A Chado case study: an ontology-based modular schema for representing genome-associated biological information
1Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720 and 2Harvard University, Molecular and Cell Biology: FlyBase, 16 Divinity Avenue, Cambridge, MA 02138, USA
*To whom correspondence should be addressed.
 |
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.
Availability: GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).
Contact: cjm{at}fruitfly.org or emmert{at}morgan.harvard.edu.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. Menda, R. M. Buels, I. Tecle, and L. A. Mueller A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes Plant Physiology, August 1, 2008; 147(4): 1788 - 1799. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Wanchana, S. Thongjuea, V. J. Ulat, M. Anacleto, R. Mauleon, M. Conte, M. Rouard, M. Ruiz, N. Krishnamurthy, K. Sjolander, et al. The Generation Challenge Programme comparative plant stress-responsive gene catalogue Nucleic Acids Res., January 11, 2008; 36(suppl_1): D943 - D946. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Papanicolaou, S. Gebauer-Jung, M. L. Blaxter, W. Owen McMillan, and C. D. Jiggins ButterflyBase: a platform for lepidopteran genomics Nucleic Acids Res., January 11, 2008; 36(suppl_1): D582 - D587. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Bowes, K. A. Snyder, E. Segerdell, R. Gibb, C. Jarabek, E. Noumen, N. Pollet, and P. D. Vize Xenbase: a Xenopus biology and genomics resource Nucleic Acids Res., January 11, 2008; 36(suppl_1): D761 - D767. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
The Gene Ontology Consortium The Gene Ontology project in 2008 Nucleic Acids Res., January 11, 2008; 36(suppl_1): D440 - D444. [Abstract] [Full Text] [PDF]
|
|