Introduction to Bio-Ontologies

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On Sunday, February 5, 2012 the Plant Ontology Consortium will host a tutorial on bio-ontologies at the New York Botanical Garden.

The successful completion of the Human Genome project has given rise to a massive expansion in the genomic, proteomic and other data available to life science research. Ontologies are a response to this expansion of data. They provide controlled vocabularies which allow biologists working in different disciplines to describe their data in common ways, thereby allowing comparisons of research results for example between different species or different diseases.

This tutorial is designed for biologists who have little or no experience with ontologies. It should be of interest to those who want to create their own ontology or make use of existing ontologies for data annotation. Although most of the examples will be drawn from the Plant Ontology, the methods described will be relevant to any domain.

9AM-9:30AM Welcome and Introductions (Dennis Stevenson, Vice President for Laboratory Research, New York Botanical Gardens)

9:30AM-11:15AM Introduction to Bio-Ontologies (Barry Smith)

What is an ontology and what is it for?
Ontology success stories in the life sciences
The bio-ontologies landscape
How to build your first ontology

11:30AM-12:30PM Introduction to the Plant Ontology (Ramona Walls)

What is the Plant Ontology and what is it for?
How the Plant Ontology is structured: anatomy and development stages
Plant Ontology relations and definitions
Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)
Different types of plant data made available through the Plant Ontology

This tutorial is open to the public. If you are interested in attending please contact Ramona Walls before February 1, 2012.

The New York Botanical Garden us located in the Bronx, NY, and is easily reached by the Metro-North Railraod or other means of transportation.

Suggested Reading

If you would like to read about bio-ontologies before the workshop, check out the following publications:

Smith et al. 2007, "The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration".

Ilic et al. 2007, "The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant".

Avraham et al. 2007, "The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations".

Some Useful Links