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Pathoplexus

Pathoplexus Non-Profit Association
Switzerland
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About

Launched: 2024
Record Updated: Sep 30, 2026
Data collection or management tool
Open scholarly dataset
Repository service
Pathoplexus is an open-source, open-access database for sharing and analyzing pathogen genomic sequence data and associated metadata, currently focused on viral pathogens of public health importance. Built on the open-source Loculus platform, it offers submitters the choice between immediate open sharing or a time-limited restricted-use period (up to one year) to protect against "scooping" while preserving data availability to the community. All data is provided free of charge via web interface and API, and open data is submitted onward to INSDC. Pathoplexus is governed by a nonprofit Swiss association (Verein) with a transparent, community-oriented governance structure, and adheres to FAIR data principles to maximize the reusability and impact of shared genomic data for research and public health response.

Domain Relevance

  • Biological sciences
  • Health sciences

Mission

Rapid, open sharing of pathogen genomic data is essential for outbreak response and public health research, but researchers who generate this data often hesitate to share it immediately, fearing their work will be used by others ("scooped") before they can publish their own analysis. Existing sequence databases frequently lack mechanisms to balance open access with fair attribution, and many also suffer from unclear governance, limited transparency, and infrastructure not tailored to the specific needs of pathogen genomics. Pathoplexus addresses these gaps by providing a purpose-built, transparent, community-governed platform that lets data generators choose short, time-limited restrictions on use while still enabling swift access for public health response — building the trust needed to encourage more open data sharing over time.

Technical Attributes

Maintenance Status

Actively Maintained

Open Code Repository

Implemented
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Technical Documentation

Implemented
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Code License

Implemented
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Open API

Implemented
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Open Data Statement

Implemented
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Technical Attribute Statements

Programming Languages

  • kotlin
  • python
  • typescript
  • Other
Other:
MDX

Technology Readiness Level

  • Actual system proven in operational environment

Code Licenses Used

  • GNU General Public License (GPL)

Content Licensing

  • Other
GNU AFFERO GENERAL PUBLIC LICENSE (AGPL)

Standards

Persistent Identifier

  • ORCiD

Community Engagement

Community Engagement

Implemented
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Community Statements

User Contribution Pathways

  • Contribute funds
  • Contribute to code
  • Contribute to working groups or interest groups

Community Engagement Activities

  • Conference participation
  • Interest, working, user, or advisory groups
  • Mailing lists and discussion forums (including Slack)
  • Social media
  • Webinars and training

Engagement with Values Frameworks

  • FAIR Guiding Principles for Scientific Data Management and Stewardship

Additional Information

Organizational History

Pathoplexus was founded in 2024 by genomic epidemiologists and public health researchers who saw a gap in pathogen data sharing: databases were either fully open, discouraging submission for fear of being "scooped," or restrictive in ways that slowed outbreak response. Built on the open-source Loculus platform, Pathoplexus offers a middle path: short, time-limited restricted-use periods paired with fast, free, open access once released. The platform has since grown to cover an expanding range of viral pathogens of public health importance, supporting real-time sharing during outbreak responses. Pathoplexus is governed as a nonprofit Swiss association (Verein), with an Executive Board and Scientific Advisory Board providing community-led oversight, and its policies evolve through ongoing member consultation. It is sustained by institutional and philanthropic support, and its open-source codebase is maintained collaboratively, letting other communities build similar platforms.

Organizational Structure

Business or Ownership Model

Non-profit organization

Funding

Primary Funding Source

  • Contributions

Revenue Sources

  • Grants (private)
  • Grants (public)
  • In-kind contributions
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