Dataset Information

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

ABSTRACT: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.

SUBMITTER: Harrison PW

PROVIDER: S-EPMC8218199 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

Harrison Peter W PW Lopez Rodrigo R Rahman Nadim N Allen Stefan Gutnick SG Aslam Raheela R Buso Nicola N Cummins Carla C Fathy Yasmin Y Felix Eloy E Glont Mihai M Jayathilaka Suran S Kadam Sandeep S Kumar Manish M Lauer Katharina B KB Malhotra Geetika G Mosaku Abayomi A Edbali Ossama O Park Young Mi YM Parton Andrew A Pearce Matt M Estrada Pena Jose Francisco JF Rossetto Joseph J Russell Craig C Selvakumar Sandeep S Sitjà Xènia Pérez XP Sokolov Alexey A Thorne Ross R Ventouratou Marianna M Walter Peter P Yordanova Galabina G Zadissa Amonida A Cochrane Guy G Blomberg Niklas N Apweiler Rolf R

Nucleic acids research 20210701 W1

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European ...[more]

PMID: 34048576

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Project description:BackgroundCOVID-19 has threatened the health of tens of millions of people all over the world. Massive research efforts have been made in response to the COVID-19 pandemic. Utilization of clinical data can accelerate these research efforts to combat the pandemic since important characteristics of the patients are often found by examining the clinical data. Publicly accessible clinical data on COVID-19, however, remain limited despite the immediate need.ObjectiveTo provide shareable clinical data to catalyze COVID-19 research, we present Columbia Open Health Data for COVID-19 Research (COHD-COVID), a publicly accessible database providing clinical concept prevalence, clinical concept co-occurrence, and clinical symptom prevalence for hospitalized patients with COVID-19. COHD-COVID also provides data on hospitalized patients with influenza and general hospitalized patients as comparator cohorts.MethodsThe data used in COHD-COVID were obtained from NewYork-Presbyterian/Columbia University Irving Medical Center's electronic health records database. Condition, drug, and procedure concepts were obtained from the visits of identified patients from the cohorts. Rare concepts were excluded, and the true concept counts were perturbed using Poisson randomization to protect patient privacy. Concept prevalence, concept prevalence ratio, concept co-occurrence, and symptom prevalence were calculated using the obtained concepts.ResultsConcept prevalence and concept prevalence ratio analyses showed the clinical characteristics of the COVID-19 cohorts, confirming the well-known characteristics of COVID-19 (eg, acute lower respiratory tract infection and cough). The concepts related to the well-known characteristics of COVID-19 recorded high prevalence and high prevalence ratio in the COVID-19 cohort compared to the hospitalized influenza cohort and general hospitalized cohort. Concept co-occurrence analyses showed potential associations between specific concepts. In case of acute lower respiratory tract infection in the COVID-19 cohort, a high co-occurrence ratio was obtained with COVID-19-related concepts and commonly used drugs (eg, disease due to coronavirus and acetaminophen). Symptom prevalence analysis indicated symptom-level characteristics of the cohorts and confirmed that well-known symptoms of COVID-19 (eg, fever, cough, and dyspnea) showed higher prevalence than the hospitalized influenza cohort and the general hospitalized cohort.ConclusionsWe present COHD-COVID, a publicly accessible database providing useful clinical data for hospitalized patients with COVID-19, hospitalized patients with influenza, and general hospitalized patients. We expect COHD-COVID to provide researchers and clinicians quantitative measures of COVID-19-related clinical features to better understand and combat the pandemic.

Project description:In 1982, the Annals of Virology published a paper showing how Liberia has a highly endemic potential of Ebola warning health authorities of the risk for potential outbreaks; this journal is only available by subscription. Limiting the accessibility of such knowledge may have reduced information propagation toward public health actors who were indeed surprised by and unprepared for the 2014 epidemic. Open access (OA) publication can allow for increased access to global health research (GHR). Our study aims to assess the use, cost and impact of OA diffusion in the context of GHR.A total of 3366 research articles indexed under the Medical Heading Subject Heading "Global Health" published between 2010 and 2014 were retrieved using PubMed to (1) quantify the uptake of various types of OA, (2) estimate the article processing charges (APCs) of OA, and (3) analyse the relationship between different types of OA, their scholarly impact and gross national income per capita of citing countries.Most GHR publications are not available directly on the journal's website (69%). Further, 60.8% of researchers do not self-archive their work even when it is free and in keeping with journal policy. The total amount paid for APCs was estimated at US$1.7 million for 627 papers, with authors paying on average US$2732 per publication; 94% of APCs were paid to journals owned by the ten most prominent publication houses from high-income countries. Researchers from low- and middle-income countries are generally citing less expensive types of OA, while researchers in high-income countries are citing the most expensive OA.Although OA may help in building global research capacity in GHR, the majority of publications remain subscription only. It is logical and cost-efficient for institutions and researchers to promote OA by self-archiving publications of restricted access, as it not only allows research to be cited by a broader audience, it also augments citation rates. Although OA does not ensure full knowledge transfer from research to practice, limiting public access can negatively impact implementation and outcomes of health policy and reduce public understanding of health issues.

Project description:This survey-based study examines health science scholars' perceptions of collaborative research behavior and sharing open research data in university settings. A total of 362 health science scholars from U.S. universities participated in an online questionnaire consisting of 59 questions. Descriptive and inferential statistical analyses of the data included frequencies, cross-tabulations, descriptive ratio statistics, and the non-parametric Kruskal-Wallis one-way analysis of variance. Four open-ended questions were also analyzed to provide further insights into the survey findings. The study reveals that health scholars share their data with colleagues within their institution or project, demonstrating a lesser inclination toward open research data sharing practices through institutional repositories and journal supplements. Motivating factors and challenges influencing researchers' decisions to share their research data were also identified. While scientific and knowledge advancement served as major incentives, health scholars working with human-related data expressed concerns about privacy and confidentiality breaches, which are primary barriers to data sharing. Some participants indicated that requirements and policies also influenced their willingness to share data. Disciplinary variations were observed regarding data-sharing practices through journal supplements, secondary data analysis, and personal communication. Furthermore, significant differences emerged between funded and non-funded scholars, impacting their practices, motivations, and challenges in sharing open research data. Important factors driving health science scholars to share open research data include resources, policy compliance, and requirements. This study contributes valuable insights for policy development by investigating factors that can foster openness and sharing of research data in the health sciences. The findings shed light on the complexities and considerations associated with open data-sharing practices, enabling stakeholders to develop effective strategies and frameworks.

Dataset Information

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

Publications

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

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