Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.
Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and sjwang@mcw.edu.
Shur-Jen
SJ
Wang
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Stanley J F
SJ
Laulederkind
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
G Thomas
GT
Hayman
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Victoria
V
Petri
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Jennifer R
JR
Smith
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Marek
M
Tutaj
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Rajni
R
Nigam
Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin.
Melinda R
MR
Dwinell
Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and.
Mary
M
Shimoyama
D000818:Animals; D002318:Cardiovascular Diseases / Q000235:genetics*; D030541:Databases, Genetic; D063990:Gene Ontology; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods; D040641:Quantitative Trait Loci / Q000235:genetics; D051381:Rats
animal models of human disease; cardiovascular disease; functional genomics; model organism database