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.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

“…We annotated the database schemas with concepts from the Crop Ontology [39], the GCP Domain Model [15], the Sequence Ontology [40] and the EDAM ontology [31]. Some of these generated WS are available in the BioCatalogue (Figures 11 and 12).…”

“…Furthermore, major plant databases, such as TAIR [8], Gramene [9], IRIS [10], MaizeGDB [11] and GnpIS [12], annotate their data using ontology terms to link different datasets and to facilitate queries across multiple databases. Guided by life science integration studies [13,14], annotating data with ontologies promotes the development of ontology-driven integration platforms [15,16]. …”

Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature

“…Crop science and PGR practitioners span diverse research communities, each with its favourite internet communication protocols (BioMoby, TAPIR, SSWAP, GDPC, etc). The CO, along with the GCP domain model ( Bruskiewich et al , 2006 , 2008 ) and associated Pantheon software, provides a common semantic and software framework for global integration of data across diverse community protocols. Generation Challenge Programme's semantics are designed to be extensible, and to allow for the addition of new semantics and novel data types as the needs of crop researchers evolve.…”