Immunology Ontology

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

2Rules

1. Introduction to biomedical ontology building

Identification of participant areas of interest in preparation for the afternoon practical session

Overview of biomedical ontology

What is an ontology for?

How ontologies can support data-driven research

Glories and miseries of the Semantic Web

How to build an ontology

Mistakes to avoid

Example

The Ontology for Biomedical Investigations (OBI)

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

3. Formats and Tools

Brief remarks on formats: XML, RDF, OWL and OBO

GO File Format Guide

Brief remarks on tools

Protégé Ontology Editor

Ontofox Slides

SPARQL

4. How are ontologies used?

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)

Immunological Ontologies

Overview

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

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.