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The Rat Genome Database, update 2007--easing the path from disease to data and back again.

Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, RGD Te - Nucleic Acids Res. (2006)

Bottom Line: The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations.In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments.We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. simont@mcw.edu

ABSTRACT
The Rat Genome Database (RGD, http://rgd.mcw.edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model. Recognizing the importance of the rat as a disease model we have employed targeted curation strategies to curate genes, QTL and strain data for neurological and cardiovascular disease areas. This work has centered on rat but also includes data for mouse and human to create 'disease portals' that provide a unified view of the genes, QTL and strain models for these diseases across the three species. The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations. In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments. We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.

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Related in: MedlinePlus

Screenshot of the RGD Neurological Disease portal showing the combined data for all neurological diseases. The various subsections of the page (A–D) are described in more detail in the text.
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fig2: Screenshot of the RGD Neurological Disease portal showing the combined data for all neurological diseases. The various subsections of the page (A–D) are described in more detail in the text.

Mentions: Building from this, we identified a subset of diseases that were clearly of high interest to the research community and developed a two-pronged approach to providing enhanced support for research in these areas. For each disease area, two methods were utilized to identify data for inclusion. Disease-related genes were identified from existing sources such as Online Mendelian Inheritance in Man (OMIM) (9), the Genetic Association Database (10), GeneCards (11) and NCBI's Genes and Disease database. In addition, genes at the Mouse Genome Database (MGD) (12) annotated with related phenotypes were included. These genes were prioritized and targeted searches of rat and human literature were undertaken to provide comprehensive annotations for functional, disease, phenotype and pathway information. In a complimentary approach, focused literature searches were conducted to identify additional genes, QTLs and strains related to the disease area. To facilitate translational studies Human and Mouse data was also included. As there is limited data on human QTL available electronically, a similar strategy was followed to identify relevant Human QTL papers for inclusion in the portal. Mouse and Human gene orthologs are already curated as part of the normal RGD gene curation process. By following this targeted approach, all rat genes, strains, QTL related to a disease area could be added to the database, along with their functional annotations (GO, pathway, phenotype, disease). Similarly, the Human and Mouse gene orthologs and Human QTL were also identified to provide comparative resources for the database. To complement the dedicated curation effort, an online portal was created to provide access to this information. To date, one disease portal has been released for neurological diseases; a second for Cardiovascular Diseases will be released in the autumn of 2006. The portal combines text data with visual elements to allow the user to quickly get an overview of knowledge in a disease area while providing hyperlinks to more details as desired. A screenshot of the Neurological portal is shown in Figure 2 and the main elements are described below:


The Rat Genome Database, update 2007--easing the path from disease to data and back again.

Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, RGD Te - Nucleic Acids Res. (2006)

Screenshot of the RGD Neurological Disease portal showing the combined data for all neurological diseases. The various subsections of the page (A–D) are described in more detail in the text.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761441&req=5

fig2: Screenshot of the RGD Neurological Disease portal showing the combined data for all neurological diseases. The various subsections of the page (A–D) are described in more detail in the text.
Mentions: Building from this, we identified a subset of diseases that were clearly of high interest to the research community and developed a two-pronged approach to providing enhanced support for research in these areas. For each disease area, two methods were utilized to identify data for inclusion. Disease-related genes were identified from existing sources such as Online Mendelian Inheritance in Man (OMIM) (9), the Genetic Association Database (10), GeneCards (11) and NCBI's Genes and Disease database. In addition, genes at the Mouse Genome Database (MGD) (12) annotated with related phenotypes were included. These genes were prioritized and targeted searches of rat and human literature were undertaken to provide comprehensive annotations for functional, disease, phenotype and pathway information. In a complimentary approach, focused literature searches were conducted to identify additional genes, QTLs and strains related to the disease area. To facilitate translational studies Human and Mouse data was also included. As there is limited data on human QTL available electronically, a similar strategy was followed to identify relevant Human QTL papers for inclusion in the portal. Mouse and Human gene orthologs are already curated as part of the normal RGD gene curation process. By following this targeted approach, all rat genes, strains, QTL related to a disease area could be added to the database, along with their functional annotations (GO, pathway, phenotype, disease). Similarly, the Human and Mouse gene orthologs and Human QTL were also identified to provide comparative resources for the database. To complement the dedicated curation effort, an online portal was created to provide access to this information. To date, one disease portal has been released for neurological diseases; a second for Cardiovascular Diseases will be released in the autumn of 2006. The portal combines text data with visual elements to allow the user to quickly get an overview of knowledge in a disease area while providing hyperlinks to more details as desired. A screenshot of the Neurological portal is shown in Figure 2 and the main elements are described below:

Bottom Line: The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations.In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments.We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. simont@mcw.edu

ABSTRACT
The Rat Genome Database (RGD, http://rgd.mcw.edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model. Recognizing the importance of the rat as a disease model we have employed targeted curation strategies to curate genes, QTL and strain data for neurological and cardiovascular disease areas. This work has centered on rat but also includes data for mouse and human to create 'disease portals' that provide a unified view of the genes, QTL and strain models for these diseases across the three species. The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations. In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments. We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.

Show MeSH
Related in: MedlinePlus