<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.0 20120330//EN" "JATS-archivearticle1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>OnlynessIsLoneliness (OIL)</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Oscar Corcho</string-name>
          <email>ocorcho@fi.upm.es</email>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Catherine Roussey</string-name>
          <email>catherine.roussey@cemagref.fr</email>
          <email>catherine.roussey@liris.cnrs.fr</email>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Cemagref</institution>
          ,
          <addr-line>24 Av. des Landais, BP 50085, 63172 Aubi ́ere</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Ontology Engineering Group, Departamento de Inteligencia Artificial, Universidad Polit ́ecnica de Madrid</institution>
          ,
          <country country="ES">Spain</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>Universit ́e de Lyon</institution>
          ,
          <addr-line>CNRS, Universit ́e Lyon 1, LIRIS UMR5205, Villeurbanne</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
      </contrib-group>
      <fpage>104</fpage>
      <lpage>107</lpage>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1 Introduction</title>
      <p>
        Our work is based on the debugging process of real ontologies that have been
developed by domain experts, who are not necessarily too familiar with DL, and
hence can misuse DL constructors and misunderstand the semantics of some
OWL expressions, leading to unwanted unsatisfiable classes. Our patterns were
first found during the debugging process of a medium-sized OWL ontology (165
classes) developed by a domain expert in the area of hydrology [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ]. The first
version of this ontology had a total of 114 unsatisfiable classes. The information
provided by the debugging systems used ([
        <xref ref-type="bibr" rid="ref3">3</xref>
        ], [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ]) on (root) unsatisfiable classes
was not easily understandable by domain experts to find the reasons for their
unsatisfiability. And in several occasions during the debugging process the
generation of justifications for unsatisfiability took several hours, what made these
tools hard to use, confirming the results described in [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ]. Using this debugging
process and several other real ontologies debugging one, we found out that in
several occasions domain experts were just changing axioms from the original
ontology in a somehow random manner, even changing the intended meaning of
the definitions instead of correcting errors in their formalisations.
      </p>
      <p>
        We have identified a set of patterns that are commonly used by domain
experts in their DL formalisations and OWL implementations, and that
normally result in unsatisfiable classes or modelling errors ([
        <xref ref-type="bibr" rid="ref1">1</xref>
        ], [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ]). Thus they are
antipatterns. [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ] define antipatterns as patterns that appear obvious but are
ineffective or far from optimal in practice, representing worst practice about how
to structure and build software. We also have made an effort to identify common
alternatives for providing solutions to them, so that they can be used by domain
experts to debug their ontologies.
      </p>
      <p>All these antipatterns come from a misuse and misunderstanding of DL
expressions by ontology developers. Thus they are all Logical AntiPatterns (LAP):
they are independent from a specific domain of interest, but dependent on the
expressivity of the logical formalism used for the representation.
2
2.1</p>
    </sec>
    <sec id="sec-2">
      <title>Pattern</title>
      <sec id="sec-2-1">
        <title>Problem</title>
        <p>The ontology developer created a universal restriction to say that C1 instances
can only be linked with property R to C2 instances. Next, a new universal
restriction is added saying that C1 instances can only be linked with R to C3
instances, with C2 and C3 disjoint. Figure 1 illustrates this problem: grey squares
represent instances of C2 C3 that cannot exist. In general, this is because the
ontology developer forgot the previous axiom in the same class or in any of the
parent classes.</p>
        <p>C1 ∀R.(C2); C1 ∀R.(C3); Disj(C2, C3); 4</p>
        <p>Notice that to be detectable, R property must have at least a value, normally
specified as a (minimum) cardinality restriction for that class, or with existential
restrictions.</p>
        <p>Covers Requirements When this antipattern appears during the debugging
process, you have to first explain to the domain expert the meaning of this
formalisation using a schema like the one of the Figure 1. Then you could ask
4 This does not mean that the ontology developer has explicitly expressed that C2 and
C3 are disjoint, but that these two concepts are determined as disjoint from each
other by a reasoner. We use this notation as a shorthand for C2 C3 ⊥.
him some questions to find out where is the problem. For example, you could
ask:
- Should C1 be linked with the R property to C2?
- Should C1 be linked with the R property to C3?
- Does C1 have to be linked only to C2 with the R property?
- Does C1 have to be linked only to C3 with the R property?
- Are you sure that C2 and C3 are disjoint?
2.2</p>
      </sec>
      <sec id="sec-2-2">
        <title>Solution</title>
        <p>If it makes sense, we propose the domain expert to transform the two universal
restrictions into only one that refers to the logical disjunction of C2 and C3.
Another alternative solution, which is used by most part of automatic debugging
tool is to remove one of the axioms.</p>
        <p>C—1——∀—R.—C2—;C—1 — —∀R—.C—3; Disj(C2, C3); ⇒ C1 ∀R.(C2 C3);
2.3</p>
      </sec>
      <sec id="sec-2-3">
        <title>Example</title>
        <p>The following section describes two definitions from HydrOntology where this
antipattern can be found and their English translations. Notice that in each
example, the antipattern corresponds to a part of the class definition.</p>
      </sec>
      <sec id="sec-2-4">
        <title>Example Problem about Transitional Water</title>
        <p>Aguas de Transici´on ∀est´a pr´oxima.Aguas M arinas
∀est´a pr´oxima.Desembocadura = 1est´a pr´oxima. ;</p>
        <p>T ransitional W ater ∀is nearby.Sea W ater ∀is nearby.River M outh
= 1is nearby. ;</p>
      </sec>
      <sec id="sec-2-5">
        <title>Example Solution about Transitional Water</title>
        <p>Aguas de Transici´on ∀est´a pr´oxima.(Aguas M arinas
= 1est´a pr´oxima. ;</p>
        <p>T ransitional W ater ∀is nearby.(Sea W ater
= 1is nearby.</p>
        <sec id="sec-2-5-1">
          <title>Desembocadura)</title>
        </sec>
        <sec id="sec-2-5-2">
          <title>River M outh)</title>
        </sec>
      </sec>
      <sec id="sec-2-6">
        <title>Example Problem about Wet Zone</title>
        <p>Zona Humeda ∀Humedal ∀es inundada.Aguas M arinas
∀es inundada.Aguas Superf iciales ≥ 1es inundada. ;</p>
        <p>W et Zone ∀W etlands ∀are inundated.Sea W ater
∀are inundated.Surf ace W ater ≥ 1are inundated. ;</p>
      </sec>
      <sec id="sec-2-7">
        <title>Example Solution about Wet Zone</title>
        <p>Zona Humeda ∀Humedal
∀es inundada.(Aguas M arinas Aguas Superf iciales) ≥ 1es inundada. ;</p>
        <p>
          W et Zone ∀W etlands ∀are inundated.(Sea W ater Surf ace W ater)
≥ 1are inundated. ;
All the information related to the debugging of the Hydrontology ontology can
be found in urlhttp://www.dia.fi.upm.es/ ocorcho/OWLDebugging/. The
debugging strategy using this antipattern is described in [
          <xref ref-type="bibr" rid="ref2">2</xref>
          ]. Other antipatterns
found during the debugging task are defined in [
          <xref ref-type="bibr" rid="ref1">1</xref>
          ] and [
          <xref ref-type="bibr" rid="ref7">7</xref>
          ]
3
        </p>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>Summary and Future Work</title>
      <p>
        This antipattern can be found in ontologies and may cause inconsistency
problems. We provide a solution to it, so that it can be used by domain experts to
debug their ontologies. In the future, we aim at implementing additional tools
to help in the identification of antipatterns in well-known inconsistent
ontologies (e.g., TAMBIS). For the time being we have started applying the OPPL
language [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ] for this task, with promising results.
      </p>
    </sec>
  </body>
  <back>
    <ref-list>
      <ref id="ref1">
        <mixed-citation>
          1.
          <string-name>
            <surname>Corcho</surname>
            <given-names>O.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Roussey</surname>
            <given-names>C.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Vilches Blazquez L.M.</surname>
          </string-name>
          <article-title>: Catalogue of Anti-Patterns for formal Ontology debugging</article-title>
          .
          <source>In Proceedings of Construction d'</source>
          <article-title>ontologies : vers un guide des bonnes pratiques</article-title>
          ,
          <source>AFIA</source>
          <year>2009</year>
          , Hammamet,
          <string-name>
            <surname>Tunisie.</surname>
          </string-name>
          (
          <year>2009</year>
          ).
        </mixed-citation>
      </ref>
      <ref id="ref2">
        <mixed-citation>
          2.
          <string-name>
            <surname>Corcho</surname>
            <given-names>O.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Roussey</surname>
            <given-names>C.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Vilches Blazquez L.M.</surname>
          </string-name>
          <article-title>: Pattern-based OWL Ontology Debugging Guidelines</article-title>
          .
          <source>In Proceedings of 1st Workshop on Ontology Patterns (WOP2009)</source>
          ,
          <string-name>
            <surname>Washington</surname>
            <given-names>DC</given-names>
          </string-name>
          , USA. (
          <year>2009</year>
          ).
        </mixed-citation>
      </ref>
      <ref id="ref3">
        <mixed-citation>
          3.
          <string-name>
            <surname>Horridge</surname>
            <given-names>M</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Parsia</surname>
            <given-names>B</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Sattler</surname>
            <given-names>U.</given-names>
          </string-name>
          :
          <article-title>Laconic and Precise Justifications in OWL</article-title>
          .
          <source>In Proceedings of the 7th International Semantic Web Conference (ISWC)</source>
          ,
          <source>Karlsruhe, Germany; LNCS</source>
          <volume>5318</volume>
          :
          <fpage>323</fpage>
          -
          <lpage>338</lpage>
          . (
          <year>2008</year>
          ).
        </mixed-citation>
      </ref>
      <ref id="ref4">
        <mixed-citation>
          4.
          <string-name>
            <surname>Iannone</surname>
            <given-names>L</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Rector</surname>
            <given-names>A</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Stevens</surname>
            <given-names>R.</given-names>
          </string-name>
          :
          <article-title>Embedding Knowledge Patterns into OWL</article-title>
          .
          <source>In proceedings of the 6th European Semantic Web Conference (ESWC2009)</source>
          , Crete, Greece.
          <source>The Semantic Web: Research and Applications</source>
          (
          <year>2009</year>
          ), pp.
          <fpage>218</fpage>
          -
          <lpage>232</lpage>
        </mixed-citation>
      </ref>
      <ref id="ref5">
        <mixed-citation>
          5.
          <string-name>
            <surname>Kalyanpur</surname>
            <given-names>A</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Parsia</surname>
            <given-names>B</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Sirin</surname>
            <given-names>E</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Cuenca-Grau</surname>
            <given-names>B.</given-names>
          </string-name>
          :
          <article-title>Repairing Unsatisfiable Classes in OWL Ontologies</article-title>
          .
          <source>In Proceedings of the 3rd European Semantic Web Conference (ESWC)</source>
          ,
          <source>Budva, Montenegro; LNCS</source>
          <volume>4011</volume>
          :
          <fpage>170</fpage>
          -
          <lpage>184</lpage>
          (
          <year>2006</year>
          )
        </mixed-citation>
      </ref>
      <ref id="ref6">
        <mixed-citation>
          6.
          <string-name>
            <surname>Koenig</surname>
            <given-names>A.</given-names>
          </string-name>
          :
          <article-title>Patterns and Antipatterns</article-title>
          .
          <source>Journal of Object-Oriented Programming</source>
          <volume>8</volume>
          (
          <issue>1</issue>
          ):
          <fpage>46</fpage>
          -
          <lpage>48</lpage>
          . (
          <year>1995</year>
          )
        </mixed-citation>
      </ref>
      <ref id="ref7">
        <mixed-citation>
          7.
          <string-name>
            <surname>Roussey</surname>
            <given-names>C.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Corcho</surname>
            <given-names>O.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Vilches Blazquez L.M.:</surname>
          </string-name>
          <article-title>A Catalogue of OWL Ontology AntiPatterns</article-title>
          .
          <source>In Proceedings of the Fifth International Conference on Knowledge Capture KCAP</source>
          <year>2009</year>
          ,
          <string-name>
            <given-names>Yolanda</given-names>
            <surname>Gil</surname>
          </string-name>
          , Natasha Noy ed. Redondo Beach, California, USA.
          <source>ISBN 978-1-60558-658-8</source>
          . pp.
          <fpage>205</fpage>
          -
          <lpage>206</lpage>
          (
          <year>2009</year>
          )
        </mixed-citation>
      </ref>
      <ref id="ref8">
        <mixed-citation>
          8.
          <string-name>
            <surname>Stuckenschmidt</surname>
            <given-names>H.</given-names>
          </string-name>
          :
          <article-title>Debugging OWL Ontologies - a Reality Check</article-title>
          .
          <source>In Proceedings of the 6th International Workshop</source>
          on Evaluation of
          <article-title>Ontology-based Tools and the Semantic Web Service Challenge (EON-SWSC-</article-title>
          <year>2008</year>
          ), Tenerife,
          <string-name>
            <surname>Spain.</surname>
          </string-name>
          (
          <year>2008</year>
          ).
        </mixed-citation>
      </ref>
      <ref id="ref9">
        <mixed-citation>
          9.
          <string-name>
            <surname>Vilches-Bl´azquez</surname>
            <given-names>LM</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Bernab´</surname>
          </string-name>
          e-
          <string-name>
            <surname>Poveda</surname>
            <given-names>MA</given-names>
          </string-name>
          , Su´
          <string-name>
            <surname>arez-Figueroa</surname>
            <given-names>MC</given-names>
          </string-name>
          ,
          <article-title>G´omez-</article-title>
          <string-name>
            <surname>P´erez</surname>
            <given-names>A</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Rodrguez-Pascual</surname>
            <given-names>AF</given-names>
          </string-name>
          :
          <article-title>Towntology &amp; hydrOntology: Relationship between Urban and Hydrographic Features in the Geographic Information Domain</article-title>
          .
          <article-title>In Ontologies for Urban Development</article-title>
          .
          <source>Studies in Computational Intelligence</source>
          , vol.
          <volume>61</volume>
          , Springer:
          <fpage>73</fpage>
          -
          <lpage>84</lpage>
          . (
          <year>2007</year>
          )
        </mixed-citation>
      </ref>
    </ref-list>
  </back>
</article>