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Covid-19: Open Data

In this page there are links to institutions, research centers, companies and groups that with their actions are realizing the purposes of Open Science: sharing data, documents, software, tools and protocols as quickly as possible. Research is open and participatory, in favor of transparency and reproducibility.

GISAID Initiative

The GISAID Initiative promotes the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19. This includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how viruses evolve and spread during epidemics and pandemics.

PROMED

The Program for Monitoring Emerging Diseases (ProMED) is a program of the International Society for Infectious Diseases (ISID). ProMED is the largest publicly-available system conducting global reporting of infectious diseases outbreaks.

ECDC - European Centre for Disease Prevention and Control

ECDC is an EU agency aimed at strengthening Europe's defences against infectious diseases.

COVIDSTAT-INFN

The National Institute of Nuclear Physics has created the COVIDSTAT-INFN Working Group and launched the website, with the aim of making available the statistical analyses of the data provided daily by the Civil Protection on the spread of the pandemic in Italy.
COVIDSTAT-INFN data, software and summary graphs are available in Open Access in the INFN digital archive. The archive for the storage of INFN scientific products (currently in pilot version) is open also to contributions from researchers from other disciplines.

COVIDier

From BiorXiv, the article of a group of researchers describing a new deep learning-based software that is enabled to classify the different genomes of Alpha coronavirus, Beta coronavirus, MERS, SARS-CoV-1, SARS-CoV-2, and bronchitis-CoV. Authors declare that COVIDier can predict how close the emerging novel genomes of SARS are to the known genomes (with accuracy 99%), and is born as an alternative to other well-known software, such as BLAST (Basic Local Alignment Search Tool - NIH).

EBSCO

In addition to collections of documents, EBSCO makes available the following resources:
COVID-19 Clinical Information
https://more.ebsco.com/EBSCO-COVID-19-ResourceCenter.html
Link to protocols.io for the import of protocols connected to Covid-19
https://www.protocols.io/groups/coronavirus-method-development-community/publications?sort=views

 

GenBank® - Genetic sequence database

Data regarding the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2, 2019-nCoV) outbreak sequences can be found in GenBank® and in the Sequence Read Archive (SRA) of NIH.
GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences, and is part of International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.
https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

Covid-19 opendata

On GitHub, a lot of examples of data processing and integration between platforms.
es: https://github.com/mcicolella/covid19-opendata

ISTAT

Mortality data.
https://www.istat.it/it/archivio/240401

Johns Hopkins University, Center for Systems Science and Engineering (JHU CSSE): Mapping 2019-nCov
Research activity on Covid-19; it is also included the development of the dashboard used by Protezione Civile Italiana
https://systems.jhu.edu/research/public-health/ncov/.

LinkedIn

In the post “The pandemic crisis of covid-19 fight with the support of open science” by Julien Hering, the author makes a list of free initiatives and projects for the solution of problems connected with Covid-19; there is also a specific section on Open Science.
https://www.linkedin.com/pulse/pandemic-crisis-covid-19-fight-support-open-science-julien-hering/

Michael Smith Genome Sciences Center (GSC)

GSC operates in genomics, proteomics, bioinformatics and molecular biology technology development, providing clinical services for BC Cancer (British Columbia, Canada) and collaborating on research projects around the world.
https://www.bcgsc.ca/

MIDAS - Models of Infectious Disease Agent Study

MIDAS is a global network of scientists and practitioners from academia, industry, government, and non-governmental agencies, who develop and use computational, statistical and mathematical models to improve the understanding of infectious disease dynamics as it relates to pathogenesis, transmission, effective control strategies, and forecasting. Many MIDAS members are conducting researches on COVID-19 and are collecting data and information about this epidemic.
https://midasnetwork.us/covid-19/

NCBI Virus

A portal that collects data on virus sequences from RefSeq, GenBank and other archives NCBI (National Library of Medicine).
https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/
Specific data on Coronavirus: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome-related%20coronavirus, %20taxid:694009/

Nextstrain

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. It provides a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Its goal is to aid epidemiological understanding and improve outbreak response.
https://nextstrain.org/
https://nextstrain.org/ncov
https://github.com/nextstrain/ncov

OpenAIRE

The OpenAIRE COVID-19 Gateway aims to aggregate COVID-19 and SARS-CoV-2 records (publications-data-software-other research outcomes), link them together and provide a single access point for their discovery and navigation.
https://www.openaire.eu/openaire-covid-19-gateway
Technical information: https://www.openaire.eu/openaire-activities-for-covid-19

EU Open Data Portal

COVID-19 Coronavirus data.
https://data.europa.eu/euodp/en/data/dataset/covid-19-coronavirus-data

Protezione Civile Italia

COVID-19 in Italy - Situation monitoring.
https://github.com/pcm-dpc/COVID-19
https://opendatadpc.maps.arcgis.com/apps/opsdashboard/index.html#/b0c68bce2cce478eaac82fe38d4138b1

re3data.org (International registry of research data repositories)

200 archives of data that respond to research by subject: Microbiology, Virology and Immunology.
https://re3data.org/search?subjects[]=204%20Microbiology,%20Virology%20and%20Immunology

Semantic Scholar: COVID-19 Open Research Dataset (CORD-19)

The Semantic Scholar team at the Allen Institute for AI has partnered with leading research groups to provide CORD-19, a free resource of more than 57,000 scholarly articles about the novel coronavirus for use by the global research community.
https://www.semanticscholar.org/

SIS - Società Italiana di Statistica

On the page on Covid-19, works are classified temporally, in order to show the evolution of research in recent weeks, and with respect to their typology, simplified into three large groups: "Web, Apps, Interviews and Videos", "Numbers, Graphs and Disclosure Articles" and "Statistical Models and Forecasts".
http://www.sis-statistica.it/ita/56/index.php?p=9980

SPARC Europe: COVID-19 and Open Science

The non-profit organization SPARC Europe (the Scholarly Publishing and Academic Resources Coalition) collected open resources, created by research communities in different areas:

The University of Cambridge, Institute for Manufacturing: Manufacturing and COVID-19: How you or your organisation could help

Specific information for UK companies, but also how researchers can help to improve the situation in different sectors.
https://www.ifm.eng.cam.ac.uk/manufacturing-and-covid-19-ways-your-company-could-help/? fbclid=IwAR0Mr6oXFI7io6qoo8TA74xNaGVxmyWf46Gl5fUhnGBgXOwROdH1nsi49vk

Worldometer

Worldometer is run by an international team of developers, researchers, and volunteers with the goal of making world statistics available to a wide audience around the world. Worldometer is a provider of global COVID-19 statistics for many caring people around the world. Its data is also trusted and used by the UK Government, Johns Hopkins CSSE, Financial Times, The New York Times, Business Insider, BBC, and many others.
https://www.worldometers.info/
https://www.worldometers.info/coronavirus/

Zenodo

On the homepage of the repository, created to host the results of research funded by the European Union, highlighting outputs that may be relevant to the Coronavirus Disease (COVID-19) or the SARS-CoV-2. Scientists are encouraged to upload their outcomes in this collection to facilitate sharing and discovery of information.
https://zenodo.org/