Gene-Ontology

The Gene Ontology (GO) is a major bioinformatics initiative to unify the vocabulary of the life sciences, specifically to represent gene and gene product attributes across all species. Specifically, the project aims to clearly represent biological knowledge. Specifically, it is planned to:

• maintain and develop the vocabulary of gene and gene product attributes
• to explain genes and gene products and to assimilate and make publicly available annotation data
• provide the necessary tools for easy access to all aspects of the data provided by the project and enable functional interpretation of experimental data using GO.

In biology and related fields, there is no universal standard terminology. The use of terms may be specific to a species.It may be specific to a research area or even a particular research group. This makes communication and data sharing difficult.

The Gene Ontology project provides an ontology with defined terms that represent the properties of gene products. The ontology covers three domains:

• cellular component, the parts of a cell or its extracellular environment;
• molecular function, the elementary activities of a gene product at the molecular level, such as binding or catalysis;
• biological process, operations or sets of molecular events with a defined beginning and end relevant to the functioning of integrated living entities: cells, tissues, organs and organisms.

Each GO term within the ontology has a term name, which may be a word or phrase, a unique alphanumeric label, a definition with cited sources, and an ontology indicating the domain to which it belongs. Terms may also have synonyms that are classified as exactly equivalent to the term name, broader, narrower, or related; references to equivalent concepts in other databases; and comments on the meaning or use of the term. The GO vocabulary is species-neutral and contains terms that apply to prokaryotes and eukaryotes, unicellular and multicellular organisms.

Example

• id: GO:0000016
• name: lactase activity
• namespace: molecular_function
• def: "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108]
• synonym: "lactase-phlorizin hydrolase activity" BROAD [EC:3.2.1.108]
• synonym: "lactose galactohydrolase activity" EXACT [EC:3.2.1.108]
• xref: EC:3.2.1.108
• xref: MetaCyc:LACTASE-RXN
• xref: Reactome:20536
• is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds.

While Gene Nomenclature focuses on genes and gene products, Gene Ontology focuses on the function of genes and gene products. It also uses a markup language to make the data (not only of the genes and their products, but also their functions) machine-readable. This is to standardize this information across all species.

The GO ontology and annotation files are freely available on the GO website in a number of formats or can be accessed online using the GO browser AmiGO. The Gene Ontology project also offers downloadable mappings of its terms to other classification systems.

1. The Gene Ontology Consortium (January 2008). "The Gene Ontology project in 2008". Nucleic Acids Research. 36(Database issue): D440-444.
2. Dessimoz Ch et al. (2017) The Gene Ontology Handbook. Methods in Molecular Biology. doi:10.1007/978-1-4939-3743-1.
3. Gaudet P et al. (2017) Primer on the Gene Ontology. The Gene Ontology Handbook. Methods in Molecular Biology. 1446: 25–37.