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COVID-19 Clinician Resource & Consumer Health Information

Resources for Clinicians   •   Clinician Care & Safety   •   Consumer Health   •   Latest Research & Citations   •   Data 

Resources for Clinicians

For clinical-related questions, please contact clinical.librarians@yale.edu or use our webform

Disease Facts & Guidance

Research & Guidelines

Tools

Staying Current

Clinician Care & Safety

Taking Care of Yourself at Yale

How to Use PPE

Making Ethical Decisions about Care

Consumer Health

Latest Research & Citations

The Cushing/Whitney Medical Library developed a public collection of COVID-19 citations to aid the research and clinical practice missions of Yale and the Yale New Haven Hospital.

ACCESS THE COLLECTION (public Zotero library)

Includes daily updates from PubMed, ClinicalTrials.gov, Disaster Lit, and preprints* from bioRxiv and medRxiv. 

How we're collecting citations

PubMed  Citations of journal articles (strategy includes a daily date limit, too)

covid-19[tw] OR COVID19[tw] OR COVID-19[nm] OR SARS-CoV-2[tw] OR SARS-CoV2[tw] OR severe acute respiratory syndrome coronavirus 2[nm] OR severe acute respiratory syndrome coronavirus 2[tw] OR 2019-nCoV[tw] OR 2019nCoV[tw] OR coronavirus[tw] OR coronavirus[mh] 

ClinicalTrials.gov: Clinical trials registrations

COVID-19 OR Covid19 in the “other terms” search box

Disaster Lit: Guidelines, reports, conference proceedings

COVID-19 OR COVID19 OR SARS-CoV-2 OR SARS-COV2 OR 2019-nCoV OR 2019nCoV OR coronavirus

bioRxiv and medRxiv: Preprints*

Utilizing the RSS feed listed here

*Preprints -- which are manuscripts made available prior to peer review -- support the rapid dissemination of information. However, this means that these documents should be critically appraised and monitored for updates. 

 

About the project

This project was developed at the request of Sten Vermund, Albert Ko, and other researchers at YSPH who helped determine the project scope and organization.

 

Data

For data-related questions, please contact: medicaldata@yale.edu

Click on a title below to expand the section.

Open Access Data and Computational Resources to Address COVID-19

  • NIH Data Science
    COVID-19 open-access data and computational resources are being provided by federal agencies, including NIH, public consortia, and private entities. These resources are freely available to researchers, and this page will be updated as more information becomes available.

Race and Ethnicity Data on COVID-19
> Bioinformatics Data (proteomic, virology, genomic, etc.)

 

  • NCBI Virus SARS-CoV-2 Interactive Data Dashboard
    Shows the collection location (country and US state), the date of collection, and the date of public availability for SARS-CoV-2 sequence data.

  • GenBank Nucleotide Sequences
    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. 

  • COVID-19 Genome Sequence Dataset
    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.
     
  • GenBank Protein Sequences
    Provides rapid, open, and unrestricted access to virus conceptually translated protein 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. 
     
  • Virological.org 
    A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.
     
  • Nextstrain.og 
    Genomic epidemiology of novel coronavirus (HCOV-19).
     
  • Severe acute respiratory syndrome coronavirus 2 data hub
    Search, retrieve, and analyze SARS-CoV-2 GenBank data.
     
  • Novel 2019 coronavirus genome
    The Shanghai Public Health Clinical Center & School of Public Health, in collaboration with the Central Hospital of Wuhan, Huazhong University of Science and Technology, the Wuhan Center for Disease Control and Prevention, the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control, and the University of Sydney, Sydney, Australia is releasing a coronavirus genome from a case of a respiratory disease from the Wuhan outbreak. The sequence has also been deposited on GenBank (accession MN908947 14.1k)
     
  • GEO Datasets
    Human transcriptional responses to SARS-CoV-2 infection. 
     
  • GISAID
    International database of hCoV-19 genome sequences and related clinical and epidemiological data
     
  • NCBI Virus: SARS-CoV-2 data hub
    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.
     
  • Sequence Read Archive (SRA)
    Provides rapid, open, and unrestricted access to virus nucleotide or metagenomic sequence data 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.
     
Geographically Based Data

  • NCBI Virus SARS-CoV-2 Interactive Data Dashboard
    Shows the collection location (country and US state), the date of collection, and the date of public availability for SARS-CoV-2 sequence data.

  • Johns Hopkins Dashboard
    This dashboard leverages data from a number of national and global sources and monitors the current scenario of COVID-19. Data is available in CSV format, and is available at the country, province, and date levels. GitHub repository containing the code behind the dashboard, as well as the WHO data behind these visualizations 

  • New York Times COVID-19 Dataset
    Researchers, students, and others in the Models of Infectious Disease Agent Study (MIDAS) create and use computational models to study transmission dynamics of a broad range of infectious diseases. Many MIDAS members are conducting research on COVID-19 and are contributing to an extraordinary international collection of data and information regarding the outbreak. This site has an affiliated GitHub repository for sharing of computable CSV files with data, software and metadata. Data is available to download in CSV format. 
     
  • Worldometer
    Worldometer provides global COVID-19 live statistics for a wide audience.
     
  • Connecticut COVID-19 Data Resources
    This data portal provides centralized access to data on the COVID-19 emergency and response, and supplements information available on the state's COVID-19 portal. It includes data on tests, hospitalizations, confirmed cases, deaths, and cases by demographic.
Data on Testing
Chemical Datasets 

  • CAS COVID-19 Dataset Properties
    The dataset is in SD file format (.sdf) and contains connection tables for nearly 50,000 chemical substances, along with related metadata such as CAS Registry Number® and physical properties for each substance. 

Datasets for Machine Learning and Machine Learning Efforts

  • MIDAS Online portal for COVID-19 Modeling Research
    Researchers, students, and others in the Models of Infectious Disease Agent Study (MIDAS) create and use computational models to study transmission dynamics of a broad range of infectious diseases. Many MIDAS members are conducting research on COVID-19 and are contributing to an extraordinary international collection of data and information regarding the outbreak. This site has an affiliated GitHub repository for sharing of computable CSV files with data, software and metadata. GitHub repository

  • COVID-19 Open Research Dataset (CORD-19)
    The Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 29,000 scholarly articles about COVID-19 and the coronavirus family of viruses for use by the global research community. This dataset can be analyzed with Natural Language Processing (NLP) methods.
     
Data on Response