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<h2>The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science</h2> <p> <br><strong>Richard Bruskiewich,<sup>1</sup> Martin Senger,<sup>1</sup> Guy Davenport,<sup>2</sup> Manuel Ruiz,<sup>3</sup> Mathieu Rouard,<sup>4</sup> Tom Hazekamp,<sup>4</sup> Masaru Takeya,<sup>5</sup> Koji Doi,<sup>5</sup> Kouji Satoh,<sup>56</sup> Reinhard Simon,<sup>7</sup> Jayashree Balaji,<sup>8</sup> Akinnola Akintunde,<sup>9</sup> Ramil Mauleon,<sup>1</sup> Samart Wanchana,<sup>1,10</sup> Trushar Shah,<sup>2</sup> Mylah Anacleto,<sup>1</sup> Arllet Portugal,<sup>1</sup> Victor Jun Ulat,<sup>1</sup> Supat Thongjuea,<sup>10</sup> Kyle Braak,<sup>2</sup> Sebastian Ritter,<sup>2</sup> Alexis Dereeper,<sup>3</sup> Milko Skofic,<sup>4</sup> Edwin Rojas,<sup>7</sup> Natalia Martins,<sup>6</sup> Georgios Pappas,<sup>6 </sup>Ryan Alamban,<sup>1</sup> Roque Almodiel,<sup>1</sup> Lord Hendrix Barboza,<sup>1</sup> Jeffrey Detras,<sup>1</sup> Kevin Manansala,<sup>1</sup> Michael Jonathan Mendoza,<sup>1</sup> Jeffrey Morales,<sup>11</sup> Rowena Valerio,<sup>1</sup> Yi Zhang,<sup>1</sup> Sergio Gregorio,<sup>1,11</sup> Joseph Hermocilla,<sup>1,11</sup> Michael Echavez,<sup>1,12</sup> Jan Michael Yap,<sup>1,12</sup> Andrew Farmer,<sup>1313</sup> Jennifer Lee,<sup>14</sup> Terry Casstevens,<sup>15</sup> Pankaj Jaiswal,<sup>15</sup> Ayton Meintjes,<sup>16</sup> Mark Wilkinson,<sup>17</sup> Benjamin Good,<sup>18,19</sup> James Wagner,<sup>18,1916</sup> David Marshall,<sup>14 </sup>Anthony Collins,<sup>7 </sup>Shoshi Kikuchi,<sup>5</sup> Thomas Metz,<sup>1 </sup>Graham McLaren,<sup>1</sup> and Theo van Hintum<sup>20</sup> Marcos Costa, Barry Peralta, Gary Schiltz, Jane Morris,</strong> </p> <p> <br> 1Crop Research Informatics Laboratory, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines<br> 2Crop Research Informatics Laboratory, International Maize and Wheat Improvement Center (CIMMYZT), Apdo. Postal 6-641, 06600 Mexico, DF, Mexico<br> 3Centre International de Recherche Agronomique pour le Développement (CIRAD), Avenue Agropolis, 34398 Montpellier, Cedex 5, France<br> 4Bioversity International, Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino), Rome, Italy<br> 5National Institute for Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan<br> 6Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA), Parque Estação Biologia Final W5 Norte, 70770-900 Brasilia, DF, Brazil<br> 7Centro Internacional de la Papa (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima 12, Peru<br> 8International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh 502324, India<br> 9International Center for Agricultural Research in the Dry Areas, P.O. Box 5466, Aleppo, Syria<br> 10National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand<br> 11Institute of Computer Science, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna 4031, Philippines<br> 12Department of Computer Science, University of the Philippines, Room 215, Melchor Hall, Diliman, Quezon City 1101, Philippines<br> 13National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA<br> 14Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK<br> 15Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA<br> 16African Centre for Gene Technologies, P.O. Box 75011, Lynnwood Ridge 0040, South Africa<br> 17Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3<br> 18School of Computing Science, Simon Fraser Universtiy, 8888 University Drive, Burnaby, BC, Canada V5A 1S6<br> 19Bioinformatics Graduate Program, Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC, Canada V5Z 4S6<br> 20Centre for Genetic Resources, The Netherlands (CGN), P.O. Box 16, 6700 AA Wageningen, The Netherlands<br> Richard Bruskiewich: Email: r.bruskiewich@cgiar.org<br> Recommended by Chunguang Du<br> Received September 22, 2007; Accepted December 14, 2007. </p> <p> </p> <p> <em>This is an open access article from Int J Plant Genomics. 2008; 2008: 369601 distributed under the Creative Commons Attribution License.</em><br></p> <p> <br> Abstract<br><br> 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. </p> <p> </p>
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