Chado

Chado

Chado is a comprehensive database schema designed to store and manage biological data, particularly in the field of genomics and genetics. It is part of the Generic Model Organism Database (GMOD) project, which aims to provide open-source software tools for managing and analyzing biological data.

Overview

Chado is a modular and extensible schema that can accommodate a wide variety of biological data types. It is designed to be flexible enough to handle the diverse needs of different model organism databases. The schema is implemented in PostgreSQL, a powerful open-source relational database system.

Structure

Chado is organized into several modules, each of which is responsible for a specific type of data. The main modules include:

• Sequence Module: This module is used to store information about biological sequences, such as DNA, RNA, and protein sequences. It includes tables for storing sequence features, annotations, and alignments.

• Genetic Module: This module handles genetic data, including information about genes, alleles, and genotypes. It supports the storage of genetic maps and linkage data.

• Phenotype Module: This module is used to store phenotype data, which describes observable traits of organisms. It allows for the association of phenotypes with genetic and environmental factors.

• Expression Module: This module manages data related to gene expression, including microarray and RNA-Seq data. It supports the storage of expression measurements and experimental conditions.

• Publication Module: This module is used to store bibliographic information about scientific publications. It allows for the association of data with relevant literature.

Features

Chado offers several features that make it suitable for managing complex biological data:

• Extensibility: Chado's modular design allows users to extend the schema to accommodate new types of data as needed.

• Interoperability: Chado is designed to work with other GMOD tools, such as Apollo and GBrowse, facilitating the integration of data analysis and visualization.

• Scalability: Chado can handle large datasets, making it suitable for use with high-throughput sequencing and other large-scale biological experiments.

Applications

Chado is used by a variety of model organism databases, including:

• FlyBase, a database for the genetics and molecular biology of Drosophila melanogaster.
• WormBase, a database for the biology and genomics of Caenorhabditis elegans and related nematodes.
• Saccharomyces Genome Database (SGD), a database for the genetics and molecular biology of Saccharomyces cerevisiae.

See Also

• Bioinformatics
• Database management system
• Genomics

References

• Stein, L. D., et al. (2002). The Generic Genome Browser: A Building Block for a Model Organism System Database. Genome Research, 12(10), 1599-1610.
• Mungall, C. J., et al. (2007). Chado: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23(13), i337-i346.

External Links

• Chado on GMOD