Rat Genome Database

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DESCRIPTION (provided by applicant): The Rat Genome Database provides a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. The goal of RGD is to provide investigators with a research platform that facilitates the elucidation of disease mechanisms by implementing standard data formats and ontologies. To meet this goal, we propose three specific aims: 1) To acquire, integrate and functionally annotate emerging genomic elements and variations along with core data to create a comprehensive genome resource. New gene models, sequence and map data and variations such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs), and splice variants will be integrated through collaborations with NCBI and Ensembl and the use of innovative data pipelines. Curators will continue to focus on functional annotation of core data using multiple ontologies. New information including chemical-gene, drug-gene interactions and their impact on biology or disease will be added. Tools will be developed for mining, analysis and visualization of new data types. Educational activities for this aim will focus on new users and new tools for existing users. 2) To create a comprehensive phenome resource including phenotype measurements and strain medical records. We will develop a phenome database and provide individual strain "medical records" to provide easy access to the richness of this information. The phenome resource will include specific educational activities focused on phenotyping protocols, breeding and the use of our new tools and strain resources. 3) To link genotypes (Aim 1) to phenotypes (Aim 2) through QTLs, molecular, cellular and physiological pathways and the disease portals. RGD will continue to curate QTL data and enhance the QTL reports to provide a navigational hub linking genotype and phenotype data. Drug and physiological pathways will be curated in addition to disease related signaling and regulatory pathways and interactive diagrams will be used to link pathways, biological processes, genomic variations and phenotype data. RGD will expand its Disease Portals to serve as integration points for genomic and phenotype data, disease model profiles, and pathway data. Educational activities will focus on tools for comparative studies between rat and human, as well as those which integrate genotype and phenotype data.