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 vaccines and diagnostic tests.  

However, much of the data remains unactionable due to:

• Data and resources scattered across multiple locations;
• Large diversity 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 global consortium aiming to enable a world-wide ecosystem of linked data and tools to support research and public health response to infectious diseases and epidemics. It will cover diverse biodata types, including host and pathogen genomics, transcriptomics, proteins, pathways and networks, imaging and cohorts. Coordinated by the SIB Swiss Institute of Bioinformatics and bringing together 12 international partners, 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 will provide 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. It will be made accessible and re-usable under the central Pathogens Portal (PP), hosted at EMBL-EBI. 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 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/. 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 (e.g., COMPARE, VEO, ReCoDID, BY-COVID) 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.

Work streams involved: Pathogens Portals and FAIR Data Management

Supporting 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.

Work streams involved: Data Analyses, Policy & Ethics, Training, Outreach and Community

Enabling trustworthy data sharing

• 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.

Work stream involved: Training, Outreach and Community 

Preparing the next generation workforce

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

Work stream involved: Training, Outreach & Community

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)

PDN is a large multi-PI consortium, bringing together interdisciplinary expertise.

PARTNERS

Our partners consist of institutions that wrote a letter of intention to collaborate with PDN if it were funded. Through its seed money program, PDN covers some expenses of its partners to support them in establishing a local pathogen data hub or portal, or in running a local workshop. Current list of partners (alphabetical order):

• CABANAnet, Costa Rica
• CaribData, Barbados
• Center for Research and Advanced Studies, Mexico
• Institute of Weed Science, Entomology and Plant Pathology, Philippines
• Kenya Medical Research Institute, Kenya
• Kilimanjaro Clinical Research Institute, Tanzania
• Morehouse School of Medicine, United States of America
• National Autonomous University of Mexico, Mexico
• National Center for Scientific and Technical Research, Morocco
• National Crop Protection Center, Philippines
• National Institute of Genetics, Japan
• National Institute of Health, Colombia
• Office of Public Health Studies, Hawaii, United States of America
• Oswaldo Cruz Institute, Brazil
• South African National Biodiversity Institute, South Africa
• University of Costa Rica, Costa Rica
• University of Puerto Rico, Puerto Rico
• Vale Institute of Technology, Brazil