Data Sources

The Research Data Alliance’s (RDA) COVID-19 Recommendations and Guidelines on Data Sharing contains information on various data repositories and data sources that Canadian health researchers can use to securely store their own datasets and/or access publicly available COVID-19 datasets. This document summarizes the data resources from the following disciplinary areas:

• Clinical Data
• Omics Data
• Epidemiology Data

Clinical data

Databases of Publicly and Privately Funded Clinical Studies

The following databases and registers provide information on registered clinical trials. In some cases, these platforms are specifically tracking COVID-19 related clinical trials.

• The WHO International Clinical Trials Registry Platform (ICTRP)
• The United States National Library of Medicine’s clinical trials register; ClinicalTrials.gov
• The European Union Clinical Trials Register
• Cytel’s COVID-19 clinical trials trackers
• Cell Trials Data tracker of COVID-19 treatments clinical trials
• Trials Tracker’s COVID-19 clinical trials tracking tool
• TrialScope’s Coronavirus Clinical Trials
• Cochrane Central Register of Controlled Trials (CENTRAL)
• European Clinical Research Infrastructure Network COVID-19 Trials Registries summary
• National Institute for Health Research COVID-19 studies registry
• Italian Medicines Agency COVID-19 clinical trials registry

Health Care and Clinical Data

The following databases and platforms include other relevant health care and clinical datasets:

• tranSMART Foundation’s  Consortium for Clinical Characterization of Covid19 by EHR (4CE)
• Health System Response Monitor
• ISARIC COVID-19 Clinical Research Resources
• ECDC COVID-19 Pandemic dashboard
• Immune Epitome Database and Analysis Resources
• ImmPort Shared Data
• ImmuneSpace

Omics Data

Virus Genomics DNA

Raw virus sequence data can be stored in and/or retrieved from one of the International Nucleotide Sequence Database Collaboration (INSDC) archives:

• DNA Data Bank of Japan (DDBJ) Sequence Read Archive (SRA)
• ENA (European Nucleotide Archive at EMBL-EBI)
• NCBI SRA

Assembled and annotated genomes can be stored in and/or retrieved from one or more of these archives:

• NCBI GenBank accessible through NCBI Virus
• DDBJ Annotated/Assembled Sequences
• ENA
• NCBI Virus

Host Genomics DNA

Gene expression data can be stored in and/or retrieved from the following repositories:

Transcriptomics of human subjects (requiring authorised access):

• Database of Genotypes and Phenotypes (dbGaP)
• European Genome-Phenome Archive (EGA)
• Japanese Genotype-phenotype Archive (JGA)

Transcriptomics from cell lines/animals:

• ArrayExpress
• Gene Expression Omnibus
• Genomic Expression Archive
• DDBJ Sequence Read Archive (DRA)
• European Nucleotide Archive
• NCBI Sequence Read Archive (SRA)

Microarray-based gene expression data:

• ArrayExpress
• Gene Expression Omnibus
• Genomic Expression Archive
  • Data on the originating sample can be retrieved from/will automatically be deposited to the corresponding sample archive:
    • DDBJ BioSample
    • EBI BioSamples
    • NCBI BioSample

Genome-Wide Association Studies (GWAS):

• GWAS Catalog
• EGA
• GWAS Central

Adaptive Immune Receptor Repertoire Sequencing (AIRR-seq) data:

• AIRR-seq specific repositories that are part of the AIRR Data Commons, (e.g. the iReceptor Public Archive or VDJServer)

Structural Data

Protein structural data can be stored in and/or retrieved from the following repositories:

• wwPDB: Worldwide Protein Data Bank  
  • for Europe: EBI PDBe and the Electron Microscopy Data Bank EMDB
  • for the USA: RCSB PDB
  • for Japan :PDBj

Drug Discovery and Therapeutics

Drug discover and therapeutics data can be stored in and/or retrieved from the following repositories:

• Global Health Drug Discovery Institute of China (GHDDI) Info Sharing Portal
• ReFRAME compound library
• Drug Discovery Cloud Computing System on Alibaba Cloud
• COVID-19 Molecular Structure and Therapeutics Hub

Proteomics data

Proteomics data can be stored in and/or retrieved from the following platforms:

For shotgun proteomics data:

• PRIDE
• MassIVE
• jPOST (Japan Proteome Standard Repository)
• iProX (integrated Proteome resources)

For targeted proteomics data:

• PASSEL
• Panorama

For repossessed results:

• PeptideAtlas
• MassIVE

Metabolomics Data

Metabolomics data can be stored in and/or retrieved from the following platforms:

• MetaboLights (in Europe)
• Metabolomics Workbench (in the USA)
• Massbank (in Japan)

Lipidomics Data

Lipidomics data can be stored in and/or retrieved from the following platform:

• MetaboLights

Epidemiology Data

Population-Level Data Sources

• Allen Institute for AI COVID-19 Open Research Dataset (CORD-19)
• Apple Inc. COVID-19-Mobility Trends Reports
• European Centre for Disease Control Geographic distribution of COVID-19 cases worldwide
• European Centre for Disease Control The European Surveillance System (TESSy)
• Institute for Health Metrics and Evaluation (IHME) Global Health Data Exchange (GHDx)
• Johns Hopkins University COVID19 dataset
• Oxford University COVID19 dataset
• The Atlantic COVID Tracking Project
• The New York Times Covid-19 Data in the United States
• The White House COVID-19 Open Research Dataset Challenge (CORD-19)
• U.S. Centre for Disease Control Cases of COVID19 in the U.S.
• University of Washington Be Outbreak Prepared
• World Bank Understanding the Coronavirus (COVID-19) pandemic through data
• World Health Organization (WHO) Novel Coronavirus (2019-nCoV) situation reports
• Worldometer COVID19 data

Date modified:

2020-11-24