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Rat Genome Database


NAR Molecular Biology Database Collection entry number 93
Twigger, S.N.1, Shimoyama, M.1, Lu, J.1, Pasko, D.1, Bromberg, S.1, Chen, C.F.1, Chen, J.1, Gopinathrao, G.1, Nigam, R.1, Ramachandran, H.1, Mathis, J.1, Nie, J.1, Maltais, L.2, Eppig, J.T.2, Maglott, D.3, Schuler, G.3, Jacob, H.J4, Tonellato, P.J.1
1Bioinformatics Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
2The Jackson Laboratory, Bar Harbor, Maine, 04609, USA
3National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
4Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
Contact simont@mcw.edu

Database Description

The Rat is uniquely suited to its role as a model of human disease and the primary focus of the Rat Genome Database (RGD, http://rgd.mcw.edu/) is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources that are constantly being expanded through ongoing literature and bulk dataset curation. Our goal is to enhance studies in the rat by providing not only a repository of genomic data but by allowing the user to view this data from a disease-centric perspective. This will facilitate interpretation and analysis of results in a holistic or systems-oriented manner. Combining this disease-centric approach with our comparative genomics tools allows interpretation of rat studies in the context of the human genome, further leveraging the benefits of the rat as a model organism. RGD has a well defined community outreach focus geared towards the researcher wishing to apply these tools and approaches. These include a Visiting Scientist program, the Rat Community Forum (an online discussion group for rat research), workshops, training seminars and an international curation network. Thus RGD provides data, tools and support to the rat research community and enables this research to be applied to studies in other model systems.

Recent Developments

Major developments in 2002 have centered around making the database more accessable to the user. Comprehensive help pages including 'How do I?' sections have been introduced to explain how the tools and data in RGD can be used to answer typical biological questions. Biological annotations were added to gene reports, including Gene Ontology annotations. Through our ongoing collaboration with MGD and LocusLink, RGD now has almost 5000 gene entries; the gene symbols and names are being systematically reviewed and updated to conform to established nomenclature guidelines. In preparation for the release of the Rat sequence, all rat ESTs have been loaded into the database along with Unigene and Tigr Cluster data, providing a valuable resource for sequence and microarray analysis. To assist users in accessing the data within the database, more comprehensive FTP flat files have been released and two new mirror sites (in Japan and China) were established.

Acknowledgements

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.

References

Twigger, S.N., et. al., Nucleic Acids Res. 2002 Jan
1;30(1):125-8


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