Paper Info
Title
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
Abstract
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 can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies ( or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas ( modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences.
Year
DOI
Venue
2007
10.1093/bioinformatics/btm189
BIOINFORMATICS
Keywords
DocType
Volume
information system,relational database,genome sequence,software development,biological database,controlled vocabulary,generic model organism database,genetics
Conference
23
Issue
ISSN
Citations 
13
1367-4803
78
PageRank 
References 
Authors
9.34
7
2
Name
Order
Citations
PageRank
Chris Mungall131636.22
David B. Emmert2789.34