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New COVID-19 Data Tools Coming Online to Help Tackle Pandemic

The UC Davis COVID-19 web app allows users to hover over states with their mouse to find information on cases, testing and deaths over time. Credit: Christopher Barker / UC Davis

Thousands of researchers across the globe have been working tirelessly to study the new coronavirus, generating enormous amounts of information. Here we highlight some recently launched or updated data tools and dashboards.

EMBL-EBI Launches COVID-19 Data Portal

Today, the European Molecular Biology Laboraty – European Bioinformatics Institute (EMBL-EBI) and partners launched the COVID-19 Data Portal, which enables sharing and data analysis on SARS-CoV-2. The initiative aims to facilitate international collaboration to accelerate scientific discovery, monitor the pandemic and help develop treatments and a vaccine for the new coronavirus.

Currently, the COVID-19 Data Portal includes datasets from the following EMBL-EBI data resources:

  • European Nucleotide Archive (ENA)
  • UniProt
  • Protein Data Bank in Europe (PDBe)
  • Electron Microscopy Data Bank (EMDB)
  • Expression Atlas
  • Europe PMC

These resources cover a wide range of data types including genomic, protein and microscopy data, as well as scientific literature.

In the coming weeks, the portal will also include genomic data from the outbreak and a dedicated Cohort Browser for searching clinical and epidemiological data. The COVID-19 Data Portal is the entry point to the wider European COVID-19 Data Platform initiative, which involves the creation of multiple SARS-CoV-2 Data Hubs. These hubs are currently being built and, once ready, will organise the flow of sequence data from the outbreak and provide comprehensive open data sharing for the European and global research communities accessible through the Data Portal.

Both the European COVID-19 Data Portal and the SARS-CoV-2 Data Hubs will use already established EMBL-EBI data infrastructures, including the Pathogen Portal and the European Nucleotide Archive (ENA). The latter is part of the COMPARE Data Hubs, which provide pathogen-focused data sharing and analysis tools, and will be connected to the European Open Science Cloud (EOSC).

Current collaborators working with EMBL-EBI to provide platform infrastructure include

The European COVID-19 Data Platform is a partnership between EMBL-EBI, ELIXIR and the European Commission. Current collaborators working with EMBL-EBI to provide the Platform infrastructure include: Erasmus Medical Centre, Technical University of Denmark, Eotvos Lorand University, National Institute for Public Health and the Environment, and the Universitaetsklinikum Heidelberg.

WHO Updates COVID-19 Dashboard with Better Data Visualization

The World Health Organization on Apr. 14 announced the release of a substantial update to its COVID-19 information dashboard. It allows access to current and reliable data on COVID-19 cases submitted directly to WHO by countries. The upgrade was developed and supported by the WHO Technology for COVID-19 initiative, a pro-bono collaboration of technology companies, brought together by WHO to fight the pandemic.

A prominent new feature is the release of the mobile-friendly version. In addition, the dashboard has a clean and modern interface and several data visualization tools to better grasp the current status of COVID-19 as the situation unfolds.

Users will now be able to view:

  • New and confirmed cases and deaths globally with daily statistics.
  • Country-specific info by clicking on any country on the interactive map.
  • Interactive chart showing reported cases by WHO region including daily and cumulative statistics.
  • Confirmed cases and deaths, and changes over time in a specific country, region, or territory, on the interactive chart.
  • A new explorer tab designed to provide complex datasets for easy access and use. It allows users to select variables across three axis, which helps see correlations and relationships that can provide insights into COVID-19 and how communities are responding to it.

UC Davis Researchers Launch COVID-19 Web Application and Data Visualization Tool

Researchers at the University of California, Davis, have developed a new web application that allows users to track COVID-19 cases and testing across the globe. The app offers a simple, intuitive way for users to track COVID-19 data at the country, state and county level.

The website app features interactive maps and graphs. It also includes a web address that tracks the user’s current view so it can be bookmarked and shared with others. The website uses open, publicly available data from the COVID Tracking Project, Johns Hopkins University and the New York Times.

Christopher Barker, an associate professor of epidemiology with the UC Davis School of Veterinary Medicine wrote the code and led the project. Barker teamed up with CalSurv programmer Jody Simpson, who developed interactive maps and streamlined the web application. CalSurv is a surveillance system that helps mosquito control agencies and public health officials monitor and respond to potential outbreaks of mosquito-borne diseases by mapping the insects that can carry deadly viruses. Although the virus causing COVID-19 is not transmitted by mosquitoes, the team was able to leverage resources at UC Davis and CalSurv to help during this emergency.

Regenstrief Institute Data Dashboard Launched for State of Indiana COVID-19 Tracking and Response

Regenstrief Institute and partners have developed a data dashboard to support COVID-19 tracking and response in the state of Indiana. The dashboard augments the state’s existing information by providing data on patients’ course of care through healthcare systems in Indiana.

Data on hospitalizations and intensive care unit stays gives state leaders a more comprehensive picture of the COVID-19 pandemic and its impact on Hoosiers and the healthcare system, as well as perspective to anticipate emerging hot spots and surges.

Partners in this effort are the Indiana State Department of Health (ISDH), Indiana Family Social Services Administration (FSSA), Indiana Management Performance Hub (MPH), Regenstrief Institute, Indiana Health Information Exchange (IHIE), Indiana University Richard M. Fairbanks School of Public Health and Indiana University School of Medicine.

The partnership makes possible access to data from the majority of Indiana’s health systems and laboratories. Access to these data during this emergency, and to the experts who help with interpretation, allows public health professionals to identify significant patterns and predict how to best respond as COVID-19 cases spread across the state.

Philips Launches National Portal for Digital Exchange of COVID-19 Patient Data in the Netherlands

In cooperation with Erasmus Medical Center (Rotterdam, The Netherlands), Jeroen Bosch Hospital (‘s-Hertogenbosch, the Netherlands) and the Netherlands Ministry of Health, Welfare and Sport (VWS), Philips has created an online portal that allows Dutch hospitals to seamlessly share COVID-19 patient information with one another.

In the fight against an escalating pandemic like COVID-19, being able to share patient data between hospitals at the ‘touch of a button’ is vitally important to optimizing the use of healthcare resources. It can, for example, assist in the seamless transfer of infected patients between hospitals to avoid local overload in critical care units. Since its launch on March 28, 95% of Dutch hospitals have already been connected to the portal for digital exchange of COVID-19 patient data.

The new COVID-19 portal, which is available to all Dutch hospitals, is not linked directly to an individual hospital’s EPD (Electronic Patient Dossier), PACS (Picture Archiving and Communication System) or pathology department systems. Instead, specific information, such as a patient’s radiology images, reports and patient summary is shared via the portal. The information is instantly available to a receiving hospital provided the originating hospital and the patient have given their explicit consent. The safety of medical data exchange remains of the utmost importance, even in times of crisis. As a result, the portal fully complies with the ISO27001 information security standard and the Dutch NEN7510 standard, which is specifically designed for information handling in the healthcare sector.

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