Chado use case: Storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Abstract

The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis tools for Rosaceae crops and Gossypium (cotton). These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform. Chado is highly normalized and uses ontologies to indicate the 'types' of data. Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen. These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic and genotypic data, ontologies and publications. We provide information about how to store these types of data in Chado using GDR and CottonGen as examples sites that were converted from an older legacy infrastructure.