The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. The use of a consistent vocabulary allows genes from different species to be compared based on their GO annotations. For each of three categories of biological information--molecular function, biological process, and cellular component--a set of terms has been selected and organized. Each set of terms uses a controlled vocabulary, and parent-child relationships between terms are defined. This combination of a controlled vocabulary with defined relationships between items is referred to as an ontology. Within an ontology, a child may be a "part of" or an example ("instance") of its parent. There are three independently organized controlled vocabularies, or gene ontologies, one for molecular function, one for biological process, and one for cellular component. Many-to-many parent-child relationships allowed in the ontologies. A gene may be annotated to any level in an ontology, and to more than one item within an ontology. The Gene Ontology project is a collaboration between three model organism databases, FlyBase (Drosophila), Saccharomyces Genome Database (SGD) and Mouse Genome Informatics (MGI).

This definition is in context to Yeast Genome. See more contextual defintions for Gene Ontology (GO).