWD/rdf/onto2.owl
</div>
<center>http://alignapi.gforge.inria.fr/format.html</center>
<hr />
$Id$
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