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

Morning Lecture

8:30am Introduction to biomedical ontology building Slides

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

How to select appropriate starting points

Mistakes to avoid

Reinventing the wheel

Confusing words with things

Example

The OBO (Open Biological and Biomedical Ontologies) Foundry

The Ontology for Biomedical Investigations (OBI)

9:15am Overview of ontologies with content relevant to immunology

Use of ontology portals and search engines

The Cell Ontology (CL) Bioportal

The Protein Ontology (PRO) Bioportal

The Gene Ontology (GO) Poster

Relation to MeSH and similar resources

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

The Infectious Disease Ontology (IDO)

Staph Aureus Ontology and Other IDO Extension Ontologies

The Vaccine Ontology (VO) Slides

9:45am 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

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.

innate immunity

allergy and allergic disease

autoimmune disease

asthma

immune tolerance

transplantation

medical countermeasures against radiological and nuclear threats

tissue engineering

wounds and injuries

HIPC

diseases of inflammation

tumor microenvironments

acquired/adaptive immunity

mucosal immunity

(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list here.)

1:10pm Participants will vote to select ca. 10 topics, for each of which we have six or so people who have some relevant domain knowledge

1:20 Participants will be divided into corresponding breakout groups. The task of each group will be to create a workplan for building an ontology (or ontologies) for their selected area. The workplan will consist minimally of

i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source

ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below

Each group should select a reporter, who will present the results of the group's work, and a recorder, who will take notes of the discussions and have control of the powerpoint slides documenting the results of these discussions.

2:20 Presentation of results: Each group is required to produce at least 4 slides summarizing the results of their work.

Slide 1: Title and author list

Slide 2: Quick comparison of the experience of using the 4 ontology browsers listed above; optional report on experience using MeSH

Slide 3: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology

Slide 4: List of the main terms in the ontology

2.50 Summation