The Pathogen Data Network (PDN) has conducted a global survey to better understand the challenges researchers face when working with pathogen data and to identify priority areas for training and support. The results pinpoint limited funding, data aggregation challenges and a shortage of skilled personnel as significant barriers — and highlight a clear demand for enhanced tools and targeted training to advance FAIR (Findable, Accessible, Interoperable, Reusable) data sharing.
A global effort to understand researchers’ needs
Sharing reliable and accurate pathogen data as quickly as possible is essential for preventing and managing infectious disease outbreaks. However, little systematic research has been conducted to understand the real-world challenges researchers face in this space.
“PDN’s international approach brings together experiences and insights that no single institution or country could provide alone. Outbreaks do not respect borders, so understanding the needs and norms of multiple countries is essential for effective collaboration.“
Jason Williams
PDN’s co-Principal Investigator
Cold Spring Harbor Laboratory (NY, US)
PDN developed and deployed this survey to reach a broader and more diverse group of stakeholders, and to capture the specific barriers and training needs they encounter when working with pathogen data. Between March and April 2025, the survey was distributed to researchers and pathogen data professionals, yielding 211 responses. Respondents included analysts, researchers, public health professionals, educators, software developers, policymakers, and data stewards from a wide range of institutions and countries.
Top challenges facing pathogen data researchers and other key findings
Respondents identified limited funding for data-related work (74%), data aggregation challenges (68%), and a shortage of skilled personnel (52%) as the most significant barriers to working with pathogen data.
Respondents also ranked the Pathogens Portal as the most important PDN resource (72%), followed by access to experts and validated analysis tools.
Training needs varied by role, but key priorities included:
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- Bioinformatics for infectious disease research (68%)
- Use of the PDN Pathogens Portal (51%)
- Visualization and communication of results (50%)
Detailed results will be presented at ISMB/ECCB 2025 in Liverpool.
An international collaboration
PDN’s international approach was key to making this work possible. By combining insights from diverse research communities, PDN can better align its tools and training with the realities researchers face in different contexts.
Supporting PDN’s mission
This work supports PDN’s mission to enable a global ecosystem of linked data and tools to accelerate research and public health responses to infectious diseases. It complements other PDN outreach efforts — including the Open Community Forum — and ensures that the network’s offerings are grounded in the priorities of the global research community.
What’s next?
The PDN Training, Outreach & Community team is now using the survey results to refine PDN’s training and engagement strategy. In response to the findings, upcoming efforts will focus on:
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- Expanding training in bioinformatics, portal usage, and data visualization
- Enhancing data aggregation tools through the Pathogens Portal
- Offering short online courses and webinars aligned with researchers’ expressed needs
This is a crucial step toward strengthening global capacity for FAIR pathogen data sharing — and ultimately, helping public health agencies and researchers around the world respond more effectively to infectious disease threats.
Workstreams involved: WS5 Training, Outreach & Community