The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, we write and maintain the ontologies themselves; second, we make cross-links between the ontologies and the genes and gene products in the collaborating databases, and third, we develop tools that facilitate the creation, maintainance and use of ontologies.
The use of GO terms by several collaborating databases facilitates uniform queries across them. The controlled vocabularies are structured so that you can query them at different levels: for example, you can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or you can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.
BBOP has been a member of the GO consortium since its inception in 1999, for which Suzanna Lewis was a founding member (with Michael Ashburner, Judy Blake, and Mike Cherry). In collaboration with Dr Paul Thomas’s group at USC we provide informatics and infrastructure supporting the GO, including:
Communication and Internal Documentation
- The GO Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D330–D338.
- Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou L-P, 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, nature.com; 2019 Oct;51(10):1429–1433. http://dx.doi.org/10.1038/s41588-019-0500-1 PMID: 31548717
- Mungall, C. J., Dietze, H., & Osumi-Sutherland, D. (2014). Use of OWL within the Gene Ontology. In M. Keet & V. Tamma (Eds.), Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) (pp. 25–36). Riva del Garda, Italy, October 17-18, 2014. http://doi.org/10.1101/010090
- 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 15;25(2):288–289. http://dx.doi.org/10.1093/bioinformatics/btn615 PMCID: PMC2639003
- Day-Richter J, Harris MA, Haendel M, Gene Ontology OBO-Edit Working Group, Lewis S. OBO-Edit–an ontology editor for biologists. Bioinformatics. 2007 Aug 15;23(16):2198–2200. http://dx.doi.org/10.1093/bioinformatics/btm112 PMID: 17545183
- Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, … Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258–61. http://dx.doi.org/10.1093/nar/gkh036 PMCID: PMC308770
- Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res. 2001 Aug;11(8):1425–1433. http://dx.doi.org/10.1101/gr.180801 PMCID: PMC311077
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H. Gene Ontology: tool for the unification of biology. Nature. nature.com; 2000. https://www.nature.com/articles/ng0500_25