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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Ontology: The Discipline and the Tool</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Doug Mayhew</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Dirk Siebert</string-name>
          <email>dirk.siebert@ifomis.uni-leipzig.de</email>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Department of Philosophy, University at Buffalo</institution>
          ,
          <addr-line>New York</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Institute for Formal Ontology and Medical Information Science, University of Leipzig</institution>
          ,
          <addr-line>04107 Leipzig, Härtelstraße 16-18, Germany doug.mayhew</addr-line>
        </aff>
      </contrib-group>
      <abstract>
        <p>The fields of philosophy and informatics entertain two somewhat different conceptions of ontology. Philosophical ontology is a branch of metaphysics dating back at least to the time of Plato and Aristotle. Ontology in informatics has its origins in the artificial intelligence research of the eighties and nineties. This means that the fields of philosophy and informatics entertain two somewhat different conceptions of ontology and the present paper discusses the relationship between these two conceptions. Differences and similarities are pointed out and variations in methodological approaches are also discussed. Efforts to combine the ontological methodologies and resources of the two fields are surveyed, and actual and potential benefits and drawbacks of such collaborations are examined.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>
        The fields of philosophy and informatics entertain two somewhat different
conceptions of ontology, with correspondingly different notions of what ontology is for.
First, we have the age-old conception of ontology as a philosophical discipline.
Second, we have the relatively new conception of ontology as an information
organization tool, a notion of ontology adapted from the philosophical conception by artificial
intelligence researchers and then adopted by the applications-oriented field of
informatics. (The philosophical conception was recognized in informatics as early as the
late sixties in data modeling research [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ].) The two conceptions have their
characteristic differences, which show up primarily in what each field thinks ontology is for. The
following is a discussion of these differences, but also of the similarities between the
two disciplines and of the ways in which they might cooperate.
      </p>
      <p>
        In philosophy, ontology is the study of what exists. Ontology is thus of a piece
with metaphysics, the branch of philosophy that studies the nature of reality, and has
been a prominent area of investigation since the beginnings of philosophical inquiry.
The individual ontological theories advanced in philosophy are universal, descriptive
classifications of the content and structure of reality as a whole. Aristotle provides a
classic example in [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ], where he describes the world using ten categories—viz.,
substance and nine kinds of attributes or accidents. Philosophical ontologies have
traditionally been expressed informally, using natural language, but Leśniewski’s [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ] use
of an artificial formal language to represent his formal theory of parts (mereology)
inaugurated philosophy’s use of artificial languages and formal logic in expressing
ontologies. Examples of contemporary philosophical endeavors which involve the
symbolical representation of ontologies can be found in [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ] and [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ].
      </p>
      <p>
        Informatics uses ontology predominantly as an information organization tool.
Many attribute the initial use of ontology in this way to artificial intelligence research
on the facilitation of knowledge sharing and re-use among software agents. As
described in [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ], ontology in this field often entails the development of customized
terminologies (with individually specified meanings for the terms) used to create
customized descriptions or models of a particular domain of some actual or constructed
reality. These are language dependent ontologies rather than universal theories. An
example in the medical domain is SNOMED [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ]. Ontologies in informatics are often
expressed as logical theories (often using one or other flavor of description logic [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ]),
semantic networks, or, more recently, in a modeling language such as UML [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ]. They
might then be converted to programming language code to become part of a software
application.
      </p>
      <p>Whereas philosophical ontology has traditionally sought to provide a general
ontology of reality as a whole, those working on ontologies in informatics develop
domain-specific ontologies designed to meet particular information processing needs
and requirements. This difference in scope points to yet another difference. The
philosopher seeks knowledge of what exists more or less for the sake of knowledge itself.
The informatician, in contrast, is interested in developing ontologies to serve more
limited and practical purposes. There is normally very little theoretical work involved,
for example, in developing an ontology of a company’s product or service line; this is
done simply to manage inventory and accounting records. The difference here is in
one’s motivation for doing ontology.</p>
      <p>There are some other differences to note. First, as indicated above, philosophical
ontologies are language-independent or universal, whereas many informatics
ontologies are restricted to the specific languages in which they are formulated. Another
difference turns on the fact that, while philosophy has traditionally been concerned with
giving ontological accounts of the natural and continuous reality that everyone
experiences, informatics is often working with the closed-world realities, for instance, of
particular businesses, the specific products or services with which those businesses
deal, the people and activities involved, and so forth—reflecting again their
underlying, specifically pragmatic motivations.</p>
      <p>Along with the differences, there are also similarities. In both fields, the general
idea—leaving aside for the moment issues of domain, scope, degree of refinement,
and method of expression—is that ontology provides a means to classify entities,
processes, and the relations that hold between them. There is also the commonly—
though not unanimously—held belief in both fields that ontology should strive for
descriptive accuracy and cross-domain communicability.</p>
      <p>Despite the many differences between the philosophical and informatics
conceptions of ontology, a number of philosophers and informaticians are now working
together in various ontology projects. Individuals from both fields are surveying the
relevant literature and exchanging ideas in efforts to improve upon their respective
uses of ontology. The benefits and drawbacks of such efforts are discussed in the last
section of the paper.</p>
    </sec>
    <sec id="sec-2">
      <title>Different Approaches</title>
      <p>
        The conceptual differences discussed above are differences between fields. There are
also different conceptual and methodological approaches to ontology within the two
fields. An account of the different approaches in philosophical ontology can be found
in [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ], and a condensed account of philosophical and informatics approaches is
provided in what follows.
      </p>
      <p>
        Approaches in traditional philosophical ontology fall under two basic divisions,
which we might call substance versus process and reductionist versus
nonreductionist. Substance-based ontologies focus on substances or things as the essential
constituents of reality. Process-based ontologies describe reality primarily in terms of
processes, flux, or change. Reductionist approaches claim that reality is accurately
described in terms of one basic type of constituent, usually either substance or process.
It is rather difficult to find examples of pure substance or process reductionism, since
almost all those who put forward a substance-based ontology also admit processes of
one sort or another and vice versa. One finds an essentially substance-based,
reductionist ontology in materialist metaphysical doctrines like that presented in [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]. An
example of process-based reductionism can be found in [
        <xref ref-type="bibr" rid="ref12">12</xref>
        ]. Non-reductionist
ontologies are concerned with providing an exhaustive ontological account of reality at
all levels, from the micro- to the macroscopic, including categories of both substance
and process. Aristotelian metaphysics is a good example, as is the ontological work in
[
        <xref ref-type="bibr" rid="ref13">13</xref>
        ] and [
        <xref ref-type="bibr" rid="ref14">14</xref>
        ].
      </p>
      <p>
        Within informatics there are also two basic divisions, the reference versus
applications division and the logic-based versus non-logic-based division. Proponents of
reference ontologies [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ] advocate the creation of overarching, descriptively adequate
ontologies accompanied by a rich formal representation. Applications ontology is
focused on low-level ontologies designed to represent the taxonomical structure of
specific domains, and proponents of applications ontology praise its advantages for
the practical purposes of many information systems. Commerce, research, and
information-based applications developed using ontological methods of organization range
from simple yet extensive domain-specific terminologies to standards development
projects involving software interoperability, information search and retrieval,
automated inferencing, and natural language processing. A good example of applications
ontology that handles a range of these tasks can be found in [
        <xref ref-type="bibr" rid="ref15">15</xref>
        ].
      </p>
      <p>
        Examples of research being done in both reference and applications ontology can
be found in [
        <xref ref-type="bibr" rid="ref16 ref17 ref18">16, 17, 18</xref>
        ]. Much of the commercial work done within ontology is
applications ontology. Among reference and applications ontologists, one can find a
further division between logic- and non-logic-based approaches. Logic-based approaches
rely primarily on description logic to develop a model of some domain.
Non-logicbased approaches, exemplified in network-based structures (e.g., connectionist
systems and semantic networks), seek to develop models that more closely resemble the
observable structure and workings of human cognition. An example of this approach
is seen in [19].
      </p>
      <p>
        Not every ontological effort in either field adheres strictly to one approach or the
other. Hybrid approaches are common in philosophy and informatics, and such
approaches often turn out to be useful in advancing both philosophical understanding
and information systems performance. The non-reductionist approach in philosophy is
itself a hybrid approach. One can find ontological projects in informatics and
especially in AI that use logic in combination with non-logic-based approaches—e.g., in
some of the latest software agent designs [20]. Then, of course, there are recent
projects that combine approaches from the two fields of philosophy and informatics [
        <xref ref-type="bibr" rid="ref16 ref17 ref18">16,
17, 18</xref>
        ]. Hybrid approaches, as one might guess, tend to be richer in what they can
express and how they express it, and thereby more complex and time consuming during
the design phase.
      </p>
    </sec>
    <sec id="sec-3">
      <title>Philosophy and Informatics Working Together</title>
      <p>Though ontology has a long history in philosophy, it is probably safe to say that today
it is known primarily from its association with artificial intelligence and informatics.
This is based partly on the fact that there are many more people involved in doing
research on ontology in informatics than in philosophy. There are, however, a few
philosophers studying ontology as a discipline reaching beyond its philosophical origins.
There are also informaticians exploring the philosophical origins of what they once
thought of primarily as an information organization tool. Efforts to combine
philosophical and informatics research in ontology are still in their infancy but growing
steadily. Let us consider some of the actual as well as some of the potential benefits
and drawbacks of philosophers and informaticians working together in ontology.</p>
      <sec id="sec-3-1">
        <title>Benefits</title>
        <p>Researchers on both sides stand to benefit, first of all, from simply being exposed to a
different perspective. Combining perspectives is a good way to initiate the
development of new ideas, and new ideas can turn into concrete improvements in the ways in
which difficult problems are confronted. Following are some of the benefits, both
mutual and one-sided, that could be reaped from the exchange of ideas and methods
across the fields of philosophy and informatics.</p>
        <p>Consider the difference between the grand-scale ontologies of philosophy and the
domain-specific ontologies of informatics. Philosophers are trained to look at the big
picture, to notice the content, structure, and relations of reality as a whole, and to
develop a general ontological theory based on their investigations. Relations between
the different aspects of reality can then be expressed in terms of the general
ontological theory. This kind of training could be passed on to informaticians willing to
exchange ideas with philosophers. Informaticians would learn how to develop a wider,
yet cohesive view of reality into which their domain specific concerns could be
integrated. One resulting potential benefit to informatics is a way to seriously improve
upon systems and software interoperability and standards development.</p>
        <p>While pure philosophical ontology is not pursued for the sake of practical ends,
there are benefits that the philosopher might gain from studying informatics. Recall
that informatics ontologies are often models of domains—e.g., law, commerce, and
administration—where the entities are created entirely by the actions, physical and
verbal, of human beings. These models can be generalized, and the result used to
uncover prevalent features of our everyday lives. Philosophical efforts to account for
that have surfaced only recently in works like [21]. Philosophical ontology should
ultimately seek to give an account of every aspect of reality, and the examination of
informatics ontologies could result in benefits to philosophers working toward this end
by providing new families of examples and also new types of problems with which to
grapple.</p>
        <p>Attention to the conceptual differences and the different approaches observed
between and within the two fields may reveal possibilities for hybrid approaches that
can take advantage of the best features on either side. This is a good first step in
developing rich and exhaustive ontologies. For example, an ontology or ontological
method like that proposed in [22], that can account for different views or partitions of
reality, would be useful in both reference and applications settings. If philosophers
and informaticians continue to compare the results of their research efforts, then
perhaps, to the benefit of both fields, a universal descriptive ontology that covers any
kind of content at every level of granularity [22] can be developed.</p>
        <p>There is a mutual benefit associated with the practice of formalizing ontologies.
The primary reason for expressing an ontology in a formal language is to help achieve
higher levels of clarity, rigor, and accuracy in ontological theories and models and to
ensure that the content of the ontology is easily communicated to other people and
perhaps more easily translated into programming code. Collaboration between
philosophers and informaticians with a background in logic may assist in the creation of
better formalizations.</p>
        <p>A further benefit that can be realized from the combined efforts of philosophy and
informatics is that each field will have more manpower working on its problems. The
more there are working on a given problem, the better the chances it will get solved.
Subjecting a body of work to more minds and different perspectives is also an
effective way to expose previously hidden difficulties. Examples in which informatics has
benefited in this respect can be found in [23] and [24].</p>
        <p>The cooperation between fields has also created openings in knowledge
engineering and consultancy that can be filled by philosophers with a background in ontology
and logic. Companies like Ontology Works, Cycorp, Kanisa, and Language and
Computing are among those that have put philosophers to work. Working in
informatics has provided some philosophers with supplemental training that will undoubtedly
be of value to them in the future.</p>
        <p>These collaborative ontological efforts promise indirect benefits to those outside
philosophy and informatics as well. If the collaboration produces improvements in
information systems design and functionality, then there are subsequent benefits passed
on to everyone who is served directly or indirectly by information systems. Clients,
customers, and patients, for example, would certainly benefit from improved
efficiency and accuracy in handling their needs. Businesses would improve their ability
to better serve the client and thereby benefit financially from a stable or perhaps even
growing clientele.</p>
      </sec>
      <sec id="sec-3-2">
        <title>Drawbacks</title>
        <p>In comparison to the actual and potential benefits attributable to the collaboration
between philosophy and informatics, the drawbacks are few. It is difficult to conceive of
any actual harm that could come from the two fields working together, but there are
foreseeable difficulties and drawbacks.</p>
        <p>An obvious difficulty arises with the attempt to assimilate concepts and approaches
with which one is not entirely familiar. A lack of mutual knowledge and experience in
the respective fields may result in the individuals talking past each other, rather than
effectively communicating their ideas. The depth of professional knowledge
possessed by a worker or researcher in one field may not easily transfer to someone in
another, especially if the two fields are quite different. At the same time, years of
training and practice in concepts and methods specific to a profession are hard to set
aside, and we tend to think and communicate our ideas in terms of what we know,
rather than in a context-free manner. Philosophy and informatics are sufficiently
different for this difficulty to surface in collaborations between the two.</p>
        <p>However, by providing the right environment for knowledge exchange this
difficulty can be largely overcome. A learning environment and centers dedicated to
philosophy and informatics research would help tremendously. (Such centers and special
interest groups are being established in Buffalo, Leipzig, Rome, Trento, and Turin.)
Along with sharing knowledge, supplemental training can help in overcoming this
difficulty.</p>
        <p>The difficulty with conceptual and methodological differences between the two
fields points to a potential drawback concerning the time limits and predefined design
guidelines imposed upon many informatics projects. Most philosophers do primarily
theoretical work, and they are not under heavy time constraints. The work done in
informatics is very often geared toward client-specific practical applications, and tasks
must normally be completed within a relatively short time. An information system is
often the backbone of operations; it is something a business, for instance, needs in
order to do what it does. In other words, the people who need information systems
cannot wait around while researchers figure out what the absolute best ontological design
should be. The specific needs of the client must be taken into account, and the
designers must develop the best system they can within the time limit set by the client.</p>
        <p>There is a potential drawback for clients in that they must settle for what the
systems designers can build for them in the time they are allotted. Put philosophers and
informaticians to work on a project like this one, and we immediately see the
drawbacks from their different perspectives. The philosopher wants to make sure that the
ontology behind the system accurately reflects the world as it is and that any logical
theory behind the design is sound and complete. The informatician may very well
want the same thing, but realize that perfection must be sacrificed in the interest of
finishing the job on time.</p>
        <p>The immediate solution to this drawback is for the philosophically minded to learn
how to work within predefined design guidelines and time limits. The ultimate
solution is, again, to establish centers where basic research in philosophical and
informatics ontology research can be carried out under conditions where time limits are
dramatically relaxed. Research would be directed at developing better design guidelines
in ways which could ultimately benefit everyone related to information systems.</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>Concluding Remarks</title>
      <p>Collaboration between philosophy and informatics is a reality from which a number
of benefits have been reaped and positive results produced. With the formation of
more special interest groups, institutes, and centers dedicated to bringing
philosophical and informatics ontology researchers together to learn from one another, it is
reasonable to assume that more advances in both fields are on the way.</p>
    </sec>
    <sec id="sec-5">
      <title>Acknowledgements References</title>
      <p>This work was supported by the Alexander von Humboldt Foundation under the
auspices of its Wolfgang Paul Program.
19. Unified Medical Language System® (UMLS®). http://www.nlm.nih.gov/research/umls/
20. Baral, C., Gelfond, M.: Reasoning Agents in Dynamic Domains. In Minker, J. (ed.):
Logic</p>
      <p>Based Artificial Intelligence, Kluwer, Dordrecht (2000) 257–279
21. Searle, J. R.: The Construction of Social Reality. Free Press, New York (1995)
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24. Kumar, A, Smith, B.: The Universal Medical Language System and the Gene Ontology:
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