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) (HHSN272201200028C), 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.

(https://immport.niaid.nih.gov/), which 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.

UB is responsible for the ontological aspects of the team’s work, which combines development of ontologies for immunology and infectious disease with dissemination and training in the use of these ontologies among NIAID-funded researchers. The ontologies are designed to enhance the degree to which 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, UB ontologies will contribute to the realization of the goals of the ImmPort system 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 UB team is led by Barry Smith, Professor of Philosophy, Neurology and Computer Science and Director of the National Center for Ontological Research. It also includes Alan Ruttenberg of the Department of Oral Biology and Alexander Diehl of the Department of Neurology. Ruttenberg’s work will focus on the development of ontology-based computational tools and strategies that can advance sharing and reuse of data through the use of open ontology standards. Diehl will contribute his expertise on the development and application of ontologies in the fields of immunology, with special reference to the Gene, Protein, Cell, and Sequence Ontologies.

For background see also: 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

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

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