Ontologies are central to our work. We create tools to describe data using ontologies, and to drive our knowledge-based inferencing pipelines. We collaborate with domain experts building ontologies, and we build our own ontologies where required.

We use the Web Ontology Language (OWL) as our base framework, and we are exploring additional richer means of representing complex knowledge.


We develop or co-develop the following ontologies:

Ontology Engineering Frameworks

We develop tools, frameworks and methodologies for building and maintaining ontologies.

  • Jenkins Continuous Integration Server
  • TermGenie

Selected References

Deegan, J, E Dimmer, and Mungall, C. J. 2010. “Formalization of Taxon-Based Constraints to Detect Inconsistencies in Annotation and Ontology Development.” BMC Bioinformatics 11 (1): 530. doi:10.1186/1471-2105-11-530. http://www.biomedcentral.com/1471-2105/11/530.

Dietze, Heiko, Tanya Z Berardini, Rebecca E Foulger, David P Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, and Mungall, C. J. 2014. “TermGenie - A Web Application for Pattern-Based Ontology Class Generation.” Journal of Biomedical Semantics 5 (1): 48. doi:10.1186/2041-1480-5-48. http://www.jbiomedsem.com/content/5/1/48.

Huntley, Rachael P, Midori A Harris, Yasmin Alam-Faruque, Judith A Blake, Seth Carbon, Heiko Dietze, Emily C Dimmer, et al. 2014. “A Method for Increasing Expressivity of Gene Ontology Annotations Using a Compositional Approach.” BMC Bioinformatics 15 (1): 155. doi:10.1186/1471-2105-15-155. http://www.biomedcentral.com/1471-2105/15/155.

Mungall, C. J., Michael Bada, Tanya Z Berardini, Jennifer Deegan, Amelia Ireland, Midori A Harris, David P Hill, and Jane Lomax. 2011. “Cross-Product Extensions of the Gene Ontology.” Journal of Biomedical Informatics 44 (1): 80–86. doi:10.1016/j.jbi.2010.02.002. http://www.berkeleybop.org/people/cjm/Mungall-GO-JBI-2010.pdf http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2910209\&tool=pmcentrez\&rendertype=abstract.

Mungall, C. J., H. Dietze, and D. Osumi-Sutherland. 2014. “Use of OWL Within the Gene Ontology.” In Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014), edited by Maria Keet and Valentina Tamma, 25–36. Riva del Garda, Italy, October 17-18, 2014. doi:10.1101/010090. http://ceur-ws.org/Vol-1265/owled2014\_submission\_5.pdf.

Mungall, C. J., Heiko Dietze, Seth J Carbon, Amelia Ireland, Sebastian Bauer, and Suzanna Lewis. 2012. “Continuous Integration of Open Biological Ontology Libraries.” http://bio-ontologies.knowledgeblog.org/405.

Smith, Barry, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, ..., Suzanna Lewis 2007. “The OBO Foundry: coordinated Evolution of Ontologies to Support Biomedical Data Integration.” Nat Biotechnol 25 (11) (November): 1251–1255. doi:10.1038/nbt1346. http://dx.doi.org/10.1038/nbt1346 http://berkeleybop.org/~cjm/papers/OBO-Foundry-NBT-2007.pdf.