The Rat Genome Database 2009: variation, ontologies and pathways

@article{Dwinell2009TheRG,
  title={The Rat Genome Database 2009: variation, ontologies and pathways},
  author={Melinda R. Dwinell and Elizabeth A. Worthey and Mary Shimoyama and Burcu Bakir-Gungor and Jeffrey DePons and Stanley J. F. Laulederkind and Timothy Lowry and Rajni Nigam and Victoria Petri and Jennifer R. Smith and Alexander Stoddard and Simon N. Twigger and Howard J. Jacob},
  journal={Nucleic Acids Research},
  year={2009},
  volume={37},
  pages={D744 - D749}
}
The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level of the whole organism, including the variations associated with disease phenotypes. To fully support use of the rat as a translational model for biological systems and human disease… 
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References

SHOWING 1-10 OF 13 REFERENCES
The Rat Genome Database (RGD): developments towards a phenome database
TLDR
RGD's development towards creating a phenome database is reported on, with improvements on helping researchers find genes responsible for disease through the use of rat models and increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology.
The Gene Ontology project in 2008
TLDR
The GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms.
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and…
Progress and prospects in rat genetics: a community view
TLDR
This work outlines achievements in rat gene discovery to date, shows how these findings have been translated to human disease, and document an increasing pace of discovery of new disease genes, pathways and mechanisms.
The generic genome browser: a building block for a model organism system database.
TLDR
The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism
TLDR
The authors describe and classify different approaches for data acquisition, storage and navigation, give a detailed description of the integrative technology behind the Pathway Studio® software solution, and present a comparison with other integrative pathway analysis platforms suitable for drug discovery tasks.
miRBase: tools for microRNA genomics
TLDR
The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described and graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts.
SNP and haplotype mapping for genetic analysis in the rat
TLDR
A survey of genetic variation based on almost 3 million newly identified SNPs is reported, providing a detailed SNP map and demonstrating its utility for mapping of quantitative trait loci in the laboratory rat.
All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity
TLDR
It is argued that the specific nature of transcription factor-DNA interactions imposes constraints on the types of motifs that are likely to be transcription factor binding sites and on the relationships between motifs recognized by members of structurally similar transcription factors.
What everybody should know about the rat genome and its online resources
TLDR
The current status of the rat genome sequence is described and the plans for its impending 'upgrade' are described, including the new SNP views at Ensembl and the key online resources providing access to therat genome.
...
...