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The Generation Challenge programme is a global crop research consortium directed toward …


Biology Articles » Agriculture » Plant Production » The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Abstract
- The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science


Richard Bruskiewich,1* Martin Senger,1 Guy Davenport,2 Manuel Ruiz,3 Mathieu Rouard,4 Tom Hazekamp,4 Masaru Takeya,5 Koji Doi,5 Kouji Satoh,56 Reinhard Simon,7 Jayashree Balaji,8 Akinnola Akintunde,9 Ramil Mauleon,1 Samart Wanchana,1,10 Trushar Shah,2 Mylah Anacleto,1 Arllet Portugal,1 Victor Jun Ulat,1 Supat Thongjuea,10 Kyle Braak,2 Sebastian Ritter,2 Alexis Dereeper,3 Milko Skofic,4 Edwin Rojas,7 Natalia Martins,6 Georgios Pappas,6 Ryan Alamban,1 Roque Almodiel,1 Lord Hendrix Barboza,1 Jeffrey Detras,1 Kevin Manansala,1 Michael Jonathan Mendoza,1 Jeffrey Morales,11 Rowena Valerio,1 Yi Zhang,1 Sergio Gregorio,1,11 Joseph Hermocilla,1,11 Michael Echavez,1,12 Jan Michael Yap,1,12 Andrew Farmer,1313 Jennifer Lee,14 Terry Casstevens,15 Pankaj Jaiswal,15 Ayton Meintjes,16 Mark Wilkinson,17 Benjamin Good,18,19 James Wagner,18,1916 David Marshall,14 Anthony Collins,7 Shoshi Kikuchi,5 Thomas Metz,1 Graham McLaren,1 and Theo van Hintum20 Marcos Costa, Barry Peralta, Gary Schiltz, Jane Morris,


1Crop Research Informatics Laboratory, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
2Crop Research Informatics Laboratory, International Maize and Wheat Improvement Center (CIMMYZT), Apdo. Postal 6-641, 06600 Mexico, DF, Mexico
3Centre International de Recherche Agronomique pour le Développement (CIRAD), Avenue Agropolis, 34398 Montpellier, Cedex 5, France
4Bioversity International, Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino), Rome, Italy
5National Institute for Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
6Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA), Parque Estação Biologia Final W5 Norte, 70770-900 Brasilia, DF, Brazil
7Centro Internacional de la Papa (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima 12, Peru
8International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh 502324, India
9International Center for Agricultural Research in the Dry Areas, P.O. Box 5466, Aleppo, Syria
10National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
11Institute of Computer Science, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna 4031, Philippines
12Department of Computer Science, University of the Philippines, Room 215, Melchor Hall, Diliman, Quezon City 1101, Philippines
13National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA
14Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
15Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA
16African Centre for Gene Technologies, P.O. Box 75011, Lynnwood Ridge 0040, South Africa
17Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
18School of Computing Science, Simon Fraser Universtiy, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
19Bioinformatics Graduate Program, Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC, Canada V5Z 4S6
20Centre for Genetic Resources, The Netherlands (CGN), P.O. Box 16, 6700 AA Wageningen, The Netherlands
*Richard Bruskiewich: Email: r.bruskiewich@cgiar.org
Recommended by Chunguang Du
Received September 22, 2007; Accepted December 14, 2007.

 

This is an open access article from Int J Plant Genomics. 2008; 2008: 369601 distributed under the Creative Commons Attribution License.


Abstract

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

 


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