Ontologies for Formal Representation of Biological Systems

Nigam Shah () and Mark Musen ()
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Nigam Shah: Stanford Medical Informatics
Mark Musen: Stanford Medical Informatics

A chapter in Handbook on Ontologies, 2009, pp 445-461 from Springer

Abstract: Summary This chapter provides an overview of how the use of ontologies may enhance biomedical research by providing a basis for a formalized, and shareable descriptions, of models of biological systems. A wide variety of artifacts are labeled as “ontologies” in the Biomedical domain, leading to much debate and confusion. The most widely used ontological artifact are controlled vocabularies (CVs). A CV provides a list of terms whose meanings are specifically defined. Terms from a CV are usually used for indexing records in a database. The Gene Ontology (GO) is the most widely used CV in databases serving biomedical researchers. The GO provides term for declaring the molecular function (MF), biological process (BP) and cellular component (CC) of gene products. The statements comprising these MF, BP and CC declaration are called annotations [51], which are predominantly used to interpret results from high throughput gene expression experiments [27, 53]. Arguably, CVs provide the most value for effort in terms of facilitating database search and interoperability.

Keywords: Gene Ontology; Conceptual Framework; Formal Representation; Resource Description Framework; Abstraction Level (search for similar items in EconPapers)
Date: 2009
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DOI: 10.1007/978-3-540-92673-3_20

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