Dataset Information

Building an Open Resources Repository for COVID-19 Research.

ABSTRACT: The COVID-19 outbreak is a global pandemic declared by the World Health Organization, with rapidly increasing cases in most countries. A wide range of research is urgently needed for understanding the COVID-19 pandemic, such as transmissibility, geographic spreading, risk factors for infections, and economic impacts. Reliable data archive and sharing are essential to jump-start innovative research to combat COVID-19. This research is a collaborative and innovative effort in building such an archive, including the collection of various data resources relevant to COVID-19 research, such as daily cases, social media, population mobility, health facilities, climate, socioeconomic data, research articles, policy and regulation, and global news. Due to the heterogeneity between data sources, our effort also includes processing and integrating different datasets based on GIS (Geographic Information System) base maps to make them relatable and comparable. To keep the data files permanent, we published all open data to the Harvard Dataverse (https://dataverse.harvard.edu/dataverse/2019ncov), an online data management and sharing platform with a permanent Digital Object Identifier number for each dataset. Finally, preliminary studies are conducted based on the shared COVID-19 datasets and revealed different spatial transmission patterns among mainland China, Italy, and the United States.

SUBMITTER: Hu T

PROVIDER: S-EPMC8969556 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Building an Open Resources Repository for COVID-19 Research.

Hu Tao T Guan Weihe Wendy WW Zhu Xinyan X Shao Yuanzheng Y Liu Lingbo L Du Jing J Liu Hongqiang H Zhou Huan H Wang Jialei J She Bing B Zhang Luyao L Li Zhibin Z Wang Peixiao P Tang Yicheng Y Hou Ruizhi R Li Yun Y Sha Dexuan D Yang Yifan Y Lewis Ben B Kakkar Devika D Bao Shuming S

Data and information management 20200901 3

The COVID-19 outbreak is a global pandemic declared by the World Health Organization, with rapidly increasing cases in most countries. A wide range of research is urgently needed for understanding the COVID-19 pandemic, such as transmissibility, geographic spreading, risk factors for infections, and economic impacts. Reliable data archive and sharing are essential to jump-start innovative research to combat COVID-19. This research is a collaborative and innovative effort in building such an arch ...[more]

PMID: 35382104

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Project description:Reference data is key to produce reliable crop type and cropland maps. Although research projects, national and international programs as well as local initiatives constantly gather crop related reference data, finding, collecting, and harmonizing data from different sources is a challenging task. Furthermore, ethical, legal, and consent-related restrictions associated with data sharing represent a common dilemma faced by international research projects. We address these dilemmas by building a community-based, open, harmonised reference data repository at global extent, ready for model training or product validation. Our repository contains data from different sources such as the Group on Earth Observations Global Agricultural Monitoring Initiative (GEOGLAM) Joint Experiment for Crop Assessment and Monitoring (JECAM) sites, the Radiant MLHub, the Future Harvest (CGIAR) centers, the National Aeronautics and Space Administration Food Security and Agriculture Program (NASA Harvest), the International Institute for Applied Systems Analysis (IIASA) citizen science platforms (LACO-Wiki and Geo-Wiki), as well as from individual project contributions. Data of 2016 onwards were collected, harmonised, and annotated. The data sets spatial, temporal, and thematic quality were assessed applying rules developed in this research. Currently, the repository holds around 75 million harmonised observations with standardized metadata of which a large share is available to the public. The repository, funded by ESA through the WorldCereal project, can be used for either the calibration of image classification deep learning algorithms or the validation of Earth Observation generated products, such as global cropland extent and maize and wheat maps. We recommend continuing and institutionalizing this reference data initiative e.g. through GEOGLAM, and encouraging the community to publish land cover and crop type data following the open science and open data principles.

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.

Dataset Information

Building an Open Resources Repository for COVID-19 Research.

Publications

Building an Open Resources Repository for COVID-19 Research.

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