Introduction to Bio-Ontologies

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

Background: The successful completion of multiple genome projects 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 available data. They provide controlled vocabularies which allow biologists working in different disciplines to describe their data in common ways, thereby allowing comparison and aggregation of research results obtained, for example, in relation to different species or different ecosystems or different diseases.

Goals: 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.


Schedule

9AM-9:15AM Welcome and Introductions (Dennis Stevenson, Vice President for Laboratory Research, New York Botanical Gardens)
9:15AM-11:00AM Introduction to Bio-Ontologies (Barry Smith)
What is an ontology and what is it for?
Ontology success stories
The bio-ontologies landscape
How to build your first ontology
11:15AM-12:00PM 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

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

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

Contents

Speakers

Barry Smith is the Director of the National Center for Ontological Research (Buffalo). He is also one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, a Consultant to the Plant Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects.

Ramona Walls is a Post-Doctoral Research Associate at the New York Botanical Garden. The primary focus of her research is the Plant ontology; she also works on the ecology and systematics of Mexican Dioscorea, plant ecophysiology, and leaf trait evolution.

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

http://wiki.plantontology.org

http://www.facebook.com/pages/Plant-Ontology-Project/164166656929608

http://obofoundry.org

http://bioportal.bioontology.org/

http://ontology.buffalo.edu/

http://ncor.us/

Event coordinators

This event is being coordinated by Plant Ontology coordinator Laurel Cooper and Plant Ontology curator Ramona Walls.

Funding Source

Funded by the National Science Foundation, award# IOS-0822201.

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