Integrating Phenotypic Data With Genomic, Genetic and Genotypic Data Using Chado

Breeders and growers of various crops have been accumulating large-scale phenotypic data over the years. The process of phenotypic data collection is labor-extensive, hence slow and expensive. The management of the data is equally challenging due to the complexity of the associated data such as pedigree, phenotypic descriptors, aliases and environment variables. In addition, it is becoming crucial to integrate the phenotypic data with the exponentially increasing genomics data to exploit both genotypic and phenotypic data in our understanding of molecular basis of traits and diversity. To efficiently integrate the phenotypic data with other genomic and genetic data in Rosaceae crops and cotton, we utilize Chado, the generic, modular and ontology-driven database schema for biological data. The newly developed Natural diversity module allows us to store large-scale phenotypic data from various projects with genotypic data. The phenotypic and genotypic data have also been integrated with the genetic and genomics data that are stored in other modules of Chado. The use of ontology in Chado provides capacity to compare the phenotypic data scored with different sets of phenotypic descriptors and units.