The Rat Genome Database (RGD): developments towards a phenome database.
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.
de la Cruz
Norberto
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Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA.
Bromberg
Susan
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Pasko
Dean
D
Shimoyama
Mary
M
Twigger
Simon
S
Chen
Jiali
J
Chen
Chin-Fu
CF
Fan
Chunyu
C
Foote
Cindy
C
Gopinath
Gopal R
GR
Harris
Glenn
G
Hughes
Aubrey
A
Ji
Yuan
Y
Jin
Weihong
W
Li
Dawei
D
Mathis
Jedidiah
J
Nenasheva
Natalya
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Nie
Jeff
J
Nigam
Rajni
R
Petri
Victoria
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Reilly
Dorothy
D
Wang
Weiye
W
Wu
Wenhua
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Zuniga-Meyer
Angela
A
Zhao
Lan
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Kwitek
Anne
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Tonellato
Peter
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Jacob
Howard
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D000818:Animals; D002874:Chromosome Mapping; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D004195:Disease Models, Animal; D005819:Genetic Markers; D016678:Genome; D023281:Genomics; D010641:Phenotype; D040641:Quantitative Trait Loci; D051381:Rats / Q000235:genetics* / Q000502:physiology; D018511:Systems Integration
D005819:Genetic Markers