Tutorial on Standards and Ontology

Barry Smith and Werner Ceusters

Keywords: Standards, ontology, terminology, ISO, HL7, SNOMED, OBO, NCI Thesaurus

Barry Smith

Director, IFOMIS, Saarland University, Saarbrücken, Germany

Curriculum Vitae

Barry Smith is Director of the Institute for Formal Ontology and Medical Information Science (IFOMIS) in Saarbrücken, Germany and Julian Park Distinguished Professor of Philosophy in the University at Buffalo (New York, USA). He studied at Oxford and Manchester, and has held faculty positions in Sheffield, Manchester, and Liechtenstein. He is Director of the National Center for Ontological Research and a principal scientist in the National Center for Biomedical Ontology, an NIH Roadmap Center. Smith is the author of some 450 scientific publications, including 15 authored or edited books. His research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the Volkswagen Foundation, and the European Union. In 2002 he received in recognition of his scientific achievements the 2.2 Million Euro Wolfgang Paul Award of the Alexander von Humboldt Foundation.

Smith’s research focus is ontology and its applications in biomedicine and biomedical informatics. He is currently also working on a variety of projects relating to terminologies and standardisation.

Werner Ceusters

Director, Ontology Research Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo NY

http://org.buffalo.edu/ceusters

Curriculum Vitae

Werner Ceusters studied medicine (1977-84), neuropsychiatry (1984-90), informatics (1988-90) and knowledge engineering (1991-93). He started a series of international research projects in medical natural language processing under the Third, Fourth and Fifth Research Frameworks of the European Commission through his R&D company Office Line Engineering nv. Since then, he has also been active in standardisation bodies related to medical terminology such as CEN/TC251/WG2 and ISO/TC215/WG3. In April 1998, he started a new company – Language & Computing nv (L&C) – to exploit the results of his research. He left L&C in 2004, his main interest being now applying and testing a new theoretically-grounded approach to ontological engineering. As of February 2006 he leads the Referent Tracking Unit of the Ontology Research Group in the New York State Center of Excellence in Bioinformatics and Life Sciences. He is also Coordinator of Bioinformatics in the University at Buffalo Health Science Faculties, and Professor of Psychiatry in the School of Medicine and Biomedical Sciences.

Abstract

As biomedical research, medical care and medical record-keeping become ever more sophisticated in their use of computers, so the standardisation of biomedical data and information becomes an ever more pressing need. Standardisation can not only help to reduce costs and promote safety in medical care, it can also provide the basis for new types of virtual biomedical research by enabling uniform data to be used for purposes of scientific reasoning in ways which transcend the confines of single institutions. To this end, however, standards must be developed which ensure not merely syntactic regimentation but also what is often called ‘semantic interoperability’.

Standards and ontologies are two distinct kinds of socio-cognitive artefacts which serve the needs of syntactic and semantic regimentation in different ways. They also confront similar difficulties in development and application, difficulties which are not only theoretical and technical, but also sociological. Standards and ontologies, if they are to be effective, must be widely used, and this means that they must be documented in ways which are clear and understandable to the relevant target audiences. Yet theoretical reflection on standards, on the conditions which must be satisfied by good standards, and on the relations between standards and ontologies, are still almost unknown.

The present tutorial is designed to fill this gap. It will serve as an introduction to the much-needed theoretical reflection on standards and ontologies as applied in the domains of health care and biomedical research. We shall examinin the work of three representative organisations influential in the realm of standardisation and ontology development in the domain of the life sciences: Health Level 7 Inc., the American College of Pathologists, and the Open Biomedical Ontologies (OBO) Consortium. The tutorial will be highly interactive. It will be divided into five parts, which can be briefly summarised as follows.

Suggested Background Reading

Barry Smith, Werner Ceusters and Rita Temmerman, Wüsteria, MIE 2005 (Studies in Health and Technology Informatics, 116), 647–652.

Gunnar O. Klein and Barry Smith, Concept Systems and ontologies: Recommendations based on discussions between realist philosophers and ISO/CEN experts concerning the standards addressing “concepts” and related terms.

Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. Journal of Biomedical Informatics. In press.

Agenda

1.         Standards and Ontology: An Introduction (BS and WC)

2.         HL7 (BS)

a.         Problems with HL7 V2

b.         The Vision of HL7 V3

c.         The RIM and Its Problems

3.         SNOMED CT (WC)

a.         Overview

b.         The Concept Orientation in SNOMED CT

c.         Reforming SNOMED CT through a Coherent Upper Level Ontology of Biomedical Reality

4.         The OBO Consortium (BS)

a.         The Gene Ontology

b.         Open Biomedical Ontologies

c.         OBO Core Ontologies

d.         The National Center for Biomedical Ontology

5.         The EU RIDE Project: A Roadmap to Semantic Interoperability in E-Health Systems (WC)

Participation

Attendees who might find this tutorial worthwhile include: developers and users of standards, developers and users of electronic health record systems, physicians and others interested in the possibilities of modern healthcare informatics systems and in the role of ontologies in biomedicine.

All participants will receive from their attendance in the tutorial familiarity with a variety of approaches to healthcare standardisation and a thorough overview of problems in existing standards and of prospects for improvement in the future. This tutorial does not require any prior detailed knowledge of standards and of the processes through which they are established, modified and applied, though some familiarity with these topics will make it easier to understand the deeper issues involved. Basic familiarity with medical informatics is required.