Immunology Ontology: Difference between revisions
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:The Immune Epitope Ontology ([http://70.167.3.46/iedb/ ONTIE]) | :The Immune Epitope Ontology ([http://70.167.3.46/iedb/ ONTIE]) | ||
:The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO]) | :The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO]) | ||
[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies Overview] | |||
3. How are ontologies used? | 3. How are ontologies used? | ||
Revision as of 12:30, 6 May 2013
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
Schedule
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.
