The GCP consortium was formally
established in 2003. The first meeting of the bioinformatics and crop
informatics development team of the GCP, designated as Subprogramme 4, was
hosted in Rome, in February 2004. The general user needs and project goals were coarsely mapped
out at this meeting, with some considerable differences in opinion voiced at
how to construct the required informatics framework for the GCP. In May 2004, a
smaller team of software experts met in Mexico to discuss project
management, identify key user needs and platform requirements, and make some
initial progress in the design of the system. Key decisions at this latter
meeting were the adoption of the “model-driven architecture” paradigm for
system development and to embrace web services as a key technology for global
integration of systems. Numerous development meetings have been convened
annually since these initial meetings to further refine and advance the design
and implementation of the platform.
particular, a milestone review of the GCP domain model and initial
software systems using the model was held in Pretoria, South Africa in
March 2006. Since that time, a number of early release versions of
software systems based on GCP platform technology have become
available, generally documented at http://pantheon.generationcp.org/
and publicly downloadable from various CropForge projects. A special
“communications” project for GCP-specific projects is also available on
CropForge at the http://cropforge.org/projects/gcpcomm to further inform prospective users on the variety of such GCP software tools
now available, and provide a venue for user discussions and feedback about the tools.
So, what can I do with the GCP platform?
vision of the platform development team of the bioinformatics and crop
informatics subprogramme of the GCP is to establish a truly easy to use
but extensible workbench providing interoperability and enhanced data
access across all GCP partner sites and, later, across the global crop
research community. As indicated above, the GCP domain model has a
scope of data type coverage that spans most of the pertinent scientific
types found in crop research from upstream laboratory experiments
through germplasm manipulations, in a georeferenced characterized field
setting. The diversity of potential data sources and analysis tools is
What the platform facilitates is transparent data flows between such
data sources and tools, whether from locally administered databases or
remote Internet-connection resources.
this light, a number of practical “use cases” may be described in
general terms, as a series of data manipulation
steps, to highlight some of the anticipated usage of the platform. As
an indication of the data retrieval and analysis scope of the GCP
platform, we describe a general integrative use case here below, in
terms of a series of defined steps.
General GCP platform analysis use case for crop improvement
- Retrieve the list of all genetic maps that include a quantitative trait locus (QTL) for a specified trait.
- Retrieve selected maps in the list, from a project database or source file containing such maps.
- Load this into a suitable mapping tool (e.g., the comparative map and trait visualization tool, CMTV).
- Extract the pairs of flanking markers for the QTL.
- From a second (crop) database, retrieve the list of all germplasm that have been genotyped with these flanking markers.
- Retrieve all the pertinent passport, genotype, and phenotype information about the germplasm in the list.
parallel to the steps (5) and (6), if available, retrieve any gene
locus candidates within (genetic/physical/sequence) map intervals which
are defined by flanking markers which are molecular sequence based.
- Retrieve gene functional information about the gene loci compiled in step (7).
- Retrieve the alleles of “interesting” genes from (8), in the list of germplasm identified in step (5).
- Plot germplasm passport, genotype, and phenotype information on geographical information maps.
- Retrieve information about the environmental characteristics of the geographical regions identified in step (10).
germplasm, for further detailed evaluation, which appears to be adapted
to target environments, which have promising phenotypic values
identified in step (6) and which contains target alleles of gene loci
identified in step (9).
- Identify genotyping
(marker) systems potentially available from step (9), for marker
assisted selected transfer of target traits from identified germplasm
to additional germplasm targets.