Ontology Documentation

The Gene Ontology defines the universe of concepts relating to gene functions (‘GO terms’), and how these functions are related to each other (‘relations’). It is constantly revised and expanded as biological knowledge accumulates. The GO describes function with respect to three aspects: molecular function (molecular-level activities performed by gene products), cellular component (the locations relative to cellular structures in which a gene product performs a function), and biological process (the larger processes, or ‘biological programs’ accomplished by multiple molecular activities).

Ongoing revisions to the ontology are managed by a team of senior ontology editors with extensive experience in both biology and computational knowledge representation. Ontology updates are made collaboratively between the GOC ontology team and scientists who request the updates. Most requests come from scientists making GO annotations (these typically impact only a few terms each), and from domain experts in particular areas of biology (these typically revise an entire ‘branch’ of the ontology comprising many terms and relations). We invite researchers and computational scientists to submit requests for either new terms or new relations in the ontology.

The GO ontology is structured as a directed acyclic graph where each term has defined relationships to one or more other terms in the same domain, and sometimes to other domains. The GO vocabulary is designed to be species-agnostic, and includes terms applicable to prokaryotes and eukaryotes, and single and multicellular organisms.

In an example of GO annotation, the gene product "cytochrome c" can be described by the Molecular Function term "oxidoreductase activity", the Biological Process term "oxidative phosphorylation", and the Cellular Component terms "mitochondrial matrix" and "mitochondrial inner membrane".

Ontologies

Molecular Function

A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.

Cellular Component

These terms describe 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., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). Unlike the other aspects of GO, cellular component concepts refer not to processes but rather a cellular anatomy.

Biological Process

A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.

Details about the ontologies