Immunology Ontologies

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What: Summer School for Quantitative Systems Immunology: Lecture and practical session on Immunology Ontology

When: Tuesday June 11

Where: Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA on June 10-14, 2013.

Who: Lindsay Cowell and Barry Smith


8:30-10:00am Lecture

1. Introduction to biological ontology

what is an ontology, how is it different from a controlled vocabulary, a computerized lexicon, and a data dictionary?

2. Overview of ontologies with content relevant to immunology

The Protein Ontology (PRO) The Gene Ontology (GO) The Cell Ontology (CL) The Immune Epitope Ontology (ONTIE) The Infectious Disease Ontology (IDO)

3. How are ontologies used?

for data annotation à la GO and GMODs
in defining data standards (example: ImmPort)
to support data analysis (example: GO enrichment of microarray data)
to support text mining and NLP, document retrieval
example: GOPubMed
to integrate heterogeneous data / heterogeneous research communities (example: the OBO (Open Biological and Biomedical Ontologies) Foundry)

1:00-3:00pm: Practical Session

Hands-on example of building a small ontology in the immunological domain

Background Reading

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.

Aravind Subramanian, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, PNAS, 102 (43), 15545–15550.