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. 2017:1446:15-24.
doi: 10.1007/978-1-4939-3743-1_2.

The Gene Ontology and the Meaning of Biological Function

Paul D Thomas  1
Affiliations

The Gene Ontology and the Meaning of Biological Function

Paul D Thomas. Methods Mol Biol. 2017.

Abstract

The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. It is specifically designed for supporting the computational representation of biological systems. A GO annotation is an association between a specific gene product and a GO concept, together making a statement pertinent to the function of that gene. However, the meaning of the term "function" is not as straightforward as it might seem, and has been discussed at length in both philosophical and biological circles. Here, I first review these discussions. I then present an explicit formulation of the biological model that underlies the GO and annotations, and discuss how this model relates to the broader debates on the meaning of biological function.

Keywords: Causal role; Function; Genome; Ontology; Selected effects.

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Figures

Figure 1.
Figure 1.. DNA replication (in yeast) as modeled using the GO.
Gene products/complexes (white) perform molecular processes (molecular function, red) in specific locations (cellular component, yellow), as part of larger biological objectives (biological process, blue).
See this image and copyright information in PMC

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