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

Chris Mungall | Zendy; David Emmert | Zendy

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

Author(s) -

Chris Mungall,

David Emmert

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm189

Subject(s) - computer science , conceptual schema , schema migration , database schema , biological database , schema (genetic algorithms) , information schema , semi structured model , interoperability , modular design , software , relational database , schema evolution , information retrieval , database , database design , world wide web , programming language , bioinformatics , biology , psychology , developmental psychology , gender schema theory

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.

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