Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages

Natalya F. Noy, Sherri De Coronado, Harold Solbrig, Gilberto Fragoso, Frank W. Hartel, Mark A. Musen

Research output: Contribution to journalArticle

Abstract

The National Cancer Institute’s (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemented by Apelon, Inc. We are exploring the use of the DL species of theWeb Ontology Language (OWL DL) - aW3C recommended standard for ontology representation - instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.

Original languageEnglish (US)
Pages (from-to)173-190
Number of pages18
JournalApplied Ontology
Volume3
Issue number3
DOIs
StatePublished - Jan 1 2008
Externally publishedYes

Fingerprint

Thesauri
thesaurus
ontology
Ontology
cancer
Knowledge representation
logic
Terminology
language
technical language
Modeling languages
Modeling
Cancer
Thesaurus
Language Modeling
Description Logics
Language
Knowledge Representation

Keywords

  • Biomedical ontologies
  • NCI thesaurus
  • OWL

ASJC Scopus subject areas

  • Computer Science(all)
  • Language and Linguistics
  • Linguistics and Language

Cite this

Noy, N. F., De Coronado, S., Solbrig, H., Fragoso, G., Hartel, F. W., & Musen, M. A. (2008). Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages. Applied Ontology, 3(3), 173-190. https://doi.org/10.3233/AO-2008-0051

Representing the NCI Thesaurus in OWL DL : Modeling tools help modeling languages. / Noy, Natalya F.; De Coronado, Sherri; Solbrig, Harold; Fragoso, Gilberto; Hartel, Frank W.; Musen, Mark A.

In: Applied Ontology, Vol. 3, No. 3, 01.01.2008, p. 173-190.

Research output: Contribution to journalArticle

Noy, NF, De Coronado, S, Solbrig, H, Fragoso, G, Hartel, FW & Musen, MA 2008, 'Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages', Applied Ontology, vol. 3, no. 3, pp. 173-190. https://doi.org/10.3233/AO-2008-0051
Noy, Natalya F. ; De Coronado, Sherri ; Solbrig, Harold ; Fragoso, Gilberto ; Hartel, Frank W. ; Musen, Mark A. / Representing the NCI Thesaurus in OWL DL : Modeling tools help modeling languages. In: Applied Ontology. 2008 ; Vol. 3, No. 3. pp. 173-190.
@article{1d09ca3366534445be65dd243ccbce8e,
title = "Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages",
abstract = "The National Cancer Institute’s (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemented by Apelon, Inc. We are exploring the use of the DL species of theWeb Ontology Language (OWL DL) - aW3C recommended standard for ontology representation - instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Prot{\'e}g{\'e}-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.",
keywords = "Biomedical ontologies, NCI thesaurus, OWL",
author = "Noy, {Natalya F.} and {De Coronado}, Sherri and Harold Solbrig and Gilberto Fragoso and Hartel, {Frank W.} and Musen, {Mark A.}",
year = "2008",
month = "1",
day = "1",
doi = "10.3233/AO-2008-0051",
language = "English (US)",
volume = "3",
pages = "173--190",
journal = "Applied Ontology",
issn = "1570-5838",
publisher = "IOS Press",
number = "3",

}

TY - JOUR

T1 - Representing the NCI Thesaurus in OWL DL

T2 - Modeling tools help modeling languages

AU - Noy, Natalya F.

AU - De Coronado, Sherri

AU - Solbrig, Harold

AU - Fragoso, Gilberto

AU - Hartel, Frank W.

AU - Musen, Mark A.

PY - 2008/1/1

Y1 - 2008/1/1

N2 - The National Cancer Institute’s (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemented by Apelon, Inc. We are exploring the use of the DL species of theWeb Ontology Language (OWL DL) - aW3C recommended standard for ontology representation - instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.

AB - The National Cancer Institute’s (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemented by Apelon, Inc. We are exploring the use of the DL species of theWeb Ontology Language (OWL DL) - aW3C recommended standard for ontology representation - instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.

KW - Biomedical ontologies

KW - NCI thesaurus

KW - OWL

UR - http://www.scopus.com/inward/record.url?scp=85013602572&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85013602572&partnerID=8YFLogxK

U2 - 10.3233/AO-2008-0051

DO - 10.3233/AO-2008-0051

M3 - Article

AN - SCOPUS:85013602572

VL - 3

SP - 173

EP - 190

JO - Applied Ontology

JF - Applied Ontology

SN - 1570-5838

IS - 3

ER -