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. 2005 Jan 1;33(Database issue):D485-91.
doi: 10.1093/nar/gki050.

The Rat Genome Database (RGD): Developments Towards a Phenome Database

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Free PMC article

The Rat Genome Database (RGD): Developments Towards a Phenome Database

Norberto de la Cruz et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1
Figure 1
Sections of the Ontology and Gene reports. The ontology report (a) provides details on an ontology term including links to data on objects annotated to it. The gene report (b) provides links to ontology terms to which it is annotated. These reciprocal links enable users to move through various ontologies and find related terms and the objects annotated to them.
Figure 2
Figure 2
A section of a map from RGD's Genome Browser showing QTL, genes and SNP tracks juxtaposed against ‘ontology tracks’. This display enables users to quickly survey biological information annotated to sequence features such as genes and QTLs and correlate the annotations with other features in the genome. The drop down menu enables the user to access multiple data reports from the ontology track. From this point, the user can obtain detailed information about the sequence feature (gene), the term to which it is annotated or the set of genes annotated to this term.
Figure 3
Figure 3
A schematic diagram illustrating the flow of data between RGD and our collaborators. More than just an exchange of information, a large amount of RGD data that has been curated and quality controlled finds its way to other major databases and genome browsers.

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