The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, the parts of a cell or its extracellular environment; molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; and biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.
For example, the gene product "cytochrome c" can be described by the molecular function term "oxidoreductase activity", the biological process terms "oxidative phosphorylation" and "induction of cell death", and the cellular component terms "mitochondrial matrix" and "mitochondrial inner membrane". The GO ontology is structured as a directed acyclic graph, and 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-neutral, and includes terms applicable to prokaryotes and eukaryotes, single and multicellular organisms.
A cellular component is just that, a component of a cell, but with the proviso that it is part of some larger object; this may be an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer).
A biological process is series of events accomplished by one or more ordered assemblies of molecular functions. Examples of broad biological process terms are cellular physiological process or signal transduction. Examples of more specific terms are pyrimidine metabolic process or alpha-glucoside transport. It can be difficult to distinguish between a biological process and a molecular function, but the general rule is that a process must have more than one distinct steps.
A biological process is not equivalent to a pathway; at present, GO does not try to represent the dynamics or dependencies that would be required to fully describe a pathway.
Molecular function describes activities, such as catalytic or binding activities, that occur at the molecular level. GO molecular function terms represent activities rather than the entities (molecules or complexes) that perform the actions, and do not specify where or when, or in what context, the action takes place. Molecular functions generally correspond to activities that can be performed by individual gene products, but some activities are performed by assembled complexes of gene products. Examples of broad functional terms are catalytic activity, transporter activity, or binding; examples of narrower functional terms are adenylate cyclase activity or Toll receptor binding.
It is easy to confuse a gene product name with its molecular function, and for that reason many GO molecular functions are appended with the word "activity".
- Ontology Structure: information about the structure of GO terms and the ontology.
- Ontology Relations: documentation on the inter-term relations used in GO
- Cellular Component Ontology: Rules governing content and stylistic aspects of GO terms in the cellular component ontology.
- Molecular Function Ontology: Rules governing content and stylistic aspects of GO terms, standard definitions and term relationships in the molecular function ontology.
- Biological Process Ontology: Rules governing content and stylistic aspects of GO terms, standard definitions and term relationships in the biological process ontology.
- Species-Specific Terms: How the Gene Ontology deals with words or phrases where the meaning varies depending on the organism.
- Documentation on specific areas of the ontology:
- GO Slim Guide: information about GO slims, cut-down versions of the ontologies useful for providing an overview of GO
- OBO 1.2 File Format Guide: the ontology file format used and recommended by the GO Consortium