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<p> The fast-moving fields of comparative genomics, molecular breeding, and bioinformatics have the potential to bring new knowledge to bear on problems encountered by resource-poor farmers. These problems include abiotic stresses (such as drought and soil salinity) and biotic stresses (such as plant diseases and pests). The Generation Challenge Programme (GCP; <span><a href="http://www.pubmedcentral.nih.gov/redirect3.cgi?&&auth=0AZxQsaX1q6Jmt4j14HDW-kHi_d1vQWuSKgIruQTA&reftype=extlink&artid=2375972&iid=159862&jid=494&FROM=Article%7CBody&TO=External%7CLink%7CURI&article-id=2375972&journal-id=494&rendering-type=normal&&http://www.generationcp.org/">http://www.generationcp.org/</a></span>) aims to exploit advances in molecular biology to harness the rich global heritage of plant genetic resources and contribute to a new generation of stress-tolerant varieties that meet the needs of these farmers and the consumers of their crops. The GCP brings together three sets of partners: member agricultural research institutes of the Consultative Group on International Agricultural Research (CGIAR; <span><a href="http://www.pubmedcentral.nih.gov/redirect3.cgi?&&auth=0CLEqJiLB6C1WvXHBmoTgPNNqAkLGV8F-UPoKXAHw&reftype=extlink&artid=2375972&iid=159862&jid=494&FROM=Article%7CBody&TO=External%7CLink%7CURI&article-id=2375972&journal-id=494&rendering-type=normal&&http://www.cgiar.org/">http://www.cgiar.org/</a></span>), advanced research institutes in developed countries, and national agricultural research and extension systems in developing countries, to undertake a long-term program of globally integrated scientific research, capacity building, and delivery of products for the above goal. </p> <p> Central to GCP activities is the development of an integrated platform of molecular biology and bioinformatics tools to be applied to the research objectives of the GCP. The resulting platform is also intended to be a “global public good” to be made freely available to all crop researchers and breeders around the world, thus enabling agricultural scientists, particularly in developing countries, to more readily apply information about elite genetic stocks, genomic knowledge, and new breeding technologies that are becoming available to their local breeding programmes. </p> <p> The goal of this GCP crop informatics platform is to provide solutions for priority end-user needs for biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. Development of the platform is driven by the following observations: </p> <p> </p> <ul style="list-style-type:lower-roman;"><li><span>GCP partners (and the international crop research community in general) are globally distributed, each research team having relatively large datasets to share and integrated datasets that reside in diverse online, but locally curated databases;</span></li> <li><span>GCP research covers a diversity of crop species;</span></li> <li><span>GCP research spans a wide range of scientific data types, including germplasm, genomic, phenotypic, as well as crop physiological and geographic information, this constellation of data types is evolving with time as new experimental technologies are created;</span></li> <li><span>GCP scientists (and crop scientists in general) need to apply a wide range of analytical tools already used by their research communities; they also need new tools to meet new or evolving needs; integration of such tools to interoperate with one another is a nontrivial task.</span></li> </ul><p> A GCP crop information platform is being developed to better meet these challenges by managing genetic resources, genomics, and crop information using the following components: </p> <p> </p> <ul style="list-style-type:lower-roman;"><li><span>shared public platform-independent set of scientific domain models, ontology, and data templates to cross-link all data types and analysis processes within the platform;</span></li> <li><span>GCP domain model-constrained web service and registry technologies to identify, share, and manage the analysis of information, as well as to integrate it across a network of diverse globally dispersed data sources connected to the Internet;</span></li> <li><span>reference implementations of platform-specific middleware using the GCP domain model;</span></li> <li><span>a suite of open-source software tools (adopted or newly developed) integrated into a workbench and accessing web-connected data sources. Included in this suite is software to provide enhanced access to high-performance computational (HPC) grid facilities enabling computationally intensive and/or high-throughput analyses of project data.</span></li> </ul><p> This paper will survey progress on some of the central components of the platform, with a special emphasis on the domain model, a reference Java middleware implementation, and Internet protocol aspects of the project. </p>
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