The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

G Thomas Hayman,Stanley J F Laulederkind,Shur-Jen Wang,Melinda R Dwinell,Jennifer R Smith,Rajni Nigam,Mary Shimoyama,Jeff De Pons,Marek Tutaj,Victoria Petri

doi:10.1093/database/baw034

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

Highlights

In response to the observation that rat researchers, unlike researchers using other model organism databases, tend to be more disease oriented [1], the Rat Genome Database (RGD) has directed a significant portion of its efforts toward disease curation
Rat researchers’ interests often revolve around hypertension and diabetes, which are the topics of two of the earliest RGD disease portals established to address the needs of these research communities
RGD, which started in 1999 curating genes primarily to the Gene Ontology (GO) [3] and Mammalian Phenotype Ontology [4], began generating disease annotations shortly thereafter using disease terms from the C branch of the Medical Subject Headings (MeSH) [5]