de la Cruz, N., Bromberg, S., Pasko, D., Shimoyama, M., Twigger, S., Chen, J. L., Chen, C. F., Fan, C., Foote, C., Gopinath, G. R., Harris, G., Hughes, A., Ji, Y., Jin, W. H., Li, D. W., Mathis, J., Nenasheva, N., Nie, J., Nigam, R., Petri, V., Reilly, D., Wang, W. Y., Wu, W. H., Zuniga-Meyer, A., Zhao, L., Kwitek, A., Tonellato, P., Jacob, H. (January 2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Research, 33. D485-D491. ISSN 0305-1048
Abstract
The Rat Genome Database (RGD) (http://rgd.mcw.edu) alms 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. (I!) Knowledge representation augmented by the implementation of a new ontology and annotation system. (ill) 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.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | BIOLOGISTS SEQUENCE sequence browser BROWSER PROJECT SYSTEM |
| Subjects: | bioinformatics > genomics and proteomics > databases > database construction bioinformatics > genomics and proteomics > databases > database optimization bioinformatics > genomics and proteomics > databases organism description > animal > mammal > rodent > rat organism description > animal > mammal > rodent > rat |
| CSHL Authors: | |
| Depositing User: | CSHL Librarian |
| Date: | January 2005 |
| Date Deposited: | 13 Jan 2012 20:29 |
| Last Modified: | 13 Jan 2012 20:29 |
| URI: | https://repository.cshl.edu/id/eprint/22551 |
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