An Introduction to Biomedical Ontology

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An introduction to the methods and resources of ontology in the biomedical domain.

Tutorial by Olivier Bodenreider

The last decade has seen a marked increase in the number of artifacts created for representing biomedical entities, their terms and their relations, often referred to as vocabularies, terminologies and ontologies. This tutorial will present some of these artifacts and examine both their structure (i.e., the way their content is organized) and their function (i.e., the applications they support.)

The ontologies surveyed in this tutorial include SNOMED CT, a comprehensive concept system for healthcare; the Logical Observation Identifiers, Names, and Codes (LOINC), a vocabulary for laboratory tests and clinical observations; the Foundational Model of Anatomy (FMA), a domain ontology of structural human anatomy; the Gene Ontology, a controlled vocabulary for the functional annotation of gene products across species; RxNorm, a controlled vocabulary of normalized names and codes for clinical drugs; the National Cancer Institute Thesaurus, a public domain terminology that provides broad coverage of the cancer domain; the International Classification of Diseases, the 115-year-old medical terminology, now part of a family of health classifications; the Medical Subject Headings (MeSH), a controlled vocabulary for the indexing and retrieval of the biomedical literature; and the Unified Medical Language System (UMLS), a terminology integration system in which all the above ontologies are integrated.

The tutorial is directed towards students and professionals with an interest in biomedicine, resource annotation, data integration, and ontological aspects of biology and clinical medicine.

Faculty

Olivier Bodenreider studied medicine and computer science in France. He is a researcher at the National Library of Medicine in Bethesda, Maryland.

References

[1] Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform:124-35. Abstract

[2] Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform. 2008:67-79. Free article in PMC

Further Reading

Giannangelo K, editor. Healthcare code sets, clinical terminologies, and classification systems. Chicago, Ill.: American Health Information Management Association; 2006.

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