Using Ontologies for Organizing Plant and Animal Genomics Data

Ontologies, such as the Gene Ontology (GO), along with others such as the Plant Ontology (PO), are being used for the systematic annotation or ‘tagging’ of data: documenting associations between genes, gene products, or sequences and the structures or processes to which they contribute. These annotations facilitate computerized searching and reasoning over large data sets from multiple sources, allowing researchers to address questions in comparative genetics, development, and genomics.


This workshop will provide an introduction to how ontologies can be used to find novel insights in the massive amounts of genomics data becoming available.

Laurel Cooper(Oregon State University) and Pankaj Jaiswal(Oregon State University)
Date: Saturday, January 14, 2012
Time: 10:20 AM-12:30 PM
Room: Royal Palm Salon 5-6
10:20 AM
Introductory Remarks

10:25 AM
GO and PO Facilitate Integration and Mining of Arabidopsis Data
Eva Huala, Carnegie Institution for Science

11:05 AM
Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa
Laurel Cooper, Oregon State University; Ramona Walls, New York Botanical Garden; Justin L. Elser, Oregon State University; Justin Preece, Oregon State University; Barry Smith, Department of Philosophy, University at Buffalo; Chris Mungall, Lawrence Berkeley National Lab; Marie A. Gandolfo, Department of Plant Biology, Cornell University; Dennis Wm. Stevenson, New York Botanical Garden; Pankaj Jaiswal, Oregon State University

11:25 AM
B73 Maize Gene Expression Atlas a Plant Ontology Use Case
Mary Schaeffer, USDA-ARS and University of Missouri; Ethalinda Cannon, Iowa State University; Sudhansu Dash, Iowa State University; John Van Hemert, Iowa State University; Jack Gardiner, Iowa State University; Bremen M Braun, USDA ARS; Darwin A Campbell, USDA ARS; Justin Preece, Oregon State University; Carson M Andorf, USDA-ARS; Scott M Birkett, Iowa State University; Lisa C Harper, USDA-ARS and University of California-Berkeley; Taner Z Sen, USDA -ARS and Iowa State University; Roger Wise, USDA-ARS / Iowa State University; Julie Dickerson, Iowa State Univeristy; Carolyn J. Lawrence, USDA ARS and Iowa State University

11:45 AM
NCBO Web Services and Development of Semantic Applications
Trish Whetzel, The National Center for Biomedical Ontology ; Nigam H. Shah, Stanford University; Natalya F. Noy, Stanford University; Michael Dorf, Stanford University; Paul A. Alexander, Stanford University; Ray Fergerson, Stanford University; Mark A. Musen, Stanford University

12:05 PM
Panel Discussion

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