The Open Biomedical Ontologies (OBO) Foundry is a collective of
ontology developers and users committed to collaboration and shared
standards. We aim to build a suite of integrated ontologies that are:
- Logically well formed
- Scientifically accurate
- Interoperable and interconnected
More details can be found on the OBO Homepage.
Back in 2002, Michael Ashburner and Suzanna Lewis initiated this grass-roots effort. The goal of OBO Foundry is to work with the community to create a suite of interoperable reference ontologies in the biomedical domain. We organize small content-development workshops to assist groups who have need of an ontology to support their research, such as anatomies, cell types, environments, and so on. From August 2005-2008 these workshops were supported through our 3-year collaboration with the National Center for Biomedical Ontology (NCBO).
BBOP currently hosts the OBO Foundry website and associated tools as a free service, such as nightly production of alternate ontology formats.
We perform continuous integration on a number of ontologies: http://build.berkeleybop.org
We are also involved in a number of ontology development efforts, such as:
- GO: The Gene Ontology (see our Gene Ontology project page)
- RO: OBO Relations Ontology
- Uberon: Uberon cross-species ontology covering anatomical structures in animals
- EnvO: Environmental Ontology
- PATO: OBO Phenotype Quality Ontology
See also the Monarch project page for more ontologies that our group is involved in through the Monarch Initiative.
This OBO Foundry blog offers tips and examples for working with ontologies and ontology-related tools.
- Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database. 2021 Oct 26;2021. http://dx.doi.org/10.1093/database/baab069 PMCID: PMC8546234
- Jackson, R.C., Balhoff, J.P., Douglass, E., Harris, N.L., Mungall, C.J., and Overton, J.A. (2019). ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics 20, 407.
- Vita R, Overton JA, Mungall CJ, Sette A, Peters B. (2018). FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. Database (Oxford). 2018 Jan 1;2018. http://10.1093/database/bax105. PubMed PMID: 29688354; PubMed Central PMCID: PMC5819722.
- Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., … Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 25(11), 1251–1255. http://doi.org/10.1038/nbt1346
- Ashburner, M., Mungall, C. J., & Lewis, S. E. (2003). Ontologies for biologists: a community model for the annotation of genomic data. In Cold Spring Harbor symposia on quantitative biology (Vol. 68, pp. 227–235).