THE CHALLENGE

Pathogens, such as the flu or Salmonella, know no borders. Global surveillance and research is the backbone of prevention of and responses to related public health emergencies. Access to globally shared data managed in a FAIR (Findable, Accessible, Interoperable, Reusable) and equitable way is crucial to continuous infectious disease surveillance and the timely development of public health measures, such as diagnostic tests.  

However, much of the data remains unactionable due to:

• Data and resources scattered across multiple locations;
• Large variety of data types;
• Lack of policies and ethical frameworks to enable effective and trustworthy data sharing. 

The Pathogen Data Network was created to address these problems.

THE PROJECT IN A NUTSHELL

PDN is a Swiss-US consortium aiming to enable a world-wide ecosystem of linked data and tools to support research and public health response to infectious diseases and major outbreak. It covers diverse biodata types, including host and pathogen genomics, transcriptomics, proteins, pathways and networks, imaging and cohorts. Coordinated by the SIB Swiss Institute of Bioinformatics, this project is funded under the NIH’s National Institute of Allergy and Infectious Diseases Bioinformatics Resource Program (NIH NIAID BRC, award number U24AI183840).

PROJECT’S OBJECTIVES

To fulfil its mission, PDN provides infrastructure, tools, training, outreach and support to infectious-disease data sharing, according to the FAIR principles for scientific data management and storage.

PDN’s value is four fold: fostering data discovery, supporting efficient surveillance and outbreak response, enabling trustworthy data sharing, preparing the next generation workforce.

Fostering data discovery to enable a worldwide perspective

• Centralized pathogen data and resources discovery: Publicly available data will be integrated with further datasets and tools from a range of pathogen-related data resources into a knowledgebase, accessible and re-usable under a central portal. These resources will include pathogen, host, intermediate host, and vector species data relevant to pathogens of concern, enabling deep integrative analyses tailored to local contexts.
• Global integration through local, national or regional nodes: Pathogens Portal Nodes (PPN) will index community-specific pathogenic data into the PP. These nodes will also provide tools and documentation for managing FAIR data, connecting users to local resources, and granting access to global datasets and computational tools.
• Sustainable infrastructure for long-term impact: PDN builds on existing, well-established infrastructure to ensure its sustainability and relevance beyond the project’s term. This includes leveraging public omics data resources, open computational workflows for continued data discovery and use, and providing capacity building for pathogen genomic data sharing.

Supporting research and innovation for efficient surveillance and outbreak response

• Wastewater surveillance as a use case: Dedicated workflows and innovative computational methods, complemented by training programs and policy/ethics research will serve to co-develop the infrastructure and governance.
• Active support during public health emergencies: In times of major outbreaks or public health events of concern, PDN will assess its tools and services to extend support beyond wastewater surveillance, ensuring focused and timely assistance in coordination with NIH-NIAID. In “peace” times, PDN will assess and integrate pathogen-specific bioinformatics pipelines based on priority lists established by national and international public health authorities and aligned with PDN expertise.
• Global engagement for inclusive governance: PDN aims to empower data producers and consumers as co-designers and beneficiaries of this global infrastructure, fostering participation, local data governance, and alignment with international policies to maximize impact.

Enabling timely data sharing

• Creating private data sharing environments (i.e. private data hubs) to facilitate collaboration on prepublication data. 
• Nurture a community of trust around infectious disease data sharing, respecting benefit sharing and scientific credit sensitivities around rapid open pathogen data re-use. This is done through the creation of an Open Community Forum.
• 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.

Preparing the next generation workforce

• Providing training on the Pathogens Portal, other products of the project and community-driven needs
• Engaging with current and potential users of the Pathogens Portal and the Nodes, to strengthen their capacity through assistance, documentation and tools for managing their data.

GET INVOLVED

Whether you are researchers, data stewards, bioinformaticians, healthcare professionals, policymakers, educators, or anyone whose work involves or is impacted by pathogen data: join the PDN community to share your challenges, vision, provide feedback on PDN initiatives, and benefit from the learnings and resources made available through the project. 

MEET THE PRINCIPAL INVESTIGATORS (PIs)

The project additionally builds on the expertise of the following SIB Groups: 

• Computational Biology group, led by Niko Beerenwinkel (ETH Zurich)

• Computational Evolution group, led by Tanja Stadler (ETH Zurich)

• Comparative Genomics group, led by Christophe Dessimoz & Natasha Glover (University of Lausanne)

• EVE Epidemiology and Virus Evolution group, led by Emma Hodcroft (Swiss Tropical and Public Health Institute)

• Microbial Evolution group, led by Richard Neher (University of Basel)

• Microbial genomics, led by Tim-Christoph Roloff Handschin and Helena Seth-Smith (University of Zurich)

• Swiss-Prot group, led by Alan Bridge and Paul Thomas