Arrow Left COVID-19 related data initiatives

COVID working groups, networks & initiatives

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    Research Data Alliance (RDA) COVID-19 Working Group

    Leveraging the global RDA data community to support COVID-19 by defining detailed guidelines on data sharing and re-use under the present COVID-19 circumstances to help researchers follow best practices to maximize the efficiency of their work.

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    GO FAIR-VODAN (Virus Outbreak Data Network)

    Health-RI is member of the rapid response VODAN implementation network. It will FAIRify COVID-19 data. Making it Findable, Accessible, Interoperable and Reusable. As a next step, localized FAIR data repositories will be developed. There, scientists can access the data with their research questions, using the Personal Health Train principle.   

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    ELIXIR support for SARS-CoV-2 research

    As the ESFRI Research Infrastructure for life science data, ELIXIR Nodes provide a range of services that can be used by researchers and consortia working on SARS-CoV-2 research.

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    OHDSI (Observational Health Data Sciences and Informatic)

    Updates on activities from the OHDSI community, including the COVID-19 virtual study-a-thon hosted in March, can be found here.

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    Wikidata: WikiProject COVID-19

    Wikidata:WikiProject COVID-19 is an international project where various research from the Netherlands participate in, among which from Maastricht University and Wageningen University. It aims at collecting and making available knowledge around SARS-CoV-2, COVID-19 and related topics. People interested in the topic are invited to visit the webpage, get a Wikidata account, and sign up.

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    COVID-19 Disease Map

    An international initiative to build disease maps, molecular biological pathways, and pathway-based models for virus-host interactions and affected processes. The initiative spans many groups including the WikiPathways and Reactome teams, the DisGeNET team, FAIRdom, and Cell Designer and is led by the MINERVA disease map team in Luxembourg.

    Contact the Maastricht based WikiPathways team via wikipathways.org or Chris Evelo.

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    Stichting Corona in Kaart Brengen (available in Dutch only)

    The ‘Stichting Corona in Kaart Brengen’ collects data reported by general practitioners and the public in order to provide better insight into the disease distribution of COVID-19 (available in Dutch only)

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    Elixir support for COVID-19 Research

    ELIXIR provides a range of services that you can use for studying the SARS-CoV-2 coronavirus and the COVID-19 disease. Furthermore an ELIXIR COVID-19 slack workspace has been set up here.

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    COVID-19 virtual biohackathon April 5-11th 2020

    The goal of COVID-19-BH20 is to create a cohesive effort and work on tooling for COVID-19 analysis. The biohackathon will lead to more readily accessible data, protocols, detection kits, protein predictions etc.

    We will also push for policy change where it comes to non-public or hard to access data because we are facing such challenges!

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    SSH COVID-19 Portal

    The Social Science and Humanities (SSH) COVID-19 portal aims to consolidate and organize the SSH expertise across the Dutch universities in a publicly available national portal, ensuring fast and direct access to academic experts.

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    ZAPI COVID-19

    The Zoonoses Anticipation and Preparedness Initiative (ZAPI) is laying the groundwork for the response to zoonotic disease outbreaks like COVID-19.

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    EOSC-life Workflow HUB

    The EOSC-Life Workflow Hub is in development to become a registry of life science workflows from multiple underlying repositories for many workflow systems. EOSC-Life participants include large EU-wide European Research Infrastructures like ELIXIR, but the Workflow Hub is developed as a separate open source community project.

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    EATRIS dedicated webpage COVID-services

    The European Research Infrastructure for Translational Medicine (EATRIS) is collecting information on all relevant activities and special services being offered by EATRIS members in response to COVID-19. EATRIS has published a dedicated webpage summarizing services and expertise that can be offered and links to other relevant initiatives. The page is being regularly updated. EATRIS also joined forces with BBMRI and ECRIN to offer a joint response service.

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    The COVID-19 Host Genetics Initiative

    The COVID-19 host genetics initiative brings together the human genetics community to generate, share and analyze data to learn the genetic determinants of COVID-19 susceptibility, severity and outcomes. 

    This initiative includes several Duch and European biobanks.

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    COVID-19 - Fertility and Pregnancy

    Gathering important resources, guidance and advice statements from international organizations and societies related to COVID-19, fertility and pregnancy.

    Also creating a collection of published data on perinatel outcomes in women with confirmed COVID-19

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    The European Research Infrastructure (ESFRI) COVID-19 services

    The European Research Infrastructure (ESFRI) is helping the scientific community by aggregating information about dedicated services offered by Research Infrastructures and communicating all relevant actions as broadly as possible. More information on the initiative can be found here.

    Contact: covid-19@esfri.eu

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    ERF-AISBL overview of research infrastructure and COVID-19 research

    The Association of European-Level Research Infrastructure Facilities (ERF-AISL) are collecting relevant information about COVID-19 initiatives on a dedicated website.This work is carried out by CERIC in the frame of ACCELERATE, funded by the European Union Framework Programme for Research and Innovation Horizon 2020, under grant agreement 731112.

    For more information, please contact: useroffice@ceric-eric.eu

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    Open-Source-COVID-19

    A global collection of Open Source projects during COVID-19. The goal of this navigation site is to help people access data, contribute to the projects, and trigger new ideas.

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    COVID-19 terra workspace

    Dedicated workspace developed by Dr. Danny Park and colleagues at the Broad Institute, which contains best-practices workflows for taking sequencer output data (either FASTQ or SRA), assembling viral genomes, and running the results against the Kraken taxonomic classifier.

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    Kaggle COVID-19 contributions

    The goal of this page is to bring together the most useful contributions from the Kaggle community's COVID-19 work into a single place. It is organized into literature review, tools and datasets.

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    Health Tech COVID-19

    The Health Tech Responds to COVID-19 website is committed to providing current information and resources on the digital health ecosystem’s response to COVID-19.

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    Smart Reporting COVID-19

    Smart reporting is offering a free COVID-19 (Coronavirus Disease 2019) structured reporting template to radiologists.

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    EMBL-EBI COVID-19  database

    The European Bioinformatics Institute (EMBL - EBI) is gathering and sharing data resources as they become available.  Researchers can now see a breakdown of relevant data hosted at EMBL-EBI on the Pathogen Portal. This includes sequences of outbreak isolates and records relating to coronavirus biology.

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    COVID-19 Open Research Dataset (CORD-19)

    In response to the COVID-19 pandemic, 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 45,000 scholarly articles, including over 33,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

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    Galaxy Project SARS-CoV-2

    Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures.

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    Research Data Alliance (RDA) COVID-19 Working Group

    Leveraging the global RDA data community to support COVID-19 by defining detailed guidelines on data sharing and re-use under the present COVID-19 circumstances to help researchers follow best practices to maximize the efficiency of their work.

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    COVID-19 and AI: A Virtual Conference (available in Dutch only)

    COVID-19 and AI: A Virtual Conference gaat in op de huidige pandemie. Gesponsord door het Stanford Institute for Human-Centered Artificial Intelligence (HAI) zal dit webinar met experts betrekking hebben op kennis van het virus en de impact op de samenleving ervan beter te begrijpen.

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    Virtual Hackathon CoronaHack AI vs. COVID-19

    A virtual hackathon bringing together Biomedical and data scientists to explore ways to combat CoronaVirus. Designed to accelerate approaches to monitoring, diagnosing and controlling the CoronaVirus. 

    This event took place April 14th - April 19th.

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    Elsevier: identify COVID-19 research collaborations & publications

    Identify potential research experts or collaborators in areas related to the coronavirus epidemic across basic science, translational research, or clinical practice. 

    From our Pure portal platform, we have gathered all researchers who have been publishing research on the topic of COVID-19. You will find more than 3600 researchers from 1835 institutes who are currently working on COVID-19 and have already published over 6500 articles.

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    EOSC-Life: available resources from Life Sciences Research Infrastructures

    To support the global effort to tackle the coronavirus pandemic, Life Sciences Research Infrastructures (LS RIs) are prioritising COVID-19 research, as detailed in the actions below. The benefits of using established Research Infrastructures are clear: they are ready and able to provide expert advice and resources to meet a variety of research needs. Although in-person visits to facilities may be restricted, many infrastructure services are still available via remote access and, where possible, the cost of access will be minimised or waived.

    Please follow the links provided by each LS RI for more information and to request access to their services.

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    Systems Biology Amsterdam (SysBA) COVID-19

    1. Model of the COVID-19 epidemics showing that most governments' policies are too-late-too-little, i.e. require change:

    https://medrxiv.org/cgi/content/short/2020.03.29.20045039v1

    2. Model of the cytokine storm elicited by COVID-19 in patients which could be used as predictor of ICU necessity and therapies

    Request for collaboration: Looking for critical forums on COVID-19 epidemic.

    Contact: Hans V. Westerhoff

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    OLVG Corona Check App

    Large scale, real-time and longitudinal tele-monitoring of COVID-19 in the general population.

    English publication

    OLVG news item (available in Dutch only)

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    Living and Working in Coronavirus Times Project and Survey

    WageIndicator Foundation is surveying / interviewing people in 140 countries to explore the COVID-19 effect on jobs, workload, working from home, job losses, and working conditions. Control variables relate to occupation, firm size, employment contract, household composition, life satisfaction, and Corona-cases in respondent’s networks at home and at the workplace. The surveys are in the national language(s). Given that a random sampled global survey is beyond budget and impossible in a brief time frame, the survey is a volunteer web-survey with snowball recruiting through many frequently visited websites with high quality search engine optimization and through social media. The results are shown in maps and graphs, updated on a daily basis. Researchers from CLARIN ERIC, SSHOC Project and the University of Amsterdam are cooperating in the project. In addition, WageIndicator collects for a few countries the COVID-19 response of companies, and has developed a data collection regarding country-level measures related to work and employment.

    The surveys are accessible here (select a country and a language in case of multilingual countries):

    The codebook is available here.

    Contact: Kea Tijdens

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    Global Alliance for Genomics & Health (GA4GH) responds to COVID-19

    Learn more about how members of the GA4GH community are contributing to the effort to fight the pandemic through the power of data sharing.

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    COVID-19 Datacoalitie (available in Dutch only)

     

    Medworq, Stizon, ExpertDoc/NHGDoc, PharmaPartners, Stichting Health Base en Andersson Elffers Felix vormen samen een brede coalitie met expertise op vele kennisgebieden, van data-infrastructuur tot data-analyse, en van veiligheid tot remote-accessoplossingen. 

    Vanuit onze gezamenlijke expertises bieden we:

    • Een veilige remote-acces-omgeving voor wetenschappelijk onderzoek.
    • Een realtime koppeling met HIS voor het ophalen van data en en het leveren van beslisondersteunende informatie.
    • ISO-gecertificeerd systeem dat voldoet aan alle privacywetgeving.
    • Groot netwerk onder huisartsen, specialisten en wetenschappers.

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    EGI COVID-19 support initiatives

    The EGI federation is the largest distributed computing infrastructure for research, and brings together hundreds of data centres worldwide and also includes the largest community cloud federation in Europe with tends of research cloud providers across most of the European countries offering IaaS cloud and storage services. As the coronavirus, and its related consequences, spread across the globe, with this call EGI is committing resources and technical support to accelerate progress on COVID-19 research.

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    OHDSI Cancer and Covid-19

    The international Observational Health Data Sciences and Informatics (OHDSI) community aims to make date health data available for research by using a common data model. Using this data model, studies can be defined, replicated and validated on datasets adhering to these data standards.

    Korean and American participants (hospitals and insurance claims databases) in OHDSI are making very recent data available to address urgent questions involving COVID-19. The Oncology work group is developing a series of analyses to understand the impact of Covid-19 on cancer patients undergoing active treatment, as well as on cancer survivors.

    Contact: Gijs Geleijnse or via LinkedIn

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    COVID Milk

    To quantify antibody concentration and efficacy in breast milk of COVID +, lactating women before and after pasteurization.

    Contact: Dutch National Human Milk Bank, Amsterdam UMC; h.vangoudoever@amsterdamumc.nl; covid.milk@amsterdamumc.nl

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    Pathophysiology of COVID19: extent of organ involvement and mechanisms of disease

    To improve understanding of COVID19 and to identify new targets for treatment, more insight in pathophysiology is urgently needed. Whole body autopsy is an important tool to study disease, and has played a key role in the understanding of disease mechanisms. This study will be done in an autopsy cohort initiated by the Amsterdam UMC. The aim is to answer the following three questions:

    1. What is the distribution of SARS-CoV2 and its entry receptor ACE? 2. What is the effect of SARS-CoV2 in different organ systems?
    2. What is the effect of SARS-CoV2 in different organ systems?
    3. What are the characteristics of the immune response in patients that died due to COVID19?

    Contact: m.bugiani@amsterdamumc.nl, eva.roos@amsterdamumc.nl, b.schurink@amsterdamumc.nl

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    ErasmusMC offers free of charge genotyping of proven COVID-19 cases

    Worldwide there are ongoing efforts by the genetics community to help understand host genetics in relation to the SARS-CoV2 virus, and COVID-19. As one of our customers you can play an important role in this effort by genotyping your samples and contributing your data to a large analysis.

    To facilitate this, Illumina and Thermofisher Scientific have kindly offered a discounted price for the Global Screening Array or Axiom Precision Medicine Array. Erasmus MC, and HuGe-F in particular, also feel the responsibility to help scientific progress in this field. We therefore offer free of charge genotyping of proven COVID-19 cases and discounted genotyping of COVID-19 related cases. The data of those samples will be returned to you for use in your own and in large-scale-scientific research.

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    WHO COVID-19 Database

    WHO is gathering the latest international multilingual scientific findings and knowledge on COVID-19. The global literature cited in the WHO COVID-19 database is updated daily (Monday through Friday) from searches of bibliographic databases, hand searching, and the addition of other expert-referred scientific articles. This database represents a comprehensive multilingual source of current literature on the topic. While it may not be exhaustive, new research is added regularly.

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    Minder IC-opnames door bloeddrukmedicijnen? (available in Dutch only)

    Met steun van de Hartstichting is een groot onderzoek gestart naar valsartan. Dit veelgebruikte medicijn tegen hoge bloeddruk kan mogelijk ernstige klachten bij covid-19 voorkomen.

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