title: The Rat Genome Database (RGD): developments towards a phenome database.
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.
authors.affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA.
authors.forename: Norberto
authors.initials: N
authors.lastname: de la Cruz
authors.forename: Susan
authors.initials: S
authors.lastname: Bromberg
authors.forename: Dean
authors.initials: D
authors.lastname: Pasko
authors.forename: Mary
authors.initials: M
authors.lastname: Shimoyama
authors.forename: Simon
authors.initials: S
authors.lastname: Twigger
authors.forename: Jiali
authors.initials: J
authors.lastname: Chen
authors.forename: Chin-Fu
authors.initials: CF
authors.lastname: Chen
authors.forename: Chunyu
authors.initials: C
authors.lastname: Fan
authors.forename: Cindy
authors.initials: C
authors.lastname: Foote
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Gopinath
authors.forename: Glenn
authors.initials: G
authors.lastname: Harris
authors.forename: Aubrey
authors.initials: A
authors.lastname: Hughes
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
authors.forename: Weihong
authors.initials: W
authors.lastname: Jin
authors.forename: Dawei
authors.initials: D
authors.lastname: Li
authors.forename: Jedidiah
authors.initials: J
authors.lastname: Mathis
authors.forename: Natalya
authors.initials: N
authors.lastname: Nenasheva
authors.forename: Jeff
authors.initials: J
authors.lastname: Nie
authors.forename: Rajni
authors.initials: R
authors.lastname: Nigam
authors.forename: Victoria
authors.initials: V
authors.lastname: Petri
authors.forename: Dorothy
authors.initials: D
authors.lastname: Reilly
authors.forename: Weiye
authors.initials: W
authors.lastname: Wang
authors.forename: Wenhua
authors.initials: W
authors.lastname: Wu
authors.forename: Angela
authors.initials: A
authors.lastname: Zuniga-Meyer
authors.forename: Lan
authors.initials: L
authors.lastname: Zhao
authors.forename: Anne
authors.initials: A
authors.lastname: Kwitek
authors.forename: Peter
authors.initials: P
authors.lastname: Tonellato
authors.forename: Howard
authors.initials: H
authors.lastname: Jacob
mesh_terms: 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
chemical_list: D005819:Genetic Markers