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It has not generally been appreciated that the Gene Ontology concepts for describing aspects of gene function assume a specific model of how gene products act to achieve biological objectives.
- Paul D. Thomas
- 10.1007/978-1-4939-3743-1_2
- 2017
- 2017
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are two ways in which the gene ontology describes locations of gene products: (1) the cellular anatomical entities, in which a gene product carries out a molecular function.
- Gene Products, Not Genes, Have Functions
- Assertions About Functions of Particular Genes Are Made by “Go Annotations”
- The Model of Gene Function Underlying The Go
- Molecular Functions Define Molecular Processes
- Cellular Components Define Places Where Molecular Processes Occur
In order to understand how gene function is represented in the GO, some basic molecular biology knowledge is required. 1. A geneis a contiguous region of DNA that encodes instructions for how the cell can make a large (“macro”) molecule (or potentially multiple different macromolecules). 2. A macromolecule is called a gene product (as it is produce...
The Gene Ontology defines the “universe” of possible functions a gene might have, but it makes no claims about the function of any particular gene. Those claims are, instead, captured as “GO annotations.” A GO annotation is a statement about the function of a particular gene. But our biological knowledge is extremely incomplete. Accordingly, the GO...
The Gene Ontology (GO) considers three distinct aspects of how gene functions can be described: molecular function, cellular component, and biological process (note that throughout this chapter, bold text will denote specific concepts, or classes, from the Gene Ontology). In order to understand what these aspects mean and how they relate to each ot...
In the GO, a molecular function is a process that can be carried out by the action of a single macromolecular machine, via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product performs. These actions are described from the two distinct but related perspectives commonl...
A cellular component is a location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which biologists describe locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitoch...
- Paul D. Thomas
- pdthomas@usc.edu
- 2017
Nov 1, 2017 · 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...
One of the most important tools for the representation and processing of information about gene products and functions is the Gene Ontology (GO). 1 GO is being developed in tandem with work on a variety of biological databases within the framework of the umbrella project OBO (for: open biological ontologies). 2 It provides a controlled vocabular...
- Barry Smith, Jennifer Williams, Steffen Schulze-Kremer
- 2003
Mar 1, 2004 · The Gene Ontology (GO) is by far the most widely used bio-ontology. It aims to formalize our knowledge about biological processes ( Fig. 1 ), molecular functions and cell components, in three...
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Feb 17, 2011 · The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians.
