Data proliferation, reconciliation, and synthesis in viral ecology
Data proliferation, reconciliation, and synthesis in viral ecology
Abstract The fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic prevention. One consequence has been a massive proliferation of host-virus association data, which comprise the backbone of research in viral macroecology and zoonotic risk prediction. These data remain fragmented across numerous data portals and projects, each with their own scope, structure, and reporting standards. Here, we propose that synthesis of host-virus association data is a central challenge to improve our understanding of the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open reconciled mammal-virus database from four key published datasets, applying a standardized taxonomy and metadata. We show that reconciling these datasets provides a substantially richer view of the mammal virome than that offered by any one individual database. We argue for a shift in best practice towards the incremental development and use of synthetic datasets in viral ecology research, both to improve comparability and replicability across studies, and to facilitate future efforts to use machine learning to predict the structure and dynamics of the global virome.
Albery Gregory F.、Gibb Rory、Becker Daniel J.、Dallas Tad A.、Sweeny Amy、Carlson Colin J.、Poisot Timoth¨|e、Ryan Sadie J.、Eskew Evan A.、Brierley Liam、Rasmussen Angela L.、Farrell Maxwell J.、Connor Ryan
Department of Biology, Georgetown UniversityCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine||Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical MedicineDepartment of Biology, University of OklahomaDepartment of Biological Sciences, Louisiana State UniversityInstitute of Evolutionary Biology, University of EdinburghCenter for Global Health Science and Security, Georgetown University Medical Center, Georgetown UniversityUniversit¨| de Montr¨|al, D¨|partement de Sciences Biologiques||Qu¨|bec Centre for Biodiversity SciencesQuantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida||Emerging Pathogens Institute, University of Florida||College of Life Sciences, University of KwaZulu NatalDepartment of Biology, Pacific Lutheran UniversityDepartment of Health Data Science, University of LiverpoolVaccine Infectious Disease Organization and International Vaccine Centre, University of Saskatchewan||Center for Global Health Science and Security, Georgetown University Medical Center, Georgetown UniversityDepartment of Ecology & Evolutionary Biology, University of TorontoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
生物科学现状、生物科学发展生物科学研究方法、生物科学研究技术微生物学
Albery Gregory F.,Gibb Rory,Becker Daniel J.,Dallas Tad A.,Sweeny Amy,Carlson Colin J.,Poisot Timoth¨|e,Ryan Sadie J.,Eskew Evan A.,Brierley Liam,Rasmussen Angela L.,Farrell Maxwell J.,Connor Ryan.Data proliferation, reconciliation, and synthesis in viral ecology[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2021.01.14.426572.点此复制
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