The Rat Genome Database 2009: variation, ontologies and pathways

  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},
  pages={D744 - D749}
The Rat Genome Database (RGD, 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… 

Figures and Tables from this paper

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
The Mouse Genome Database is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes, serving to further the use of the mouse as a model system for studying human biology and disease.
Pathway Resources at the Rat Genome Database: A Dynamic Platform for Integrating Gene, Pathway and Disease Information
  • V. Petri
  • Biology
    Handbook of Research on Computational and Systems Biology
  • 2011
In this chapter, the pathway resources that RGD currently offers are presented and issues covered include: the biological pathway, the concept and the ontology, pathway literature curation and annotation of genes, interactive pathway diagrams, and tools and resources to access and navigate between pathway data.
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.
Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database
The Rat Genome Database (RGD) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, and cellular components for genes, quantitative trait loci, and strains.
The Rat Genome Database Pathway Portal
The Pathway Portal resources at RGD are presented, and future directions are discussed.
Sequencing of the rat genome and databases.
This chapter is designed to overview the existing sequence and its utility, as well as provide a glimpse of some of the databases and bioinformatic tools available to the investigator.
Original article The Rat Genome Database Pathway Portal
The Rat Genome Database has adopted a multi-tiered approach to pathway data acquisition and presentation and resources and tools are continuously added or expanded toffer more comprehensive pathway data sets as well as enhanced pathway data manipulation, exploration and visualiza-tion capabilities.
The pathway ontology – updates and applications
The content of the Pathway Ontology has increased by over 75% since first presented and the implementation of pipelines promote an enriched provision of pathway data.
The emerging role for rat models in gene discovery
The rat models, bioinformatics tools, and technologies that are changing the landscape of translational research are outlined and a perspective on how rat models will continue to positively impact biomedical research is provided.
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks
The GeneSense server was developed to integrate gene annotation and PPI networks in an expandable architecture that incorporates selected databases with the aim to assemble, analyze, evaluate and disseminate protein-protein association information in a comprehensive and user-friendly manner.


The Rat Genome Database (RGD): developments towards a phenome database
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
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
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.
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
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
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
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
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
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.