Immunology Ontologies

This page has been created to support the ontology work of the Immunology Database and Analysis Portal (ImmPort) portal within the framework of the Bioinformatics Integration Support Contract (BISC), which is funded by the NIH’s National Institute of Allergy and Infectious Diseases (NIAID). ImmPort is designed to enable scientists to easily access and exchange interoperable complex data sets to accelerate scientific discovery. It provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID.

The ontologies documented below are designed to enhance the degree to which immunology research results are expressed in a consistent fashion across communities and disciplines, thus advancing not only the analysis and integration of data but also its discoverability by scientists who were not involved in its creation. In this way, they will contribute to the realization of the goals of ImmPort to accelerate a more collaborative and coordinated research environment and create an integrated database. that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research, as well as the development of optimal methods for data collection, storage, exchange and interoperability.

The team of University at Buffalo ontologists with primary responsibility for this work includes:

• Barry Smith, Professor of Philosophy, Neurology and Computer Science and Director of the National Center for Ontological Research.
• Alexander Diehl, UB Department of Neurology
• Alan Ruttenberg, UB Department of Oral Biology and Institute for Healthcare Informatics.

For further background see: http://www.buffalo.edu/news/releases/2009/01/9857.html

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

Collaborations

Collaboration between Immport, CyTOF and the Cell Ontology

Portals

Immunology Database and Analysis (ImmPort) Portal

HIPC: Human Immunology Project Consortium

Program for Research on Immune Modeling and Experimentation PRIME

Immune Epitope Database and Analysis Resource

Publications

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. , The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration, Nature Biotechnology, 25 (11), November 2007, 1251-1255.

Cowell LG, Smith B, Infectious Disease Ontology, in Vitali Sintchenko, Infectious Disease Informatics, New York: Springer, December 2009, 373-395.

Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG, An improved ontological representation of dendritic cells as a paradigm for all cell types, BMC Bioinformatics, February 2009, 10:70.

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.

Goldfain A, Smith B, Cowell LG, Towards an Ontological Representation of Resistance: The Case of MRSA, Journal of Biomedical Informatics, 2011 (Feb.), 44:1, 35-41.

Scheuermann RH, Ceusters W, Smith B, Toward an Ontological Treatment of Disease and Diagnosis, Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, 2009, 116-120.

Goldfain A, Smith B, Cowell LG, 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.

Goldfain A, Smith B, Cowell LG, [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).

Cox AP, Jensen M, Duncan W, Weinstock-Guttman B, Szigeti K, Ruttenberg A, Smith B, Diehl AD, 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.

Yu AC, Smith B, Schwartz S, [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

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

April 8, 2013: 1st ImmPort Ontology Group Web Conference

April 22, 2013: 2nd ImmPort Ontology Group Web Conference