GeneOntology

Version 2024-10-27,
source
released 19 Sept 2012

License

Creative Commons Attribution 4.0 Unported License

Repository

https://geneontology.org/docs/ontology-documentation/

Developed By

GO consortium

The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.

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Dataset Overview

Data Type

Gene product function annotations, text, ontologies

Citation

Publication:

Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. DOI: 10.1038/75556 [abstract | full text]
The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. DOI: 10.1093/genetics/iyad031 [abstract | full text]

Data citation

https://zenodo.org/records/10536401

Dataset Card Authors

Donghui Li, Ana-Maria Istrate

Dataset Card Contact

Ana-Maria Istrate, virtualcellmodels@chanzuckerberg.com

Uses

Primary Use Cases

GO annotations provide description of gene product functions in a computable format. Its primary use is as a source of biological knowledge extracted from the literature as well as from other computational methods.

Sample use cases and references:

GO Enrichment Analysis: Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 2022 Jan;31(1):8-22. DOI:10.1002/pro.4218 [abstract | full text]
Gene function look up: AmiGO: Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan;25(2):288-289. DOI:10.1093/bioinformatics/btn615 [abstract | full text]
Systems biology: GO-CAMs: Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet. 2019 Oct;51(10):1429-1433. DOI: 10.1038/s41588-019-0500-1 [abstract | full text]

Dataset Structure

A standard GO annotation minimally contains:
- a gene product; may be a protein, an miRNA, a tRNA, etc.
- a GO term
- a reference, usually a PMID, but DOIs and GO Reference (GO_REF) are also used.
- an evidence code, using a GO Evidence Code, which describes the type of evidence: experimental evidence, sequence similarity or phylogenetic relation, as well as whether the evidence was reviewed by an expert biocurator. If not manually reviewed, the annotation is described as ‘automated’.

For detail, refer to https://geneontology.org/docs/go-annotations/.