A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science
AbstractThe COVID-19 pandemic proved how sharing of genomic sequences in a timely manner, as well as early detection and surveillance of variants and characterization of their clinical impacts, helped to inform public health responses. However, the area of (re)emerging infectious diseases...
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JMIR Publications
2025-02-01
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| Series: | JMIR Public Health and Surveillance |
| Online Access: | https://publichealth.jmir.org/2025/1/e63996 |
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| author | Clara Amid Martine Y van Roode Gabriele Rinck Janko van Beek Rory D de Vries Gijsbert P van Nierop Eric C M van Gorp Frank Tobian Bas B Oude Munnink Reina S Sikkema Thomas Jaenisch Guy Cochrane Marion P G Koopmans |
| author_facet | Clara Amid Martine Y van Roode Gabriele Rinck Janko van Beek Rory D de Vries Gijsbert P van Nierop Eric C M van Gorp Frank Tobian Bas B Oude Munnink Reina S Sikkema Thomas Jaenisch Guy Cochrane Marion P G Koopmans |
| author_sort | Clara Amid |
| collection | DOAJ |
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AbstractThe COVID-19 pandemic proved how sharing of genomic sequences in a timely manner, as well as early detection and surveillance of variants and characterization of their clinical impacts, helped to inform public health responses. However, the area of (re)emerging infectious diseases and our global connectivity require interdisciplinary collaborations to happen at local, national and international levels and connecting data to understand the linkages between all factors involved. Here, we describe experiences and lessons learned from a COVID-19 pilot study aimed at developing a model for storage and sharing linked laboratory data and clinical-epidemiological data using European open science infrastructure. We provide insights into the barriers and complexities of internationally sharing linked, complex cohort datasets from opportunistic studies for connected data analyses. An analytical timeline of events, describing key actions and delays in the execution of the pilot, and a critical path, defining steps in the process of internationally sharing a linked cohort dataset are included. The pilot showed how building on existing infrastructure that had previously been developed within the European Nucleotide Archive at the European Molecular Biology Laboratory-European Bioinformatics Institute for pathogen genomics data sharing, allowed the rapid development of connected “data hubs.” These data hubs were required to link human clinical-epidemiological data under controlled access with open high dimensional laboratory data, under FAIR (Findable, Accessible, Interoperable, Reusable) principles. Based on our own experiences, we call for action and make recommendations to support and to improve data sharing for outbreak preparedness and response. |
| format | Article |
| id | doaj-art-8de30fa5e2ce49b89e5bdbd0f3d1b510 |
| institution | DOAJ |
| issn | 2369-2960 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | JMIR Publications |
| record_format | Article |
| series | JMIR Public Health and Surveillance |
| spelling | doaj-art-8de30fa5e2ce49b89e5bdbd0f3d1b5102025-08-20T03:11:40ZengJMIR PublicationsJMIR Public Health and Surveillance2369-29602025-02-0111e63996e6399610.2196/63996A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open ScienceClara Amidhttp://orcid.org/0000-0001-6534-7425Martine Y van Roodehttp://orcid.org/0000-0002-8427-0264Gabriele Rinckhttp://orcid.org/0000-0001-6428-3431Janko van Beekhttp://orcid.org/0000-0001-7463-9411Rory D de Vrieshttp://orcid.org/0000-0003-2817-0127Gijsbert P van Nierophttp://orcid.org/0000-0003-1622-8248Eric C M van Gorphttp://orcid.org/0000-0001-6415-6678Frank Tobianhttp://orcid.org/0000-0003-2380-0003Bas B Oude Munninkhttp://orcid.org/0000-0002-9394-1189Reina S Sikkemahttp://orcid.org/0000-0001-7331-6274Thomas Jaenischhttp://orcid.org/0000-0002-9464-571XGuy Cochranehttp://orcid.org/0000-0001-7954-7057Marion P G Koopmanshttp://orcid.org/0000-0002-5204-2312 AbstractThe COVID-19 pandemic proved how sharing of genomic sequences in a timely manner, as well as early detection and surveillance of variants and characterization of their clinical impacts, helped to inform public health responses. However, the area of (re)emerging infectious diseases and our global connectivity require interdisciplinary collaborations to happen at local, national and international levels and connecting data to understand the linkages between all factors involved. Here, we describe experiences and lessons learned from a COVID-19 pilot study aimed at developing a model for storage and sharing linked laboratory data and clinical-epidemiological data using European open science infrastructure. We provide insights into the barriers and complexities of internationally sharing linked, complex cohort datasets from opportunistic studies for connected data analyses. An analytical timeline of events, describing key actions and delays in the execution of the pilot, and a critical path, defining steps in the process of internationally sharing a linked cohort dataset are included. The pilot showed how building on existing infrastructure that had previously been developed within the European Nucleotide Archive at the European Molecular Biology Laboratory-European Bioinformatics Institute for pathogen genomics data sharing, allowed the rapid development of connected “data hubs.” These data hubs were required to link human clinical-epidemiological data under controlled access with open high dimensional laboratory data, under FAIR (Findable, Accessible, Interoperable, Reusable) principles. Based on our own experiences, we call for action and make recommendations to support and to improve data sharing for outbreak preparedness and response.https://publichealth.jmir.org/2025/1/e63996 |
| spellingShingle | Clara Amid Martine Y van Roode Gabriele Rinck Janko van Beek Rory D de Vries Gijsbert P van Nierop Eric C M van Gorp Frank Tobian Bas B Oude Munnink Reina S Sikkema Thomas Jaenisch Guy Cochrane Marion P G Koopmans A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science JMIR Public Health and Surveillance |
| title | A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science |
| title_full | A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science |
| title_fullStr | A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science |
| title_full_unstemmed | A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science |
| title_short | A Call for Action: Lessons Learned From a Pilot to Share a Complex, Linked COVID-19 Cohort Dataset for Open Science |
| title_sort | call for action lessons learned from a pilot to share a complex linked covid 19 cohort dataset for open science |
| url | https://publichealth.jmir.org/2025/1/e63996 |
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