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<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Enhancing Terminological Knowledge With Upper Level Ontologies</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Selja Sepp a¨l a¨</string-name>
          <email>seljamar@buffalo.edu</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Amanda Hicks</string-name>
          <email>aehicks@ufl.edu</email>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>University at Buffalo</institution>
          ,
          <addr-line>Buffalo, NY</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>University of Florida</institution>
          ,
          <addr-line>Gainesville, FL</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
      </contrib-group>
      <pub-date>
        <year>2015</year>
      </pub-date>
      <fpage>179</fpage>
      <lpage>182</lpage>
      <abstract>
        <p>In this communication, we advocate the use of upper level ontologies such as the Basic Formal Ontology (BFO) to enhance terminological resources and research. First, we present common issues in ontologized terminological work. Then, we review two projects that illustrate the potential advantages of integrating rigorous formal upper level ontologies. Finally, we discuss possible challenges and conclude with a summary of the benefits that such ontologies can bring to both terminological theory and practice.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>Terminologies encode lexical and background
knowledge that experts have about their domain
of expertise. These resources can be
associated with a more explicit ontology-like
representation of the entities in the relevant domain. Such
representations may include, for example,
nonlexicalized concepts. This extends mere
terminologies to more sophisticated knowledge
representations. Being language independent,
ontologized terminologies have the advantage of
integrating multilingual terminologies. When
augmented with axioms, they can be used in reasoning
systems.</p>
      <p>
        Terminological works, where they refer to
ontologies at all, generally use Gruber’s definition of
an ontology as “an explicit specification of a
conceptualization.”
        <xref ref-type="bibr" rid="ref4">(Gruber, 1995)</xref>
        . Ontologies built
on the basis of this definition thus depend on
peoples’ concepts. As a result, the Gruber approach
may lead to several distinct ontological
representations of the same domain, whether expressed in
the same natural language or in different ones.
This definition may also lead to a multiplication
of ontological terms expressing categories and
relations to represent the same or distinct conceptual
systems.
      </p>
      <p>
        However, a multiplication of ontological
metalanguages (categories and relations) tends to
create knowledge silos
        <xref ref-type="bibr" rid="ref11">(Smith and Ceusters, 2010)</xref>
        .
In particular, when these metalanguages are
domain-specific. Even within a single domain,
using distinct metalanguages can limit
interoperability of systems using ontological representations
of terminologies. Furthermore, from the
terminological research viewpoint, a multiplication of
categories and relations hinders the advancement
of our understanding of conceptual systems, of
the internal structure of terms and definitions, etc.
To avoid these limitations, we propose that
terminologists developing terminological resources and
carrying out research would greatly benefit from
using an upper level ontology, such as the
Basic Formal Ontology (BFO), to integrate resources
and research.
      </p>
      <p>In this communication, we present and discuss
existing works integrating upper level ontologies,
and underline the main advantages of augmenting
terminological knowledge with categories and
relations from an upper level ontology such as BFO.
2</p>
    </sec>
    <sec id="sec-2">
      <title>Limitations of Ontological</title>
    </sec>
    <sec id="sec-3">
      <title>Terminologies</title>
      <p>
        Lack of rigorously defined categories and
relations. The interpretation of the
metalanguage is left to our intuitive understanding of
the terms used for expressing the used
categories and relations.
is a overloading
        <xref ref-type="bibr" rid="ref5">(Guarino, 1998)</xref>
        : the is a
relation used for structuring the domain
ontology does not distinguish the genuine is a
subsumption relation from the instance of
relation, and sometimes even from the
part of relation.
      </p>
      <p>Multiplication of domain-specific,
sometimes ad hoc, categories and relations.</p>
      <p>
        When upper level categories are used,
limitation to a few top-most categories, which are
completed with domain-specific ones
        <xref ref-type="bibr" rid="ref3 ref6">(Faber,
2002; Kageura, 2002)</xref>
        .
      </p>
      <p>The above limitations result in practical and
research-related consequences for terminological
works, which can be summarized as follows:
Confusing and incompatible representations
of the same domain.</p>
      <p>Non-interoperable terminologies, which
hinders the possibility of sharing and reusing
terminological resources.</p>
      <p>Non-generalizable observations of
terminological phenomena, which hinders research
towards a proper understanding of
contentrelated principles governing term formation,
definition composition, and conceptual
system organization. This eventually hinders the
development of widely (re)usable
terminological tools, for example, for creating new
terms and writing definitions.</p>
      <p>Non-comparable results of terminological
research for lack of a common well-defined
domain- and language-independent
metalanguage, which hinders the development of a
mature integrated science.</p>
      <p>These shortcomings can be addressed by
adopting well-defined domain- and
languageindependent upper level categories and relations
(ontological metalanguage) of the sort accounted
for in formal upper level ontologies.
180
3</p>
    </sec>
    <sec id="sec-4">
      <title>Enhancing Terminologies with Upper</title>
    </sec>
    <sec id="sec-5">
      <title>Level Ontologies</title>
      <p>A formal upper level ontology can be defined as
“a representation of the categories of objects and
of the relationships within and amongst categories
that are to be found in any domain of reality
whatsoever.” (Spear, 2006)</p>
      <p>
        To illustrate the potential advantages for
terminology of using formal upper level ontologies, we
describe two projects that integrate such
ontologies. There are a few upper level ontologies that
can be used by mid-level or domain-specific
ontologies to define and relate their categories in a
non-ambiguous manner, using logical axioms if
needed. The projects described hereafter use,
respectively, the Descriptive Ontology for Linguistic
and Cognitive Engineering (DOLCE)
        <xref ref-type="bibr" rid="ref7">(Masolo et
al., 2001)</xref>
        and the Basic Formal Ontology (BFO)
        <xref ref-type="bibr" rid="ref1">(Arp et al., 2015)</xref>
        .
3.1
      </p>
      <sec id="sec-5-1">
        <title>The KYOTO Project</title>
        <p>
          The KYOTO project aims at representing
domainspecific terms in a computer-tractable axiomatized
formalism to allow machines to reason over texts
in natural language
          <xref ref-type="bibr" rid="ref13">(Vossen et al., 2010)</xref>
          . The
system developed in this project comprises a platform
for multilingual text mining and information
extraction that was tested on documents from the
environmental domain. The semantics of the terms
are defined through the KYOTO ontology which
is based on DOLCE. WordNets and specialized
vocabularies of different languages are linked to
ontology classes on the basis of a mapping of the
English WordNet to the KYOTO ontology. “This
basic ontology and the mapping to WordNet are
used to model the shared and language-neutral
concepts and relations in the domain.”
          <xref ref-type="bibr" rid="ref13">(Vossen et
al., 2010, 4)</xref>
          The system can thus “detect similar
data across documents in different languages, even
if expressed differently.” (Vossen et al., 2010, 2)
        </p>
        <p>In Vossen et al. (2013), the authors extracted
statements from texts about the Chesapeake Bay
using Kybots, scripts based on ontological and
linguistic patterns in annotated text. The results of
baseline fact extraction were compared with
Kybot extraction and Cterm extraction, both of which
utilize the KYOTO ontology. The result was that
the baseline and Kybot profiles had high recall,
100% and 91% respectively. The baseline had
low precision (18%), whereas the precision of the
Kybot profiles was better, though not optimal, at
31%. In short, leveraging ontological information
in domain-specific fact extraction NLP resulted in
high recall and improved precision.
3.2</p>
      </sec>
      <sec id="sec-5-2">
        <title>The BFO-Based Ontological Analysis</title>
      </sec>
      <sec id="sec-5-3">
        <title>Framework</title>
        <p>
          The second project consists in analyzing the
contents of definitions using the categories and
relations of BFO
          <xref ref-type="bibr" rid="ref10 ref8 ref9">(Seppa¨la¨, 2012; Seppa¨la¨, 2015b)</xref>
          .
The author puts forward an ontological
analysis framework that is domain- and
languageindependent and that can be used in any kind of
terminological conceptual analysis task. The
categories and their characteristics are also used as
models that serve to predict the contents of
definitions. These may be used as templates in tools to
help in definition writing.
        </p>
        <p>The results of the pilot study reported in
Seppa¨la¨ (2012; 2015b) show that these
BFOTemplates account for about 75% of the contents
of definitions of terms from 15 distinct domains.
The rest of the definition contents can be described
using the BFO categories and relations.</p>
        <p>The well-defined BFO vocabulary can thus be
used as a metalanguage to describe definition
contents, term formation, and the organization of
conceptual systems in a way that research
findings can be compared and integrated. In
practice, BFO-based ontologized terminologies would
have the advantage of being interoperable, as it
is already the case for the mid-level and
domainspecific ontologies (and the corresponding
terminologies) that extend BFO, such as the Ontology
for Biomedical Investigations (OBI) and the
Ontology for Biobanking (OBIB)1.
4</p>
      </sec>
    </sec>
    <sec id="sec-6">
      <title>Possible Obstacles to Use of Upper</title>
    </sec>
    <sec id="sec-7">
      <title>Level Ontologies</title>
      <p>Using upper level ontologies may sometimes
prove challenging. Possible issues may be:
Upper level ontologies evolve and their
categories are, at times, still under development.
1For a full list, see http://ifomis.
uni-saarland.de/bfo/users. For an
illustration of interoperability and its advantages, see the
presentation on The OBIB Ontology for Biobanking, by
Chris Stoeckert, Jie Zheng, and Mathias Brochhausen
http://ncorwiki.buffalo.edu/index.php/
CTS_Ontology_Workshop_2015.</p>
      <p>In those cases, it may not be straightforward
under which category to place a term.</p>
      <p>Specifications of the upper level ontology
may be sparse and lacking, and sometimes
too formal (OWL, first order logic) to be
easily understood by terminologists.</p>
      <p>An adequate use requires familiarity with the
upper level ontology chosen.</p>
      <p>
        A solution to such issues would be to use
existing mappings of WordNet to upper level
ontologies as aids for integration. A future mapping
of WordNet to BFO should facilitate the
integration of BFO in terminological projects
        <xref ref-type="bibr" rid="ref10 ref9">(Seppa¨la¨,
2015a)</xref>
        .
5
      </p>
    </sec>
    <sec id="sec-8">
      <title>Conclusion</title>
      <p>We saw that ontologized terminologies present a
number of shortcomings that can be addressed by
integrating a formal upper level ontology. We
illustrated the advantages of such an enhancement
by reviewing two projects that use such
ontologies. To summarize, the main benefits of using
a language- and domain-independent upper level
ontology are, on the practical side, the possibility
to integrate multilingual and multi-domain
terminological resources with one another and with
information system tools. The latter can thus use the
inferences drawn on the basis of the upper level
ontology to reason over and manipulate
multilingual natural language texts. Using a well-defined
formal upper level ontology as a basis for
terminological work would make sharing and reuse of
terminologies easier: identifying and sharing
common terms, constructing new definitions using the
same building blocks (information types and
logical axioms), etc. Such a framework avoids
semantic conflicts and need for mapping.</p>
      <p>On the research side, using a well-defined
ontological metalanguage allows: carrying out
rigorous and comparable conceptual analysis work
in terminology; making language- and
domainindependent generalizations about term formation,
definition content structure, and terminological
systems’ organization, which can help develop
empirically based content standards and writing
aid tools; creating comparable research results that
contribute to developing a mature integrated
terminological science.</p>
      <p>Moreover, a metalanguage using the categories
and relations of an upper level ontology for
describing terminological data (for example, terms’,
definitions’, and conceptual systems’ structure)
can fruitfully complement any terminological
resource whether or not already ontologized.
Cimiano et al. (2011) propose, for example, a model
to formally link lexicons (with relevant linguistic
descriptions) to ontologies.</p>
      <p>Using more specifically a BFO-based
metalanguage would further enhance our understanding
of the relationship between the lexical,
linguistic, conceptual, and ontological levels of
terminologies. Indeed, BFO is a realist ontology that
represents the things that exist in the world and
the relations between them, independently of our
conceptualizations thereof. A BFO-based
metalanguage may thus provide an additional level of
understanding to existing descriptive frameworks.</p>
      <p>We therefore encourage terminologists to fully
embrace the best ontological practices to enhance
their research and resources.</p>
    </sec>
    <sec id="sec-9">
      <title>Acknowledgments</title>
      <p>This work was supported in part by the Swiss
National Science Foundation (SNSF) and by
the NIH/NCATS Clinical and Translational
Science Awards to the University of Florida UL1
TR000064. The content is solely the
responsibility of the authors and does not necessarily
represent the official views of the SNSF, the National
Institutes of Health, or the NCTE. Thanks also to
Aure´lie Picton and Barry Smith.</p>
    </sec>
  </body>
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