Immunology Ontologies

Ontologies

The Protein Ontology (PRO)

The Gene Ontology (GO)

The Cell Ontology (CL)

The Immune Epitope Ontology (ONTIE)

The Infectious Disease Ontology (IDO)

Ontology for Biomedical Investigations (OBI)

Ontology for General Medical Science ([http://code.google.com/p/ogms/ (OGMS))

Ontology Consortia

OBO (Open Biological and Biomedical Ontologies) Foundry

Portals

ImmPort: Bioinformatics for the Future of Immunology

HIPC: Human Immunology Project Consortium

Program for Research on Immune Modeling and Experimentation PRIME

Immune Epitope Database and Analysis Resource

Publications

Diehl AD, Augustine AD, Blake JA, Cowell LG, et al. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011; 44(1).

Meehan TF, Masci AM, Abdulla A, Cowell LG, et al. Logical development of the cell ontology. BMC Bioinformatics. 2011; 12.

Anna M. Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith and Lindsay G. Cowell, An improved ontological representation of dendritic cells as a paradigm for all cell types, BMC Bioinformatics, February 2009, 10:70.

Albert Goldfain, Barry Smith and Lindsay G. Cowell, Towards an Ontological Representation of Resistance: The Case of MRSA, Journal of Biomedical Informatics, 2011 (Feb.), 44:1, 35-41.

Lindsay Grey Cowell and Barry Smith, “Infectious Disease Ontology”, in Vitali Sintchenko, Infectious Disease Informatics, New York: Springer, December 2009, 373-395.

Richard H. Scheuermann, Werner Ceusters, and Barry Smith, “Toward an Ontological Treatment of Disease and Diagnosis”, Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, 2009, 116-120.

Albert Goldfain, Barry Smith and Lindsay G. Cowell, Dispositions and the Infectious Disease Ontology, in Antony Galton and Riichiro Mizoguchi (eds.), Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.

Albert Goldfain, Barry Smith and Lindsay Cowell, [http://ontology.buffalo.edu/smith/articles/ICBO2012/IDO_Lattice.pdf Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository”, Proceeedings of the Third International Conference on Biomedical Ontology, Graz, July 23-25, 2012 (CEUR, vol. 897).

Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith and Alexander D. Diehl, Ontologies for the Study of Neurological Disease, Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology, Graz, July 22, 2012.

Alexander C. Yu, Barry Smith, Stanley Schwartz, [http://ontology.buffalo.edu/medo/ACAAI-2012.pdf Formal and Computable Representations of Allergic Diseases in the Electronic Health Record: An Approach Based on the Ontology of General Medical Science, 2012 Annual Meeting of the American College of Allergy, Asthma & Immunology (ACAAI), November 8-13, 2012, Anaheim, California (Poster).

Events

Lecture and practical session on Immunology Ontology as part of Summer School for Quantitative Systems Immunology, Boston, MA, June 11, 2013