Open-Access Data and Computational Resources to Address COVID-19

The Broad Terra cloud workspace for best practices with COVID-19 genomics data

• Raw COVID-19 sequencing data from the NCBI Sequence Read Archive (SRA)
• Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics
• Jupyter Notebook produces quality control plots for workflow output

The CDC is providing a variety of data on COVID-19 in the United States.

View listed clinical studies related to the coronavirus disease (COVID-19). Studies are submitted in a structured format directly by the sponsors and investigators conducting the studies. Submitted study information is generally posted on ClinicalTrials.gov within 2 days after initial submission and site content is updated daily. Full website content is also available through the API.

Freely available dataset of 45,000 scholarly articles, including over 33,000 with full text, on COVID-19, SARS-CoV-2, and related coronaviruses. This machine-readable resource is provided to enable the application of natural language processing and other AI techniques.

See the CORD-19 Challenge, developed in partnership with Kaggle. Amazon Web Services has a CORD-19 search website.

Read the accompanying call to action from the White House Office of Science & Technology Policy and learn more about the creation of CORD-19.

The COVID-DPR provides whole slide images of histopathologic samples relevant to COVID-19, including biopsy samples and autopsy specimens. The current focus of the repository includes tissue from the lungs, heart, liver, and kidney. The repository contains examples of H1N1, SARS, and MERS for comparison. 

A centralized sequence repository for all strains of novel corona virus (SARS-CoV-2) submitted to the National Center for Biotechnology Information (NCBI). Included are both the original sequences submitted by the principal investigator as well as SRA-processed sequences that require the SRA Toolkit for analysis.

The European Bioinformatics Institute (EMBL-EBI), part of the European Molecular Biology Laboratory, has a COVID-19 Data Portal to facilitate data sharing and analysis and ultimately contribute to the European COVID-19 Data Platform. EMBL-EBI is part of the International Nucleotide Sequence Database Collaboration (INSDC); the National Center for Biotechnology Information (NCBI) is the U.S. partner of the INSDC.

Provides rapid, open, and unrestricted access to virus nucleotide sequences and is the repository being recommended by NIAID and CDC for investigator and public health submissions. Due to the scale of data indexing, there may be a delay before new submissions are indexed and retrievable with a term-based query. 

Human transcriptional responses to SARS-CoV-2 infection

GCP is hosting a repository of public datasets and offering free hosting and queries of COVID datasets. Learn more about the free hosting and queries of COVID datasets.

NLM curated literature hub for COVID-19

The National COVID Cohort Collaborative, N3C is one of the largest repositories of longitudinal COVID-19 real-world deidentified linked clinical, CMS, Mortality and Viral Variants data in an open science secure collaboration analytics environment.  More information about N3C and how to get access can be found at https://covid.cd2h.org/onboarding

SARS-CoV-2 focused content from NCBI Virus, including links to related resources. Search, filter, and download the most up-to-date nucleotide and protein sequences from GenBank and RefSeq (taxid 2697049). Generate multiple sequence alignments and phylogenetic trees for sequences of interest. Provides one-click access to the Betacoronavirus BLAST database and relevant literature in PubMed.

The Inter-university Consortium for Political and Social Research (ICPSR) has launched a new repository of data examining the impact of the novel coronavirus global pandemic. This repository is a free, self-publishing option for researchers to share COVID-19 related data.

Small molecule compounds, bioactivity data, biological targets, bioassays, chemical substances, patents, and pathways

The RCSB Protein Data Bank is offering access to COVID-19 related PDB structures for research and related images and videos for education. 

A database of carefully validated SARS-CoV-2 protein structures, including many structural models which have been re-refined or re-processed. The resource is being updated weekly by Minor Lab at the University of Virginia as new SARS-CoV-2 structures are being deposited to the Protein Data Bank.