A Chado case study: an ontology-based modular schema for representing genome-associated biological information

Motivation: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Results: Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly ...

• Type: Conference
• Year: 2007
• Where: ISMB
• Authors: Chris Mungall, David B. Emmert
• Keywords: Computational Biology, Database Schema, ISMB 2007, Model Organism, Relational Database Schema