Immunology Ontology: Difference between revisions
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Hands-on example of building a small ontology in the immunological domain | Hands-on example of building a small ontology in the immunological domain | ||
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==Background Resources (will be reviewed in class)== | ==Background Resources (will be reviewed in class)== | ||
Revision as of 16:06, 9 June 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)
- Staph Aureus Ontology and Other IDO Extension Ontologies
- The Vaccine Ontology (VO) Slides
- The Ontology for Biomedical Investigations (OBI)
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 Resources (will be reviewed in class)
Examples
[HIPC example http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/]
[Allergy example http://ncor.buffalo.edu/2013/Immunology/allergy-example.docx]
Portals
1. The Open Biological and Biomedical Ontologies
2. Bioportal
3. Ontobee
4. EBI Ontology Lookup Service
5. MeSH
Software
Literature
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.
