Journal article
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data
Database : the journal of biological databases and curation, Vol.2011, pp.bar051-bar051
2011
Handle:
https://hdl.handle.net/2376/112273
PMCID: PMC3225077
PMID: 22120662
Abstract
Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.
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Details
- Title
- The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data
- Creators
- Sook Jung - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Naama Menda - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Seth Redmond - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Robert M Buels - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Maren Friesen - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Yuri Bendana - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Lacey-Anne Sanderson - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Hilmar Lapp - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Taein Lee - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Bob MacCallum - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Kirstin E Bett - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Scott Cain - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Dave Clements - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Lukas A Mueller - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164Dorrie Main - Department of Horticulture and Landscape, Washington State University, Pullman, WA 99164
- Publication Details
- Database : the journal of biological databases and curation, Vol.2011, pp.bar051-bar051
- Academic Unit
- Horticulture, Department of; Plant Pathology, Department of
- Publisher
- Oxford University Press
- Identifiers
- 99900547726401842
- Language
- English
- Resource Type
- Journal article