2103
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 in a systems biology approach can be used to find novel insights in the massive amounts of genomics data becoming available.
Date: Saturday, January 11, 2014
Time: 8:00 AM-10:10 AM
Room: Royal Palm Salon 5-6
Organizers:
Laurel Cooper , Pankaj Jaiswal and Sushma Naithani
8:00 AM
Introductory Remarks


8:35 AM
Using the MapMan ontology to decipher diurnal regulation across species
Bjorn Usadel, Forschungzentrum Juelich & RWTH Aachen

8:55 AM
9:15 AM
VitisCyc: A Metabolic Pathway Database for Grapevine
Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Rajani Raja, Department of Botany & Plant Pathology, Oregon State University; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

9:30 AM
Leaf Ontogeny and Ontology
Barbara A. Ambrose, The New York Botanical Garden

10:10 AM
Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics
Laurel Cooper, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Elizabeth Arnaud, Bioversity International; Dennis Wm. Stevenson, New York Botanical Garden; Sinisa Todorovic, Oregon State University; Eugene Zhang, Oregon State University; Christopher Mungall, Berkeley Bioinformatics Open-Source Projects; Barry Smith, University at Buffalo; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

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