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What’s in an ‘is a’ link?

William R. Hogan¹

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1. University of Pittsburgh

PDF (273.3 KB)

Document Type:

Poster

Date:

Received 25 July 2009 15:02 UTC; Posted 27 July 2009

Subjects:

Bioinformatics

Tags:

• biomedical ontology
• realist ontology
• relations
• SNOMED CT

Abstract:

Introduction

Several researchers have demonstrated that current medical terminologies and ontologies use relations in inconsistent and ambiguous ways,¹ despite Woods’ seminal work that first illustrated the problem.² The goal of the present work is to catalog the different ways in which SNOMED CT uses the is a relation. The rationale for creating the catalog is to serve as a basis for systematically improving the semantics of terminologies and ontologies so as to improve their accessibility to machine inference.

Methods

I reviewed the literature to find ontological mistakes that change the interpretation of the is a relation, without respect to any particular terminology. I then reviewed the stated relationships table of SNOMED CT, Jan 2009 version, placing them into categories from the literature, and creating new categories when existing categories did not apply.

Results

I found nine categories of misuse of the is a relation in SNOMED CT (see Table in poster), eight from the literature and one from my analysis. SNOMED CT had an example of every misuse found in the literature.

Discussion

The January 2009 version of SNOMED CT violates its intended interpretation of the is a relation, which is nearly identical to the definition of Smith et al.¹ I cataloged nine categories of misuse of is a, and found an example of each in SNOMED CT. This study demonstrates for the first time that (1) certain common ontological mistakes, not previously identified as causing misuse of is a, lead to ambiguity in the interpretation of is a, (2) the stated relationships of SNOMED CT are the source of mistakes in the use of the is a relation, (3) SNOMED CT has at least one example of every problem with is a elucidated from the broader literature.

References
1. Smith B, Ceusters W, Klagges B, et al. Relations in biomedical ontologies. Genome Biol.2005;6(5):R46.
2. Woods W. What’s in a link: Foundations for semantic networks. In: Bobrow D, Collins A, eds. Representation and understanding. New York: Academic Press; 1975:35-82.

Collection:

International Conference on Biomedical Ontology

Presented at:

International Conference on Biomedical Ontology, Buffalo, NY, 24 July 2009

Discussion

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Hogan, William. What’s in an ‘is a’ link?. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3462.1> (2009)

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