Experiences Using Logic Programming in Bioinformatics
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
Detecting distant homologies on protozoans metabolic pathways using scientific workflows
International Journal of Data Mining and Bioinformatics
Journal of Biomedical Informatics
Ontology consolidation in bioinformatics
APCCM '10 Proceedings of the Seventh Asia-Pacific Conference on Conceptual Modelling - Volume 110
Editorial: BioDB: An ontology-enhanced information system for heterogeneous biological information
Data & Knowledge Engineering
Integrative data mining in functional genomics of brassica napus and arabidopsis thaliana
IEA/AIE'10 Proceedings of the 23rd international conference on Industrial engineering and other applications of applied intelligent systems - Volume Part III
A set of ontologies to drive tools for the control of vector-borne diseases
Journal of Biomedical Informatics
Evolution of the Sequence Ontology terms and relationships
Journal of Biomedical Informatics
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
Applied Ontology - Biomedical Ontologies
Flexible case-based retrieval for comparative genomics
Applied Intelligence
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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@fruitfly.org or emmert@morgan.harvard.edu.