Systems Biology and Ontologies

Systems biology is a scientific approach that emphasizes the structure and dynamic behavior of complex biological systems and their inherent interactions (Hoehndorf, et al 2011). This approach involves the of integration experimental and computational research and often involves genome-wide “omics” studies (Kitano, 2002). Analyses of these vast datasets have the potential to improve our understanding of the molecular basis of phenotypes, development and species evolution. Effective inter-specific comparisons at the systems biology scale demand common vocabularies (ontologies), structured in a way that permits computer-aided reasoning about relationships among different kinds of entities. Thus, ontologies have become indispensable tools for data curation and analysis in the life sciences. The Gene Ontology and the Plant Ontology, along with many others, 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 datasets from multiple sources, allowing researchers to address questions in comparative genetics, development, and genomics. The goals of the workshop are to demonstrate how the integration of ontologies and systems biology approaches can be used to find novel insights in the massive amounts of genomics data becoming available.
Date: Saturday, January 10, 2015
Time: 8:00 AM-10:10 AM
Room: Pacific Salon 2
Pankaj Jaiswal , Laurel Cooper and Sushma Naithani
8:00 AM
Welcoming Remarks

8:25 AM
8:45 AM
New Phytologist and the Plant Ontology: Working Together to Enhance Journal Content
Sarah Lennon, New Phytologist; Laurel Cooper, Department of Botany & Plant Pathology, Oregon State University; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University; Helen Ougham, Institute of Biological, Environmental & Rural Sciences (IBERS); Dennis Wm. Stevenson, New York Botanical Garden

9:05 AM
Inferring Gene Ontologies from Molecular Networks
Michael Kramer, Department of Medicine, University of California, San Diego

9:45 AM
The Interplay of DNA Methylation, Histone Modification and Gene Activity in Soybean Seed Development
Jer-Young Lin, University of California; Min Chen, University of California; Julie Pelletier, University of California; Russell Baden, University of California; John Harada, University of California; Robert B Goldberg, University of California

10:05 AM
Concluding Remarks

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