Data tools, data curation & services

Castor is offering its platform for free for COVID-19 studies (to date more than 60 studies are making use of this). 

Contact: covid19@castoredc.com

Check our Health-RI tips for COVID-19 research

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If you are doing research on COVID-19, you can apply for accelerated access to the national high performance computing and data infrastructure for research. Further support initiatives from SURF for COVID-19 are outlined here.

Contact: helpdesk@surfsara.nl (please include COVID-19 Fast Track) in the subject line.

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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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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 Dutch and European biobanks.

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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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Health-RI is inventorying existing COVID-19 related data collections, images and samples. As a next step, all relevant data sets will be labeled as ‘COVID-19’ in BBMRI.nl catalogue. In time, new data sets will be added and enhanced with information on what specifics make these data or samples relevant. 

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Podium, a ‘webshop’ system will give access to data collections, efficiently and safely. It can be used by researchers and organizations alike to manage and facilitate the research request workflow of data/samples/images. 

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the Personal Health Train principles to make optimal use of the distributed data. Health-RI also offers expertise on more traditional methods of connecting data. 

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ealth-RI hosts and supports a solid pipeline for managing large quantities of radiology images, pseudonymisation of DICOM images and making these available for research (CTP and XNAT). 

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Answers to many ELSI related questions can be found on the ELSI Servicedesk. Together with the ELSI Servicedesk and several partners, Health-RI is working on urgent needs that have arisen in the context of COVID-19. For example: how do we organize patients’ consent or objection in a fast, legally and ethically sound way when collecting data or samples for COVID-19 research. Furthermore, guidelines and formats for the access and use of collected data and samples are being developed. As new guidelines or procedures become available, these will be published on the ELSI Servicedesk. To ensure that we will address the right needs, we welcome your experiences, hurdles and issues. Please email to info@health-ri.nl (put “ELSI” in the subject line).

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

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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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Collaborative project for curation biological processes involved in the COVID-19 disease after SARS-Cov-2 infection.

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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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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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The i2b2 community is working to combine national and international analyses of the COVID-19 affliction on its patients. Dr. Zak Kohane and several members of its Board of Directors have launched an urgent initiative with organizations around the world to rapidly collect aggregated data on hospitalized patients that are COVID-19 positive. The goal of this effort is to quickly publish the initial results.

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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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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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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.

Furthermore, in April,l EMBL’s European Bioinformatics Institute (EMBL-EBI) and partners launched the COVID-19 Data Portal, which enables the sharing and analysis of data related to the new coronavirus, 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

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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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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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Imaging COVID-19 AI initiative is a multicenter European project to enhance computed tomography (CT) in the diagnosis of COVID-19 by using artificial intelligence.

For more information on NL involvement, please contact partners from ETZ Tilburg & NKI-AVL Amsterdam.

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Het MUMC wil een algoritme gebruiken dat snel kan bepalen of iemand is besmet met het coronavirus en wat het ziekteverloop kan zijn.

Het algoritme blijft in Chinese handen maar scans gaan naar een Japans serverpark, zodat ze buiten het gezag van de Chinese overheid blijven.

De invoering wacht nog op goedkeuring van Inspectie voor de Gezondheidszorg en Raad van Bestuur van het MUMC, die de Europese regels voor privacybescherming wil toetsen.

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Element AI offers a free platform to assist clinical researchers, scientific researchers, public health authorities and frontline workers that are working towards finding a cure to mitigate this pandemic. Element AI have developed a platform that connects structured and unstructured datasets that enables users to query using natural language.

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Using our renowned research platform EmmaResearch, we introduced on March 30, a COVID-19 symptoms clinical registration app, called Coronaz, to assist elderly and chronically ill patients to recognize early symptoms of Corona. People fill in a daily symptom list and are warned if they reach a yellow/orange/red zone with instructions. We supply the research data open source to interested research parties. The data will also be used by a spin-off of Radboud University AI dept. to look for causal relationships between illness and symptoms.

This initiative is also looking for collaborations with hospitals and research institutes with the latest knowledge on COVID-19 symptoms (positive, false positive and false negative) and methodologies for designing optimal questionnaire structures.

Contact details: 

Medicine Men BV
Ir. Oscar van Dijk
oscar@medicinemen.nl
+31 85 1307020

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Evidencio offers a cloud-based platform to easily create, distribute, maintain, and evaluate medical guidelines regarding the diagnosis and treatment of COVID-19. Promoting guideline adherence, enabling quick evaluation of actual use and outcomes of COVID-19 guidelines in clinical practice, and using this feedback to quickly improve and share new protocol versions in a centralized manner are now more important than ever.

Evidencio offers tooling with which existing medical guidelines can be presented as interactive flowcharts. This tooling can be made directly available to physicians, can be used free of charge and functions independent of any electronic health record (EHR) system. Upon entering requested patient characteristics, the interactive flowchart automatically generates patient-tailored diagnosis or treatment recommendations based on the latest evidence or expert opinion. Optionally, prediction models can be included to guide medical decision-making based on predicted probabilities for individual patients.

Upon completion, the flowchart along with patient-tailored recommendations can be exported to each EHR system for registration purposes. Patient characteristics entered can be stored directly in the secure data environment of Castor EDC as discrete pseudonymized data for the purpose of scientific research. In addition, all steps of the flowchart are automatically logged as well as protocol deviations and argumentation why these deviations occurred. Therewith, highly relevant information is collected regarding actual use and adherence to COVID-19 guidelines in clinical practice. This information, along with relevant outcome data, can than be used to evaluate, compare, and improve COVID-19 guidelines with unprecedented speed and efficiency.

Evidencio complies with necessary rules and regulations. The platform contains a content management system that allows scientific committees to create, maintain, and evaluate interactive guideline-based flowcharts, including version and role management.

Contact details:

R.G. Pleijhuis, M.D., Ph.D.
Chief Medical Officer Evidencio
E-mail: r.g.pleijhuis@evidencio.com

Visiting address:
Irenesingel 19
7481 GJ Haaksbergen
The Netherlands

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Centralized creation, validation and distribution of prediction models:

Assessment of individual probability of response to treatment, the probability of developing hazardous side effects, or identification of patients who are likely to benefit most from ICU admission: prediction models are considered important tools to support medical decision-making. However, there is an urgent and unmet need for standardized, high-quality prediction models that are transparent, externally validated in the target population, and integrable in digital guidelines and EHR systems.

Evidencio.org offers a cloud-based platform to create, validate, and distribute COVID-19 prediction models. Using the platform, researchers can easily create a functional, user-friendly calculator in a transparent and standardized manner. These calculators can than be externally validated semi-automatically to evaluate algorithm performance based on anonymized patient data from local hospitals. Also, multiple prediction models can be compared head-to-head to select the best performing model in a certain patient population or subgroup.

The best performing prediction models can than be shared with physicians worldwide, making them directly available for clinical use. The standardized manner in which all prediction models hosted on the platform are constructed, strongly facilitates integration of interactive prediction models in digital protocols, guidelines, third party apps, and electronic health record (EHR) systems. Hosting prediction models on a centralized location prevents the undesirable circulation of different models and model versions.

Contact details:

R.G. Pleijhuis, M.D., Ph.D.
Chief Medical Officer Evidencio
E-mail: r.g.pleijhuis@evidencio.com

Visiting address:
Irenesingel 19
7481 GJ Haaksbergen
The Netherlands

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For your organization that has access to the Mendeley Data platform it is possible to pull out any data sets that have been discussed regarding  Covid-19.  For Covid-19 keyword, we can discover more than 170000 results of data sets worldwide.

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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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De huidige crisis ten gevolge van de uitbraak van het virus COVID-19, zorgt immers voor nieuwe en onvoorziene knelpunten bij het klinisch onderzoek in Nederland.

De Dutch Clinical Research Foundation (DCRF) wil zich echter ook nu inzetten voor het inventariseren van knelpunten bij het opzetten, uitvoeren en publiceren van klinisch onderzoek. 

Om de voortgang en de kwaliteit van klinisch onderzoek in de toekomst veilig te stellen, heeft de DCRF een COVID-19 kernteam opgericht. Het kernteam heeft in overleg met vertegenwoordigers van de aangesloten koepels een enquête voorbereid, met het doel inzicht te krijgen in deze knelpunten. Met de resultaten wil het team vervolgens kijken welke activiteiten nodig en mogelijk zijn om de knelpunten op te lossen en de aanpak daarvan te harmoniseren.

Heeft u de enquête nog niet ontvangen, maar wilt u hem wel graag invullen, vraag hem via e-mail aan bij secretariaat@dcrfonline.nl.

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SLIM is a GDPR compliant cloud based application. 

The SLIM software is available for free for COVID-19 studies (currently two COVID-19 studies are using it)

Contact:  Padualaan 8, 3584 CH Utrecht
Phone: +31 6 55 11 70 69 (Sandor)

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NanoString is making available to all researchers utilizing nCounter Gene Expression panels and/or Custom CodeSets for mRNA gene expression profiling (800-plex, results within 48 hours) , a specific COVID-19 Panel Plus product that can be spiked-in. The COVID-19 Panel Plus is a beta product for experimental Research Use Only (RUO) Probes included are compatible for use with most nCounter Immunology Gene Expression Panels .

COVID-19 Panel Plus beta cannot be used as an individual assay (as with all Panel Plus products)

Separately, probes for SARS-CoV-2 compatible with Elements and PlexSet Reagents as well as pre-amplification primers for low input experiments will also be made available. Additonally incorporation into our GeoMx Digital Spatial Profling platform for high multiplex Protein and mRNA on FFPE tissue (i.e. spatial transcriptomics) will be available as well.

Contact: Patrick van Houts, nanoString technology

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This is the bio.tools COVID-19 subdomain, containing software tools relevant to COVID-19 and SARS-CoV-2. bio.tools is the ELIXIR-funded bioinformatics tools and services discovery portal maintained by the Danish ELIXIR node in cooperation with bioinformatics groups across Europe, including at the LUMC.

Contact: Magnus Palmblad

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

English publication

OLVG news item (available in Dutch only)

The Athena pipeline is a reference-based variant calling pipeline for (Illumina) Next Generation Sequencing data on the Sevenbridges cloud platform. By reliably detecting low-frequency genetic events, Athena is highly suitable for antiviral studies for COVID-19 and diagnostics. Free for use for any COVID-19 research.

Contact DDL Bio-IT department for a free license.

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If you want to collect clinical data, the WHO case record forms should be used. The March 23^rd 2020 NOVEL CORONAVIRUS (COVID-19) - RAPID VERSION can be downloaded here. Castor has made these forms available in xml format, ready to use in any research data capture system of your choice.  If needed, the iCRF generator can be used for conversion.

Data created with these Case Record Forms will be made interoperable in the future. An initiative from VODAN, together with GO-FAIR, AmsterdamUMC (CovidPredict: central national patient database), RadboudUMC and a Health-RI  team, are working on a semantic data model and code book to make that possible. They are also expanding the Case Record forms with specific parameters for a.o. radiology related data (e.g. CORAD scores). The latest version of this model can be found in BioPortal or Github.

Contact: Luiz Bonino

Check our Health-RI tips for COVID-19 research

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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nextstrain.org aims to provide a real-time snapshot of evolving pathogen populations and to provide interactive data visualizations to virologists, epidemiologists, public health officials, and community scientists. Through interactive data visualizations, we aim to allow exploration of continually up-to-date datasets, providing a novel surveillance tool to the scientific and public health communities.

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Philips maakt in het kader van de bestrijding van COVID-19 een online portaal beschikbaar waarmee ziekenhuizen in Nederland patiëntinformatie met elkaar kunnen delen van patiënten die naar een ander ziekenhuis worden verplaatst. Met dit portaal kan een ziekenhuis radiologische beelden, verslagen, laboratoriumuitslagen en andere relevante informatie over een patiënt beschikbaar maken voor het ontvangende ziekenhuis. Hiermee kan de spreiding van COVID-19 patiënten binnen Nederland worden ondersteund.

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SIB experts and resources are taking part in the global effort to develop dedicated data services, analysis tools, training offer - and to improve knowledge sharing to fight the COVID-19 pandemic. This list is updated regularly as new tools and findings become available.

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Informatie uit de eerstelijnszorg draagt bij aan het beter in kaart brengen van de COVID-19 epidemie in Nederland en het kunnen identificeren van hoog-risicopatiënte. De bijdrage van de huisarts speelt hierbij een cruciale rol. Voor het RIVM is het van belang dat de huisarts bij iedere patiënt die verdacht wordt van een COVID-19 besmetting een aantal vragen beantwoordt. Deze vragen zijn opgenomen in een landelijk COVID-19 protocol. Dit protocol is vanaf heden beschikbaar in NHGDoc in de vorm van een korte vragenlijst.

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EHDEN is offering to harmonise organisations’ clinical data to a standard model, while preserving patients’ privacy. This will make it easier to aggregate and jointly analyse data from different sources, something that is essential if we are to stop the outbreak and save lives.

The project is offering its expertise to organisations that have amassed data from COVID-19 patients and want help converting it to a standardised data format so that it can be used as part of wider studies on the disease. They have launched a ‘Call for data partners’ through which organisations with clinical data on COVID-19 can apply to benefit from this offer.

Organisations have until 14 May to apply; a panel of bioinformatics experts will review the applications as they are received.

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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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The COVID-19 HPC Consortium encompasses computing capabilities from some of the most powerful and advanced computers in the world. We hope to empower researchers around the world to accelerate understanding of the COVID-19 virus and the development of treatments and vaccines to help address infections. Consortium members manage a range of computing capabilities that span from small clusters to some of the very largest supercomputers in the world.

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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Retrieving information from electronic health records (EHR's) is difficult, because healthcare data is complex. We have developed a solution that organizes EHR data into logical categories and that uses text analytics to make the information in text accessible. CTCUE is currently being used in 15 hospitals (UMC, STZ and general) and specifically in the Amsterdam UMC study: antihypertensives in hospitalized COVID-19 infected patients.

Contact: 
CTcue
Science Park 406
1098 XH AMSTERDAM
roel@ctcue.com
085 600 103

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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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Discover COVID-19 research data on Figshare

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To build a public open dataset of chest X-ray and CT images of patients which are positive or suspected of COVID-19 or other viral and bacterial pneumonias (MERS, SARS, and ARDS.). Data will be collected from public sources as well as through indirect collection from hospitals and physicians. All images and data will be released publicly in this GitHub repo.

This project is approved by the University of Montreal's Ethics Committee #CERSES-20-058-D

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