Pathogen Data Network

Swiss Institute Of Bioinformatics, Geneva

Investigators

Abstract

Abstract: The Pathogen Data Network (PDN) will nucleate global networks around the mobilization of various biodata types, covering host and pathogen genomics, transcriptomics, proteins, pathways and networks, imaging and cohorts. The integration and linkage of these data for the purposes of research and public health response will be made possible through the development of a technical framework covering specifications, standards, interfaces and reference software implementations. All the publicly available data to be integrated with further datasets and tools from a range of pathogen-related data resources will be made accessible and re-usable under the Pathogens Portal (PP), hosted at EMBL-EBI, and within distributed local Pathogen Portals (LPP), hosted globally and enabling additional functionalities to be customized for the specific local context. To foster data mobilization, PDN will establish a network of FAIR Local Data Hubs (LDH) based on reference software implementations to be deployed on locally controlled cloud infrastructure, ideally in countries having signed the Nagoya Protocol. To achieve trustworthy sharing of the mobilized data to international repositories, legally compliant with local regulations as well as aligned to international practice, we will also address in-depth issues of trust and ownership and work to provide data-sharing guidelines options for international and national organizations, ensuring alignment of the PDN project with international practice and its wide adoption by end users. This will cover LDH focusing on Low and Middle Income Countries. In parallel, we will establish a LDH Managers' community of practice to share knowledge and expertise, with a focus on capacity building, harmonization and preparedness. Data Hubs (DH) hosted centrally will continue existing in parallel, supporting those that lack capacity, resource or expertise to deploy and maintain a LDH. LDH would be able to host personal sensitive data that may not be openly shared but can be made discoverable and accessible for research and public health under proper legal and ethical frameworks. The Pathogen Analysis System (PAS) will be extended with additional workflows from selected use cases spanning global sewage data, foodborne viruses and linked clinical-epidemiological data. PDN will enable its users to run analyses centrally for DH, and locally or remotely for LDHs. An extensive and global support, outreach and training program will fuel the adoption of the network concept, the connection of infrastructure to its interfaces, and the use of open pathogen data by the global scientific community - both for research and for decision-making. In summary, PDN will develop the networks and all the underpinning components at the technical-, analytical-, trust-, training- and outreach-levels to truly enable data mobilization and sharing, and the subsequent data integration and linking into a global knowledgebase network serving research needs thanks to open access to data, and public health needs, as well as preparedness and response, thanks to timely access to controlled-access data and a dedicated surveillance and outbreak dashboard.