Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Generation Challenge Programme (GCP) Domain Modeling And Crop Information Platform

Richard M. Bruskiewich¹ , Guy Davenport² , Reinhard Simon³ , Manuel Ruiz⁴ , Andrew Farmer⁵ , Thomas Metz¹ , Tom Hazekamp⁶ , Masaru Takeya⁷ , Jennifer Lee⁸ , C. Graham McLaren¹ , Theo van Hintum⁹

¹  International Rice Research Institute (IRRI) Los Baños, Laguna, Philipppines

²  Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) Km. 45, Carretera Mexico-Veracruz El Batan, Texcoco, Edo. de México CP 56130 México

³  Centro Internacional de la Papa (CIP) Avenida La Molina 1895, La Molina Apartado Postal 1558, Lima 12 Peru

⁴  Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) 42, rue Scheffer 75116 Paris, France

⁵  National Center for Genome Resources 2935 Rodeo Park Drive East Santa Fe, New Mexico 87505 USA

⁶  International Plant Genetic Resources Institute Via dei Tre Denari 472/a 00057 Maccarese (Fiumicino) Rome ITALY

⁷  National Institute for Agrobiological Sciences (NIAS) 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

⁸  Scottish Crop Research Institute/ University of Dundee Nethergate, Dundee, DD1 4HN, Scotland, UK

⁹  Wageningen Universiteit & Researchcentrum (WUR) Postbus 9101 6700 HB Wageningen

The Generation Challenge Programme (GCP; http://www.generationcp.org) is a global research consortium involving 18 international agricultural institutes (see separate PAG poster about the GCP). The scientific research goals of the GCP focus on comparative biology across crop species, high-throughput molecular characterization of genetic resources diversity for allele mining, and deployment of efficient gene transfer technologies into plant breeding programmes.
One core informatics activity of the GCP is the development of an integrated crop information platform for the support of the genomics-driven plant breeding within the consortium. This platform will integrate the information resources of the consortium members, and provide the link to the global bioinformatics and biodiversity community. Research and development activities toward this goal include the adoption and extension of a common set of scientific domain models and ontology, to cross-link all data types and analysis processes within an internet integrated crop information platform.
The modeling of the domain spans entities for germplasm (including passport information and genealogy), genotyping, phenotyping, geographical information systems (GIS) and genomics data. Where possible existing models will be adopted or further developed. The resulting models are being embedded into a layered software architecture built primarily on Java language technologies, software that strives to develop integrated use cases involving the cross-linkage of genetic mapping, germplasm, genomics and GIS information into cohesive scenarios. The platform itself provides for the integration of both GCP developed tools and compatible open-source bioinformatics software tools. The project is entirely open sourced and licensed, with the software posted to a GForge-based project management site called CropForge (http://cropforge.irri.org) and technical documentation hosted in a Wiki-based site called CropWiki (http://cropwiki.irri.org/gcp).
This presentation will discuss the structure and status of GCP scientific domain modeling and its implementation in the GCP crop information platform.