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Handbook on Ontologies pp 445–461Cite as

Ontologies for Formal Representation of Biological Systems

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Part of the book series: International Handbooks on Information Systems ((INFOSYS))

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.

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Notes

  1. 1.

    An automated technique for simultaneously analyzing thousands of different DNA sequences or proteins affixed to a thumbnail-sized “chip” of glass or silicon. DNA microarrays can be used to monitor changes in the expression levels of genes in response to changes in environmental conditions or in healthy vs. diseased cells. Protein arrays can be used to study protein expression, protein–protein interactions, and interactions between proteins and other molecules. From – www.niaaa.nih.gov/publications/arh26-3/165-171.htm

  2. 2.

    High-throughput technologies are large-scale, usually automated, methods to purify, identify, and characterize DNA, RNA, proteins and other molecules. They allow rapid analysis of very large numbers of samples.

  3. 3.

    For this current discussion, a formal representation means a computer-interpretable standardized form that can be the basis for creating unambiguous descriptions of biological systems 2.1.

  4. 4.

    We use “models” to mean a schematic description of a system or phenomenon that accounts for its known or inferred properties and can be used for further study of its characteristics.

  5. 5.

    Source public domain, non copy righted image.

  6. 6.

    The cell cycle is a complicated biological process and comprises of the progression of events that occur in a cell during successive cell replication. The process can be described at varying level of details ranging from a high level qualitative description to a detailed system of differential equations. However, for most biological processes the representation is primarily in terms of qualitative interactions.

  7. 7.

    http://www.w3.org/2001/sw/SW-FAQ

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Authors and Affiliations

  1. Stanford Medical Informatics, Stanford, CA, USA, 94305

    Nigam Shah & Mark Musen

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  1. Nigam Shah
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Correspondence to Nigam Shah .

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Editors and Affiliations

  1. Inst. Informatik, Universität Koblenz-Landau, Universitaetsstr. 1, Koblenz, 56016, Germany

    Steffen Staab

  2. Inst. Angewandte Informatik und, Universität Karlsruhe, Karlsruhe, 76128, Germany

    Rudi Studer

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Shah, N., Musen, M. (2009). Ontologies for Formal Representation of Biological Systems. In: Staab, S., Studer, R. (eds) Handbook on Ontologies. International Handbooks on Information Systems. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92673-3_20

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