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- provided a full description of ontowrap

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...@@ -15,17 +15,15 @@ There are many different APIs for ontologies. Even if the Alignment ...@@ -15,17 +15,15 @@ There are many different APIs for ontologies. Even if the Alignment
API is independent from these APIs, it is often convenient to interact API is independent from these APIs, it is often convenient to interact
with them. with them.
For that purpose, we have designed the <tt>ontowrap</tt> API which For that purpose, we have designed the <tt>ontowrap</tt> API which
provides a minimal interaction with provides a minimal interaction with the major ontology APIs (OWL API
</p> and Jena, soon SKOS API).
<p style="background-color: yellow;">
</p> </p>
<h2>The <tt>ontowrap</tt> architecture</h2> <h2>The <tt>ontowrap</tt> architecture</h2>
<p> <p>
An implementation of <tt>ontowrap</tt> is a OntologyFactory and an An implementation of <tt>ontowrap</tt> is a <tt>OntologyFactory</tt> and an
Ontology class. <tt>Ontology</tt> class.
The ontology factory is used for creating a new <tt>Ontology</tt> The ontology factory is used for creating a new <tt>Ontology</tt>
object. object.
</p> </p>
...@@ -43,22 +41,37 @@ loading ontologies. ...@@ -43,22 +41,37 @@ loading ontologies.
<p> <p>
There are three interfaces for ontologies: There are three interfaces for ontologies:
<ul> <dl>
<li><tt>Ontology</tt> simply describes an ontology. Its entities are <dt><tt>Ontology</tt></dt><dd>simply describes an ontology. Its entities are
identified by simple URIs and no assumption is made about the fact identified by simple URIs and no assumption is made about the fact
that the ontology has been loaded. Hence, the interface on the that the ontology has been loaded. Hence, the interface on the
entities is very limited.</li> entities is very limited.</dd>
<li><tt>LoadedOntology</tt> describes an ontology that has been loaded <dt><tt>LoadedOntology</tt></dt><dd>describes an ontology that has been loaded
in main memory. Thus, an implementation of this class is bound to in main memory. Thus, an implementation of this class is bound to
an ontology API. However, the connection with the API is very an ontology API. However, the connection with the API is very
limited: it is possible to know the type of entity (class, limited: it is possible to know the type of entity (class,
property, etc.) and its names and comments. This does not put property, etc.) and its names and comments. This does not put
burden on developers when connecting an API and this applies to burden on developers when connecting an API and this applies to
"lightweight" ontologies such as unstructured thesauri.</li> "lightweight" ontologies such as unstructured thesauri.</dd>
<li><tt>HeavyLoadedOntology</tt> is supposed to offer broad access to <dt><tt>HeavyLoadedOntology</tt></dt><dd>is supposed to offer broad access to
the ontology by obtaining the relations between entities the ontology by obtaining the relations between entities
(superClasses, properties, etc.).</li> (super-classes, properties, etc.).</dd>
</ul> </dl>
These three interfaces extend each others so that
the <tt>Ontology</tt> interface is the minimal one.
</p>
<p>
Switching implementations of the API is obtained through:
<div class="fragment">
OntologyFactory.setDefaultFactory("fr.inrialpes.exmo.ontowrap.owlapi30.OWLAPI3OntologyFactory");
</div>
and then ontologies can be loaded through:
<div class="fragment">
Ontology o = OntologyFactory.getFactory().loadOntology(new URI(...));
</div>
There is a built-in caching mechanism which attempts at avoiding
loading twice the same ontology under the same implementation.
</p> </p>
<h2><tt>Ontology</tt></h2> <h2><tt>Ontology</tt></h2>
...@@ -68,83 +81,163 @@ There are three interfaces for ontologies: ...@@ -68,83 +81,163 @@ There are three interfaces for ontologies:
describes the ontology but nothing from its content. describes the ontology but nothing from its content.
</p> </p>
<pre> <dl>
public URI getURI(); <dt>
public URI getFile(); <tt>public URI getURI();<br />
public URI getFormURI(); // Can be null public void setURI( URI uri );</tt>
public String getFormalism(); // Can be null </dt>
public O getOntology(); <dd>
Provides the URI identifying the ontology.
public void setURI( URI uri ); </dd>
public void setFile( URI file ); <dt>
public void setFormURI( URI u ); <tt>public URI getFile();<br />
public void setFormalism( String name ); public void setFile( URI file );</tt>
public void setOntology( O o ); </dt>
</pre> <dd>
Provides the URL from where the ontology can be loaded.
</dd>
<dt>
<tt>public URI getFormURI();
public void setFormURI( URI u );</tt>
</dt>
<dd>
Provides the URI identifying the knowledge representation formalism
(may be null).
</dd>
<dt>
<tt>public String getFormalism();<br />
public void setFormalism( String name );</tt>
</dt>
<dd>
Provides a String indicating the knowledge representation formalism
("OWL", "SKOS", etc.; may be null).
</dd>
<dt>
<tt>public O getOntology();<br />
public void setOntology( O o );</tt>
</dt>
<dd>
Provides the ontology object itself when it has been loaded.
</dd>
</dl>
<h2><tt>LoadedOntology</tt></h2> <h2><tt>LoadedOntology</tt></h2>
<p> <p>
<tt>LoadedOntology</tt> <tt>LoadedOntology</tt> extends <tt>Ontology</tt> and provides a minimal interface to the content of
the ontologies. This interface is made of two main parts:
<ul>
<li>One part dealing with the various types of objects in the
ontology (classes, properties, instances, etc.)</li>
<li>One part dealing with their names and the annotations they are
assigned.</li>
</ul>
</p> </p>
<pre>
public boolean isEntity( Object o );
public boolean isClass( Object o );
public boolean isProperty( Object o );
public boolean isDataProperty( Object o );
public boolean isObjectProperty( Object o );
public boolean isIndividual( Object o );
public Set<? extends Object> getEntities();
public Set<? extends Object> getClasses();
public Set<? extends Object> getProperties();
public Set<? extends Object> getObjectProperties();
public Set<? extends Object> getDataProperties();
public Set<? extends Object> getIndividuals();
public int nbEntities();
public int nbClasses();
public int nbProperties();
public int nbDataProperties();
public int nbObjectProperties();
public int nbIndividuals();
<dl>
<dt><tt>
public int nbEntities();<br />
public int nbClasses();<br />
public int nbProperties();<br />
public int nbDataProperties();<br />
public int nbObjectProperties();<br />
public int nbIndividuals();<br />
</tt></dt>
<dd>
Provides the number of corresponding entities defined in the ontology.
</dd>
<dt><tt>
public Set&lt;? extends Object> getEntities();<br />
public Set&lt;? extends Object> getClasses();<br />
public Set&lt;? extends Object> getProperties();<br />
public Set&lt;? extends Object> getObjectProperties();<br />
public Set&lt;? extends Object> getDataProperties();<br />
public Set&lt;? extends Object> getIndividuals();<br />
</tt></dt>
<dd>
Provides the sets of corresponding entities defined in the ontology.
</dd>
<dt><tt>
public boolean isEntity( Object o );<br />
public boolean isClass( Object o );<br />
public boolean isProperty( Object o );<br />
public boolean isDataProperty( Object o );<br />
public boolean isObjectProperty( Object o );<br />
public boolean isIndividual( Object o );<br />
</tt></dt>
<dd>
Tells if a particular object is of the correponding type in the ontology.
</dd>
<dt><tt>
public String getEntityName( Object o, String lang ) throws OntowrapException;<br />
public String getEntityName( Object o ) throws OntowrapException;
</tt></dt>
<dd>
Provide the name of an object in this ontology or its name depending
on a particular language. This primitive is not very precise and must
be used with caution: some entities may have no names (identified
by <tt>rdfs:label</tt> property) and some entities may have several
names. In the former case, the interface should try to extract a
fragment from the URI of the entity, but it may reveal
impossible. Hence the answer would null. In the latter case, which
name is returned is unspecified. This primitive is more robust in SKOS
terminologies where it is possible to specify a <tt>skos:preferedLabel</tt>.
</dd>
<dt><tt>
public Set&lt;String> getEntityNames( Object o , String lang ) throws OntowrapException;<br />
public Set&lt;String> getEntityNames( Object o ) throws OntowrapException;
</tt></dt>
<dd>
Provide the names (identified by <tt>rdfs:label</tt> property) of an
object in this ontology or its name depending on a particular language.
</dd>
<dt><tt>
public Set&lt;String> getEntityComments( Object o , String lang ) throws OntowrapException;<br />
public Set&lt;String> getEntityComments( Object o ) throws OntowrapException;
</tt></dt>
<dd>
Provide the comments (identified by <tt>rdfs:comment</tt> property) of an
object in this ontology or its comments depending on a particular language.
</dd>
<dt><tt>
public Set&lt;String> getEntityAnnotations( Object o, String lang ) throws OntowrapException;<br />
public Set&lt;String> getEntityAnnotations( Object o ) throws OntowrapException;
</tt></dt>
<dd>
Provide the annotations (found under <tt>owl:AnnotationProperty</tt>s) of an
object in this ontology or its annotations depending on a particular
language (when these are available).
</dd>
<dt><tt>
public void unload(); public void unload();
</pre> </tt></dt>
<dd>
Free the memory occupied by this ontology.
</dd>
</dl>
<h2><tt>HeavyLoadedOntology</tt></h2> <h2><tt>HeavyLoadedOntology</tt></h2>
<pre> <p>
/* Capability methods */ <tt>HeavyLoadedOntology</tt> extends <tt>LoadedOntology</tt> and
public boolean getCapabilities( int Direct, int Asserted, int Named ); provides an interface to the entities in the ontologies. In
particular, it provides informations about relations between these
/* Class methods */ entities.
public Set<Object> getSubClasses( Object c, int local, int asserted, int named ); </p>
public Set<Object> getSuperClasses( Object c, int local, int asserted, int named );
public Set<Object> getProperties( Object c, int local, int asserted, int named );
public Set<Object> getDataProperties( Object c, int local, int asserted, int named );
public Set<Object> getObjectProperties( Object c, int local, int asserted, int named );
public Set<Object> getInstances( Object c, int local, int asserted, int named );
/* Property methods */
public Set<Object> getSubProperties( Object p, int local, int asserted, int named );
public Set<Object> getSuperProperties( Object p, int local, int asserted, int named );
public Set<Object> getRange( Object p, int asserted );
public Set<Object> getDomain( Object p, int asserted );
/* Individual methods */
public Set<Object> getClasses( Object i, int local, int asserted, int named );
</pre>
<h2><tt>Additional services</tt></h2>
<pre>
</pre>
<h2>Unified interface</h2>
<p> <p>
The proposed solution goes in two ways: Unfortunately, various APIs would return different kind of answers to
such queries depending on:
<ul>
<li>if they consider only entities defined in
the ontologies or any entity referenced (<tt>local</tt>);</li>
<li>if they consider only asserted statements or statements entailed
in some way (<tt>asserted</tt>);</li>
<li>if they consider only named entities or any entities, including
anonymous ones (<tt>named</tt>).</li>
</ul>
In order to unify the behaviour of the APIs, Ontowrap uses the
following solution:
<ul> <ul>
<li>Having only one <tt>getSuperClasses( Class )</tt> primitive but <li>Having only one <tt>getSuperClasses( Class )</tt> primitive but
appending to it a number of boolean arguments defining if the appending to it a number of boolean arguments defining if the
...@@ -161,61 +254,104 @@ the requirements of the application and to raise an exception (or ...@@ -161,61 +254,104 @@ the requirements of the application and to raise an exception (or
change API) if this is not the case. change API) if this is not the case.
</p> </p>
<p>Hence, for instance (dummy): <p>Hence, for instance:
<pre> <div class="fragment">
if ( !onto.getCapabilities( OntologyFactory.GLOBAL, OntologyFactory.INHERITED, 0 ) ) { if ( !onto.getCapabilities( OntologyFactory.GLOBAL, OntologyFactory.INHERITED, 0 ) ) {
throw new AlignementException( onto+" : cannot provide both global and inherited answers"); throw new AlignementException( onto+" : cannot provide both global and inherited answers");
} else { } else {
Set&lt;Object&gt; sups = onto.getSuperClasses( class, OntologyFactory.GLOBAL, Set&lt;Object&gt; sups = onto.getSuperClasses( class, OntologyFactory.GLOBAL,
OntologyFactory.INHERITED, OntologyFactory.DIRECT ); OntologyFactory.INHERITED, OntologyFactory.DIRECT );
} }
</pre> </div>
These primitives always answer, but the answers are only correct if These primitives always answer, but the answers are only correct if
the modalities asked in argument are supported. the modalities asked in argument are supported by the implementation.
</p> </p>
<h4>General methods</h4>
<dl>
<dt><tt>public boolean getCapabilities( int Direct, int Asserted, int Named );</tt></dt>
<dd>Tests the capabilities of the ontology implementation.</dd>
</dl>
<h4>Class methods</h4>
<dl>
<dt><tt>public Set&lt;Object> getSubClasses( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of subclasses of the specified class.</dd>
<dt><tt>public Set&lt;Object> getSuperClasses( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of superclasses of the specified class.</dd>
<dt><tt>public Set&lt;Object> getProperties( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of properties defined on the specified class.</dd>
<dt><tt>public Set&lt;Object> getDataProperties( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of data properties defined on the specified class.</dd>
<dt><tt>public Set&lt;Object> getObjectProperties( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of object properties defined on the specified class.</dd>
<dt><tt>public Set&lt;Object> getInstances( Object c, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of objects belonging to the specified class.</dd>
</dl>
<h4>Property methods</h4>
<dl>
<dt><tt>public Set&lt;Object> getSubProperties( Object p, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of subproperties of the specified property.</dd>
<dt><tt>public Set&lt;Object> getSuperProperties( Object p, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of superproperties of the specified property.</dd>
<dt><tt>public Set&lt;Object> getRange( Object p, int asserted );</tt></dt>
<dd>Returns the set of range constraints defined on the specified property.</dd>
<dt><tt>public Set&lt;Object> getDomain( Object p, int asserted );</tt></dt>
<dd>Returns the set of domain constraints defined on the specified property.</dd>
</dl>
<h4>Individual methods</h4>
<dl>
<dt><tt>public Set&lt;Object> getClasses( Object i, int local, int asserted, int named );</tt></dt>
<dd>Returns the set of classes to which the specified individual belongs.</dd>
</dl>
<!--h2><tt>Additional services</tt></h2>
<p> <p>
Of course, similar reasoning must be applied to the other primitives. </p-->
</p>
<h2>Implementations</h2> <h2>Implementations</h2>
<p> <p>
</p> Here are the available implementations:
<center> <center>
<table> <table border="0">
<tr> <tr>
<td>API</td><td>Version</td><td>Implementation</td><td>Availability</td> <td>API</td><td>Version</td><td>Implementation</td><td>Availability</td><td>classname</td>
</th> </th>
<tr> <tr>
<td><a href="">Jena</a></td><td>2.5</td><td>HeavyLoadedOntology</td><td>Since 3.5</td> <td><a href="http://jena.sourceforge.net/">Jena</a></td><td>2.5</td><td>HeavyLoadedOntology</td><td>Since 3.5</td><td><tt>ow.jena25.JENAOntologyFactory</tt></td>
</tr>
<tr>
<td><a href="http://jena.sourceforge.net/">Jena</a></td><td>2.6</td><td>HeavyLoadedOntology</td><td>Since 4.0</td><td><tt>ow.jena25.JENAOntologyFactory</tt></td>
</tr> </tr>
<tr> <tr>
<td><a href="">OWL API</a></td><td>1.0</td><td>HeavyLoadedOntology</td><td>Since /3.5</td> <td><a href="http://owlapi.sourceforge.net/">OWL API</a></td><td>1.0</td><td>HeavyLoadedOntology</td><td>Since /3.5</td><td><tt>ow.owlapi10.OWLAPIOntologyFactory</tt></td>
</tr> </tr>
<tr> <tr>
<td><a href="">OWL API</a></td><td>2.0</td><td>HeavyLoadedOntology</td><td>Discontinued (3.4-3.6)</td> <td><a href="http://owlapi.sourceforge.net/">OWL API</a></td><td>2.0</td><td>HeavyLoadedOntology</td><td>Discontinued (3.4-3.6)</td><td><tt>ow.owlapi20.OWLAPIOntologyFactory</tt></td>
</tr> </tr>
<tr> <tr>
<td><a href="">OWL API</a></td><td>3.0</td><td>HeavyLoadedOntology</td><td>Since 4.0</td> <td><a href="http://owlapi.sourceforge.net/">OWL API</a></td><td>3.0</td><td>HeavyLoadedOntology</td><td>Since 4.0</td><td><tt>ow.owlapi30.OWLAPI3OntologyFactory</tt></td>
</tr> </tr>
<tr> <tr>
<td><a href="">SKOS API</a></td><td></td><td>LoadedOntology</td><td>In progress (4.x)</td> <td><a href="http://skosapi.sourceforge.net/">SKOS API</a></td><td></td><td>LoadedOntology</td><td>In progress (4.x)</td><td><tt></tt></td>
</tr> </tr>
</table> </table>
</center> </center>
<tt>ow</tt> stands for <tt>fr.inrialpes.exmo.ontowrap</tt>.
</p>
<h2>Miscellaneous</h2> <h2>Miscellaneous</h2>
<p>
The Alignment API was first designed on top of what was the first
published OWL API<sup>1</sup> (the Manchester/Karlsruhe OWL API). Since
it was an API for OWL, I assumed that anybody else would implement it.
Too bad, we soon had the Jena API<sup>2</sup> and plenty of others<sup>3</sup>. Instead of
implementing a common API (a common set of interfaces like the OWL
API), each new player designed its own.
</p>
<p>Here are the historical <a href="owlapi.html">howto notes</a> for starting quickly with OWL-API (Outdated notes about the OWL API and its integration in the Alignment API).</p> <p>Here are the historical <a href="owlapi.html">howto notes</a> for starting quickly with OWL-API (Outdated notes about the OWL API and its integration in the Alignment API).</p>
<address>$Id$</address> <address>
<small>
<hr />
<center>http://alignapi.gforge.inria.fr/ontowrap.html</center>
<hr />
$Id$
</small>
</address>
</body> </body>
</html> </html>
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