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

Sook Jung,Dorrie Main,Chun-Huai Cheng,Jing Yu,Stephen Ficklin,Taein Lee

doi:10.1093/database/baw010

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. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org)

Highlights

The database schema Chado [1] is a part of GMOD, the Generic Model Organism Database project, a collection of open source software tools for managing, visualizing, storing and disseminating genetic and genomic data
The sequence module is central for the storage of sequence features, their relationships and has the most well-defined use cases for Chado as described in detail by Mungall et al [1]
Phenotypic descriptors used for cultivar evaluation or breeding projects as well as QTL can be stored using Trait Ontology, allowing users to view all the phenotypic data, QTL and germplasm that are associated with a specific trait ontology term

Summary

Introduction

The database schema Chado [1] is a part of GMOD, the Generic Model Organism Database project (www.gmod. org), a collection of open source software tools for managing, visualizing, storing and disseminating genetic and genomic data. The database schema Chado [1] is a part of GMOD, the Generic Model Organism Database project Org), a collection of open source software tools for managing, visualizing, storing and disseminating genetic and genomic data. There are >40 software projects in GMOD, providing functionality such as genome visualization and editing, database tools, comparative genome visualization, genome annotation, community annotation and gene expression visualization. Chado is the only database schema in GMOD. It was originally developed for the FlyBase database to integrate Drosophila genomic sequences and annotation data with genetic and phenotypic data [1]. The schema was designed to be generic, extensible and open-source, so it could be used to build databases for any model organism with

Objectives

Conclusion