PROJECT SUMMARY

Funded by the NIH NIAID BRC program (award number U24AI183840), the Pathogen Data Network is a global consortium aiming to provide infrastructure, tools, training, outreach and support to FAIR infectious-diseases data sharing and reuse. It will cover diverse biodata types, including host and pathogen genomics, transcriptomics, proteins, pathways and networks, imaging and cohorts. 

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 PortalRefers to the Pathogens Portal, a resource hosted and developed by the EMBL-EBI that enables researchers, clinicians and policymakers access the latest and most comprehensive datasets on pathogens. Link to the resource: https://www.pathogensportal.org/ (PPRefers to the Pathogens Portal, a resource hosted and developed by the EMBL-EBI that enables researchers, clinicians and policymakers access the latest and most comprehensive datasets on pathogens. Link to the resource: https://www.pathogensportal.org/), hosted at EMBL-EBI, and within distributed local Pathogen Portals (LPPRefers to local, national or regional pathogens portals hosted and developed by a local community. Links to various existing resources can be found here: https://www.pathogensportal.org/national-data-portal. Within the Pathogen Data Network initiative, it also refers to the reference software implementation that will be provided to enable local communities to rapidly deploy their own local pathogens portal.), hosted globally and enabling additional functionalities to be customized for the specific local context. The Data Portal services will span all pathogens determined to be of interest to NIH-NIAID, gradually also capturing host, intermediate host and vector species of relevance to the listed pathogen species and groups.

Outside pandemic and other emergency periods requiring specific response, PDN will develop around a use case on environmental surveillance, with dedicated workflows implemented on the central Pathogen Analysis System, training and policy research. With strong community engagement and components emphasizing the need for local data governance and alignment with international policy, PDN will foster an integrative and participative approach to maximize global buy-in and impact. During public health events of concern, such as major outbreaks, PDN will actively assess the value of the tools and services that it can offer also beyond the environmental surveillance domain to provide focused urgent support following appropriate discussion and agreement with NIH-NIAID.

OBJECTIVES

1. Provide a knowledgebase (KB) with central and distributed elements to allow access to integrated infectious diseases-related data, focusing on recognized pathogens of high concern. The KB will link data from various molecular methods in support of deep integrative analyses that inform our knowledge of pathogens and infectious disease and guide public health responses to outbreaks.
2. Develop innovative computational methods. A selected use case on wastewater surveillance will serve to co-develop the infrastructure and governance.
3. Enable and empower all data consumers and producers to engage as designers and beneficiaries of this key global infrastructure. Global engagement is required for the richest data foundation to emerge to support research and public health responses.
4. Nurture a community of trust around infectious disease data sharing, respecting benefit sharing and scientific credit sensitivities around rapid open pathogen data sharing.
5. Develop and present evidence-based policy options for pathogen data-sharing from omics data. Options will target the greatest openness in data where possible while respecting controls on access where necessary.
6. Build sustainable infrastructure that will persist and thrive beyond the term of the PDN project, through the use of existing established and sustained infrastructure, such as public omics data resources and open computational workflows and options created in COMPARE, VEO, ReCoDID, and BY-COVID.

CONSORTIUM