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The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 2005 Jan 01;33(Database issue):D485-91 PMID: 15608243 PMCID: PMC540004

Pubmed ID

15608243

Abstract

The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.

Author List

de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H

Author

Mary E. Shimoyama PhD Associate Professor in the Biomedical Engineering department at Medical College of Wisconsin




Scopus

2-s2.0-13444273396   44 Citations

MESH terms used to index this publication - Major topics in bold

Animals
Chromosome Mapping
Database Management Systems
Databases, Nucleic Acid
Disease Models, Animal
Genetic Markers
Genome
Genomics
Phenotype
Quantitative Trait Loci
Rats
Systems Integration
jenkins-FCD Prod-353 9ccd8489072cb19f5b9f808bb23ed672c582f41e