The GO project has developed three structured ontologies that describe gene products in terms of :their
- associated biological processes,
- cellular components
- molecular functions
in a species-independent manner.
The following areas are outside the scope of GO, and terms in these domains will not appear in the ontologies:
Gene products: e.g. cytochrome c is not in the ontologies, but attributes of cytochrome c, such as oxidoreductase activity, are.
Processes, functions or components that are unique to mutants or diseases: e.g. oncogenesis is not a valid GO term, as “causing cancer” is the result of reprogrammed, not normal cells and thus it is not the normal function of a gene.
Attributes of sequence such as “intron” or “exon” parameters belong in a separate sequence ontology; see the Open Biological and Biomedical Ontologies website for more information.
Protein domains or structural features.
Environment, evolution and expression.
Anatomical or histological features above the level of cellular components, including cell types.
These terms describe a component of a cell that is part of a larger object, such as 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 term describes a series of events accomplished by one or more organized 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”. The general rule to assist in distinguishing between a biological process and a molecular function is that a process must have more than one distinct steps.
A biological process is not equivalent to a pathway. At present, the GO does not try to represent the dynamics or dependencies that would be required to fully describe a pathway.
Molecular function terms describes activities that occur at the molecular level, such as “catalytic activity” or “binding activity”. GO molecular function terms represent activities rather than the entities (molecules or complexes) that perform the actions, and do not specify where, 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” and “transporter activity”; examples of narrower functional terms are “adenylate cyclase activity” or “Toll receptor binding”.