The generation challenge programme platform: semantic standards and workbench for crop science

Richard Bruskiewich; Martin Senger; Guy Davenport; Manuel Ruiz; Mathieu Rouard; Tom Hazekamp; Masaru Takeya; Koji Doi; Kouji Satoh; Marcos Costa; Reinhard Simon; Jayashree Balaji; Akinnola Akintunde; Ramil Mauleon; Samart Wanchana; Trushar Shah; Mylah Anacleto; Arllet Portugal; Victor Jun Ulat; Supat Thongjuea; Kyle Braak; Sebastian Ritter; Alexis Dereeper; Milko Skofic; Edwin Rojas; Natalia Martins; Georgios Pappas; Ryan Alamban; Roque Almodiel; Lord Hendrix Barboza; Jeffrey Detras; Kevin Manansala; Michael Jonathan Mendoza; Jeffrey Morales; Barry Peralta; Rowena Valerio; Yi Zhang; Sergio Gregorio; Joseph Hermocilla; Michael Echavez; Jan Michael Yap; Andrew Farmer; Gary Schiltz; Jennifer Lee; Terry Casstevens; Pankaj Jaiswal; Ayton Meintjes; Mark Wilkinson; Benjamin Good; James Wagner; Jane Morris; David Marshall; Anthony Collins; Shoshi Kikuchi; Thomas Metz; Graham McLaren; Theo Van Hintum

doi:10.1155/2008/369601

The generation challenge programme platform: semantic standards and workbench for crop science

Richard Bruskiewich, Martin Senger, Guy Davenport, Manuel Ruiz, Mathieu Rouard, Tom Hazekamp, Masaru Takeya, Koji Doi, Kouji Satoh, Marcos Costa, Reinhard Simon, Jayashree Balaji, Akinnola Akintunde, Ramil Mauleon, Samart Wanchana, Trushar Shah, Mylah Anacleto, Arllet Portugal, Victor Jun Ulat, Supat ThongjueaKyle Braak, Sebastian Ritter, Alexis Dereeper, Milko Skofic, Edwin Rojas, Natalia Martins, Georgios Pappas, Ryan Alamban, Roque Almodiel, Lord Hendrix Barboza, Jeffrey Detras, Kevin Manansala, Michael Jonathan Mendoza, Jeffrey Morales, Barry Peralta, Rowena Valerio, Yi Zhang, Sergio Gregorio, Joseph Hermocilla, Michael Echavez, Jan Michael Yap, Andrew Farmer, Gary Schiltz, Jennifer Lee, Terry Casstevens, Pankaj Jaiswal, Ayton Meintjes, Mark Wilkinson, Benjamin Good, James Wagner, Jane Morris, David Marshall, Anthony Collins, Shoshi Kikuchi, Thomas Metz, Graham McLaren, Theo Van Hintum

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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.

Original language	English
Article number	369601
Number of pages	6
Journal	International Journal of Plant Genomics
Volume	2008
DOIs	https://doi.org/10.1155/2008/369601
Publication status	Print publication - 2008

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Bruskiewich, R., Senger, M., Davenport, G., Ruiz, M., Rouard, M., Hazekamp, T., Takeya, M., Doi, K., Satoh, K., Costa, M., Simon, R., Balaji, J., Akintunde, A., Mauleon, R., Wanchana, S., Shah, T., Anacleto, M., Portugal, A., Ulat, V. J., ... Van Hintum, T. (2008). The generation challenge programme platform: semantic standards and workbench for crop science. International Journal of Plant Genomics, 2008, Article 369601. https://doi.org/10.1155/2008/369601

@article{0bc5178df3e4449898f1c7a900e788f3,

title = "The generation challenge programme platform: semantic standards and workbench for crop science",

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.",

author = "Richard Bruskiewich and Martin Senger and Guy Davenport and Manuel Ruiz and Mathieu Rouard and Tom Hazekamp and Masaru Takeya and Koji Doi and Kouji Satoh and Marcos Costa and Reinhard Simon and Jayashree Balaji and Akinnola Akintunde and Ramil Mauleon and Samart Wanchana and Trushar Shah and Mylah Anacleto and Arllet Portugal and Ulat, {Victor Jun} and Supat Thongjuea and Kyle Braak and Sebastian Ritter and Alexis Dereeper and Milko Skofic and Edwin Rojas and Natalia Martins and Georgios Pappas and Ryan Alamban and Roque Almodiel and Barboza, {Lord Hendrix} and Jeffrey Detras and Kevin Manansala and Mendoza, {Michael Jonathan} and Jeffrey Morales and Barry Peralta and Rowena Valerio and Yi Zhang and Sergio Gregorio and Joseph Hermocilla and Michael Echavez and Yap, {Jan Michael} and Andrew Farmer and Gary Schiltz and Jennifer Lee and Terry Casstevens and Pankaj Jaiswal and Ayton Meintjes and Mark Wilkinson and Benjamin Good and James Wagner and Jane Morris and David Marshall and Anthony Collins and Shoshi Kikuchi and Thomas Metz and Graham McLaren and {Van Hintum}, Theo",

year = "2008",

doi = "10.1155/2008/369601",

language = "English",

volume = "2008",

journal = "International Journal of Plant Genomics",

issn = "1687-5370",

publisher = "Hindawi Publishing Corporation",

}

Bruskiewich, R, Senger, M, Davenport, G, Ruiz, M, Rouard, M, Hazekamp, T, Takeya, M, Doi, K, Satoh, K, Costa, M, Simon, R, Balaji, J, Akintunde, A, Mauleon, R, Wanchana, S, Shah, T, Anacleto, M, Portugal, A, Ulat, VJ, Thongjuea, S, Braak, K, Ritter, S, Dereeper, A, Skofic, M, Rojas, E, Martins, N, Pappas, G, Alamban, R, Almodiel, R, Barboza, LH, Detras, J, Manansala, K, Mendoza, MJ, Morales, J, Peralta, B, Valerio, R, Zhang, Y, Gregorio, S, Hermocilla, J, Echavez, M, Yap, JM, Farmer, A, Schiltz, G, Lee, J, Casstevens, T, Jaiswal, P, Meintjes, A, Wilkinson, M, Good, B, Wagner, J, Morris, J, Marshall, D, Collins, A, Kikuchi, S, Metz, T, McLaren, G & Van Hintum, T 2008, 'The generation challenge programme platform: semantic standards and workbench for crop science', International Journal of Plant Genomics, vol. 2008, 369601. https://doi.org/10.1155/2008/369601

TY - JOUR

T1 - The generation challenge programme platform: semantic standards and workbench for crop science

AU - Bruskiewich, Richard

AU - Senger, Martin

AU - Davenport, Guy

AU - Ruiz, Manuel

AU - Rouard, Mathieu

AU - Hazekamp, Tom

AU - Takeya, Masaru

AU - Doi, Koji

AU - Satoh, Kouji

AU - Costa, Marcos

AU - Simon, Reinhard

AU - Balaji, Jayashree

AU - Akintunde, Akinnola

AU - Mauleon, Ramil

AU - Wanchana, Samart

AU - Shah, Trushar

AU - Anacleto, Mylah

AU - Portugal, Arllet

AU - Ulat, Victor Jun

AU - Thongjuea, Supat

AU - Braak, Kyle

AU - Ritter, Sebastian

AU - Dereeper, Alexis

AU - Skofic, Milko

AU - Rojas, Edwin

AU - Martins, Natalia

AU - Pappas, Georgios

AU - Alamban, Ryan

AU - Almodiel, Roque

AU - Barboza, Lord Hendrix

AU - Detras, Jeffrey

AU - Manansala, Kevin

AU - Mendoza, Michael Jonathan

AU - Morales, Jeffrey

AU - Peralta, Barry

AU - Valerio, Rowena

AU - Zhang, Yi

AU - Gregorio, Sergio

AU - Hermocilla, Joseph

AU - Echavez, Michael

AU - Yap, Jan Michael

AU - Farmer, Andrew

AU - Schiltz, Gary

AU - Lee, Jennifer

AU - Casstevens, Terry

AU - Jaiswal, Pankaj

AU - Meintjes, Ayton

AU - Wilkinson, Mark

AU - Good, Benjamin

AU - Wagner, James

AU - Morris, Jane

AU - Marshall, David

AU - Collins, Anthony

AU - Kikuchi, Shoshi

AU - Metz, Thomas

AU - McLaren, Graham

AU - Van Hintum, Theo

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

UR - http://www.mendeley.com/research/generation-challenge-programme-platform-semantic-standards-workbench-crop-science-1

U2 - 10.1155/2008/369601

DO - 10.1155/2008/369601

M3 - Article

SN - 1687-5370

VL - 2008

JO - International Journal of Plant Genomics

JF - International Journal of Plant Genomics

M1 - 369601

ER -

The generation challenge programme platform: semantic standards and workbench for crop science

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