Paper Info
Title
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. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org).
Year
DOI
Venue
2016
10.1093/database/baw058
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
DocType
Volume
ISSN
Journal
2016
1758-0463
Citations 
PageRank 
References 
3
0.41
11
Authors
6
Name
Order
Citations
PageRank
Sook Jung1789.52
Taein Lee2485.84
Stephen P Ficklin3506.19
Jing Yu4273.09
Chun-Huai Cheng5414.72
Dorrie Main6758.44