The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database
Open accessAbstract
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.
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The Disease Ontology data were further extended and newer ontologies such as Rat Disease Ontology and Mammalian Phenotype Ontology were added to facilitate comparison of target-disease and target-phenotype associations across multiple species.
“The Disease Ontology (DO) (8) data were further extended and newer ontologies such as Rat Disease Ontology (9) and Mammalian Phenotype Ontology (10) were added to facilitate comparison of target-disease and target-phenotype associations across multiple species.”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [9]
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TCRD and pharos 2021: mining the human proteome for disease biology
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- Authors
- Hayman, G. T., Laulederkind, S. J. F., Smith, J. R., Wang, S.-J., Petri, V., Nigam, R., Tutaj, M., De Pons, J., Dwinell, M. R., & Shimoyama, M.
- Affiliations
- Medical College of Wisconsin (US)
- Corresponding author
- Hayman, G. Thomas
- ORCID
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2016
- Volume
- 2016
- Pages
- baw034
- ISSN
- 1758-0463 (ISSN-L)
- PMC
- PMC4805243
- OpenAlex
- W2310108216
- Cited by
- 27
- References
- 23
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 1 · 2023: 2 · 2022: 3 · 2021: 1 · 2020: 2 · 2019: 3 · 2018: 3 · 2017: 4 · 2016: 5
- FWCI
- 2.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Database (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (HL-64541, HL064541, HL-094271, R01HL094271, R01HL064541)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Keywords
- Rat Genome Database, disease ontology, rat genetics, biomarkers, genetic association, therapeutic target
- MeSH terms
- Animals, Disease, Humans, Software, Species Specificity, Genome, Genetic Predisposition to Disease, Databases, Genetic, Mice, Rats, Molecular Sequence Annotation, Gene Ontology
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