ELIXIR-CONVERGE D9.2 Document where code from the various regional/national data hubs is available; training documentation on data submission by the platforms - relates to tasks 9.1-9.2
Creators: name: Neves, Aitana
name: Dolanski-Aghamanoukjan, Lorenz
name: Maier, Wolfgang
name: Pergl, Robert
name: Akerström, Wolmar Nyberg
name: Hjerde, Erik
name: Cuesta, Isabel
name: Popleteeva, Marina
name: Oulas, Anastasia
name: Mohamed, Anliat
name: Tonazzolli, Arianna
name: Pilvar, Diana
name: Calhoun, Erin
name: Åberg, Espen
name: Erard, Frédéric
name: Rasche, Helena
name: Messak, Imane
name: van Helden, Jacques
name: Lara, Maria
name: Rahman, Nadim
name: Karathanasis, Nestoras
name: Willassen, Nils-Peder
name: Zmora, Pawel
name: Monzón, Sara
name: Hiltemann, Saskia
name: Singhroha, Sunny
name: Klemetsen, Terje
name: Denecker, Thomas
name: Waheed, Zahra
Publisher: name: Zenodo
Year: 2023
Subjects: ELIXIR-CONVERGE
ELIXIR
SARS-COV-2
COVID-19
COVID-19 Data Platform
COVID-19 Data Portal
data brokering
RDMKit

description: Deliverable 9.2 relates to tasks 9.1 and 9.2 on strengthening the central Covid-19 Data Portal and coordinating nascent and established data hubs in mobilising data into the central portal. To achieve this, an active network of regional and national SARS-CoV-2 data hubs managers was established. To get existing data flowing, we first organised a technical workshop on data brokering to the ENA, from which an online tutorial and RDMkit documentation were published. Then, in order to support nascent and more established nodes in mobilising data, we started addressing the various challenges and gaps identified: (i) Importance to build a case for the regional/national data hub and brokering model, also for mid- and long-term funding: a survey was conducted on 11 countries to identify use cases, funding mechanisms and assess sustainability of the developed infrastructures and tools. We aim to publish it in F1000 (ELIXIR Gateway); (ii) Maturity assessment to oversee data hub development and identify potential areas of improvement: a maturity model for pathogen data hubs was developed and is readily available online. (iii) Sensitive data remains siloed and not shared on public open data repositories, calling for the need to federate pathogen data hubs through a central system enabling privacy-preserving data queries and controlled data access following FAIR principles: an opinion paper is being finalised to present and discuss a model of Federated One Health Surveillance Platforms, beyond Covid-19. A proof-of-concept of how a data hub might be “fairified” was also conducted in the Czech Republic. (iv) Training in analytical pipelines and documentation - several actively followed workshops were organised on Galaxy and available pipelines and tools have been documented. (v) Need to better understand the legal aspects of SARS-CoV-2 data sharing: a dedicated workshop was organised to identify the common needs and start addressing them. Legal experts should be further invited to the table given the many open questions remaining. The pandemic has demonstrated the importance of genomic surveillance. This deliverable establishes the foundations to strengthen SARS-CoV-2 data hubs and importantly, scale and expand them to other pathogens and use cases serving both research and surveillance through a federation of hubs.