The DisGeNET knowledge platform for disease genomics: 2019 update
Open accessAbstract
One of the most pressing challenges in genomic medicine is to understand the role played by genetic variation in health and disease. Thanks to the exploration of genomic variants at large scale, hundreds of thousands of disease-associated loci have been uncovered. However, the identification of variants of clinical relevance is a significant challenge that requires comprehensive interrogation of previous knowledge and linkage to new experimental results. To assist in this complex task, we created DisGeNET (http://www.disgenet.org/), a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, including the scientific literature. DisGeNET covers the full spectrum of human diseases as well as normal and abnormal traits. The current release covers more than 24 000 diseases and traits, 17 000 genes and 117 000 genomic variants. The latest developments of DisGeNET include new sources of data, novel data attributes and prioritization metrics, a redesigned web interface and recently launched APIs. Thanks to the data standardization, the combination of expert curated information with data automatically mined from the scientific literature, and a suite of tools for accessing its publicly available data, DisGeNET is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.
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GO21 is a biological knowledge graph containing genes, proteins, drugs and diseases as entities, created based on several widely used biological databases.
“GO21 is a biological knowledge graph containing genes, proteins, drugs and diseases as entities, created based on several widely used biological databases, including Gene Ontology [9], Disgenet [34], CTD [35], UMLS [36], DrugBank [37], ClassyFire [38], MeSH [39] and PPI [40].”
From Modeling Heterogeneous Hierarchies with Relation-specific Hyperbolic Cones (2021) · cites this paper as [34]
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ClinVar: improving access to variant interpretations and supporting evidence
Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Jang, W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1153 · Cited by 4,196 · cited 4× · see citing works
“Contrastingly,DisGeNETprovides189 genes,6ofthemfromCURATEDresources(inbluein Figure6A),aswellas353variants(mostofthemfrom ClinVar,anexpertcuratedresourceonclinicalgenomics).”
BackgroundInfluentialMouse Genome Database (MGD) 2019
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- Authors
- Piñero, J., Ramírez-Anguita, J. M., Saüch-Pitarch, J., Ronzano, F., Centeno, E., Sanz, F., & Furlong, L. I.
- Affiliations
- Universitat Pompeu Fabra (ES)
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
- Corresponding author
- Furlong, Laura I
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-11-04
- Volume
- 48
- Issue
- D1
- Pages
- D845-D855
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7145631
- OpenAlex
- W2983166786
- Cited by
- 2,639
- References
- 3
- Citations by year
- 2026: 191 · 2025: 447 · 2024: 535 · 2023: 511 · 2022: 474 · 2021: 344 · 2020: 133 · 2019: 3
- FWCI
- 79.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc)
- Funders
- ISCIII-FEDER (PI13/00082, PI17/00230, CPII16/00026)
- IMI-JU
- EU-FP7 (FP7/2007–2013)
- EU H2020 Programme (676559)
- Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya
- Research Programme on Biomedical Informatics
- Spanish National Bioinformatics Institute
- ISCIII
- FEDER (PT13/0001/0023)
- MINECO (MDM-2014-0370)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- DisGeNET, disease-associated genes, genetic variants, knowledge management platform, data standardization, literature mining, variant prioritization, disease characteristics, genomic medicine, data interoperability
- MeSH terms
- Disease, Humans, User-Computer Interface, Genetic Variation, Genome, Human, Internet, Genomics, Databases, Genetic, Genetic Loci, Data Mining
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