Abstract
Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
Highlights
CottonGen serves as the central data repository and analysis resource for the cotton research community, providing access to an integrated and comprehensive online information system to enable basic, translational, and applied cotton research [1]
The current Cotton Trait Ontology contains 223 traits of 12 trait classes associated with 303 trait descriptors and will continue to be updated and validated as new data is imported to CottonGen
To accommodate the data mining needs that came with these new types and large volumes of data, various web interfaces were developed by the CottonGen team, such as MegaSearch [68], MapViewer [63], breeding information management system (BIMS) [13], Chado Loader, Chado Data Display, and Chado Search modules [69], or Tripal modules that other database teams developed such as the Synteny Viewer and Tripal BLAST [8]
Summary
CottonGen serves as the central data repository and analysis resource for the cotton research community, providing access to an integrated and comprehensive online information system to enable basic, translational, and applied cotton research [1]. CottonGen was expanded to include annotated genome and transcriptome sequences and enhanced with tools for easier data sharing, mining, visualization, and retrieval of cotton research data. The Tools Quick Start is organized into genomics, genetics, breeding, and general sections; each section provides links to appropriate pages to access available data, tools, or general information about CottonGen. New features that can quickly familiarize researchers to CottonGen data and functionality include the dynamic data overview page, where researchers can browse the current data types and numbers in CottonGen and access short video tutorials. We describe the currently available data and interfaces, with a focus on new features
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