3177
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. This approach involves the integration of experimental and computational research and often involves genome-wide “omics” studies. Analyses of these vast datasets have the potential to improve our understanding of the molecular basis of phenotypes, gene expression, molecular interactions, development, response to perturbation in the genotype and its interaction with the environment and species evolution.

Common vocabularies (ontologies), structured in a way that permits computer-aided reasoning about relationships among different kinds of entities, can facilitate inter-specific comparisons at the systems biology scale. 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 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.

The goals of the workshop are to demonstrate (1) development, integration and usage of ontologies and (2) novel systems biology approaches being used to find insights by analyzing the massive amounts of genomics and genetics data becoming available.

Date: Saturday, January 9, 2016
Time: 8:00 AM-10:10 AM
Room: Pacific Salon 2
Organizers:
Pankaj Jaiswal , Laurel Cooper and Sushma Naithani
8:00 AM
Welcoming Remarks


8:05 AM
Planteome: A resource for Common Reference Ontologies and Applications for Plant Biology
Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University; Laurel Cooper, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Austin Meier, Oregon State University; Marie-Angélique Laporte, Bioversity International; Christopher Mungall, Berkeley Bioinformatics Open-Source Projects; Barry Smith, University at Buffalo; Ethan KS. Johnson, Oregon State University; Megan Seymour, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Xu Xu, Oregon State University; Ryan S. Kitchen, Oregon State University; Botong Qu, Oregon State University; Eugene Zhang, Oregon State University; Elizabeth Arnaud, Bioversity International; Seth Carbon, Lawrence Berkeley National Laboratory; Sinisa Todorovic, Oregon State University; Dennis Wm. Stevenson, New York Botanical Garden

8:35 AM
Functional Annotation at Scale: Pipelined Analysis of Phytozome Data and Results from Large Inter-Species Comparisons.
Joseph W. Carlson, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Richard D Hayes, DOE Joint Genome Institute; Shengqiang Shu, DOE Joint Genome Institute; Jeremy L. Phillips, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

8:50 AM
QTLNetMiner - Linking Crop Traits to Genes through Data Integration and Text Mining
Keywan Hassani-Pak, Rothamsted Research; Ajit Singh, Rothamsted Research; Christopher Rawlings, Rothamsted Research

9:05 AM
An Integrated System-Wide Maize Atlas: From Transcriptome to Proteome Networks
Justin W. Walley, Iowa State University; Ryan C Sartor, UCSD; Robert Schmitz, University of Georgia; Zhouxin Shen, University of California, San Diego; Joseph Ecker, Salk Institute for Biological Studies & Howard Hughes Medical Institute; Steven Briggs, University of California, San Diego

9:20 AM
Rice Stress-Response Gene-Network: An Example of Community Curation in WikiPathways for Plants
Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University; Christina Partipilo, Department of Botany & Plant Pathology, Oregon State University; Bijayalaxmi Mohanty, National University of Singapore; Dong-Yup Lee, National University of Singapore; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

9:35 AM
Systems Biology Approach to Understand the Rice Plant Metabolic and Transcriptional Regulation Under Abiotic Stress
Meiyappan Lakshmanan, Bioprocessing Technology Institute; Bijayalaxmi Mohanty, National University of Singapore; Dong-Yup Lee, National University of Singapore

9:50 AM
AgroPortal : A Proposition for Ontology-Based Services in the Agronomic Domain
Clement Jonquet, Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM); Esther Dzalé-Yeumo, French National Institute for Agricultural Research (INRA); Elizabeth Arnaud, Bioversity International; Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle

10:05 AM
Workshop overview


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