- The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. [PMID: 27009807]
G Thomas Hayman, Stanley J F Laulederkind, Jennifer R Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff De Pons, Melinda R Dwinell, Mary Shimoyama
Database : the journal of biological databases and curation 2016:2016
4 Citations (Google Scholar as of 2017-03-06)
Abstract: The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu. © The Author(s) 2016. Published by Oxford University Press.
- The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. [PMID: 25355511]
Mary Shimoyama, Jeff De Pons, G Thomas Hayman, Stanley J F Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth Worthey, Melinda Dwinell, Howard Jacob
Nucleic acids research 2015:43(Database issue)
56 Citations (Google Scholar as of 2017-03-06)
Abstract: The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.