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VEuPathDB

VEuPathDB.org
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About

Launched: 1999
Record Updated: Sep 30, 2026
Annotations system
Data resource
Open scholarly dataset
The Eukaryotic Pathogen, Vector and Host Informatics Bioinformatics Resource Center (VEuPathDB.org) is a robust, scalable, cost-effective, production-quality resource providing tens of thousands of researchers worldwide with FAIR (Findable, Accessible, Interoperable, Reusable) access to genomic information and other large-scale datasets relevant to infectious disease pathogens, and their interactions with plants and animals (including humans and invertebrate vectors of disease). Computational platforms and analytical tools facilitate the collection, analysis, management, integration, and mining of genomic-scale datasets, expediting discovery research and translational application. Component websites include AmoebaDB, ClinEpiDB, CryptoDB, DataExplorer, FungiDB, GiardiaDB, HostDB, MicrobiomeDB, MicrosporidiaDB, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, TriTrypDB, VectorBase, and OrthoMCL.

Domain Relevance

  • Agricultural biotechnology
  • Basic medicine
  • Biological sciences
  • Computer and information sciences
  • Educational sciences
  • Health biotechnology
  • Health sciences
  • Veterinary science

Mission

To provide open access to data and tools enabling data mining, discovery, and hypothesis generation, thereby advancing human & veterinary health, agricultural food security, and biosecurity.

Key Achievements

For >25 years, VEuPathDB has exemplified diversified funding, with support from multiple sources worldwide. As traditional funders have become unwilling or unable to support even demonstrably cost-effective infrastructure – culminating in the termination of direct NIH support in 2024 – VEuPathDB has pioneered a voluntary subscription model, informed by a survey of ~2K researchers in 81 countries, and backed by bridge funds from the Wellcome Trust, Coefficient Giving, and others. VEuPathDB has also integrated sophisticated tools to capture community knowledge, extract & harmonize metadata, summarize functional genomics data, infer function via orthology, enable users to formulate their own questions, and support dataset analysis & dissemination. >42K citations reflect high impact on parasitology, mycology & vector biology research. Release 71 (8/26) marks the migration of production databases onto new infrastructure designed to maximize sustainability, scalability, and performance.

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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Open Product Roadmap

In Progress
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Technical Attribute Statements

Programming Languages

  • java
  • javascript
  • kotlin
  • mysql
  • perl
  • python
  • r
  • typescript

Technology Readiness Level

  • Actual system proven in operational environment

Code Licenses Used

  • Apache License, Version 2.0

Content Licensing

  • Creative commons licenses

Standards

Metadata

  • JSON
  • RDF
  • REST
  • SPARQL
  • Web Ontology Language (OWL)

Security

FISMA

Hosting Options

  • Through solution only

Community Engagement

Community Engagement

Implemented
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Community Statements

User Contribution Pathways

  • Contribute funds
  • Contribute to education or training
  • Contribute to governance
  • Contribute to user research or user testing
  • Contribute to working groups or interest groups

Community Engagement Activities

  • Community calls
  • Conference participation
  • Interest, working, user, or advisory groups
  • Social media
  • Staff roles with responsibility for community engagement
  • Webinars and training

Engagement with Values Frameworks

  • FAIR Guiding Principles for Scientific Data Management and Stewardship

Additional Information

Organizational History

VEuPathDB began in the late 1990s as standalone resources (ToxoDB, PlasmoDB) organizing genomic data for individual eukaryotic pathogens. Under the auspices of the NIH/NIAID Bioinformatics Resource Center program, these were consolidated as a production database (ApiDB) in 2004, and progressively expanded to accommodate other protozoan parasites, including trypanosomatids (TriTrypDB, 2009; Gates Fdn & Wellcome Trust), fungal pathogens (FungiDB, 2011; Burroughs Wellcome Fund), and VectorBase (established as an independent BRC in 2004; integrated into VEuPathDB in 2020). This resource has grown to accommodate thousands of curated datasets: genome sequences & annotation, variation & comparative data, orthology-based inference, functional genomics (epigenomics, transcriptomics, proteomics, metabolomics, etc), structural data, interactomes, localization, pathways, phenotypic datasets, field & clinical isolates (with relevant metadata) … along with appropriate search & visualization tools.

Organizational Structure

Business or Ownership Model

Fiscal sponsorship (academic institution)

Full-time Staff

More than 20

Non-profit Status

501(c)3

Funding

Primary Funding Source

  • Contributions

Revenue Sources

  • Grants (private)
  • Grants (public)
  • In-kind contributions
  • Individual memberships
  • Institutional memberships

Financial Reporting Level

  • Other
Solution budget only

Funding Needs

See: https://veupathdb.org/veupathdb/app/static-content/faq.html#funding
Since termination of the Wellcome Trust Resource Grant program in 2021, Gates funding for ClinEpiDB in 2022, and the VEuPathDB BRC contract from NIH in Sept 2024, stop-gap bridge funding has been provided by The Burroughs Wellcome Fund, The Chan Zuckerberg Initiative, Coefficient Giving (formerly Open Philanthropy), The Fdn for the Advancement of Science & Medicine, Univ Pennsylvania, The Wellcome Trust, and other sources; Penn and Univ Georgia have also agreed to waive institutional overhead for the duration of this transitional period.
We anticipate that new infrastructure will permit continued support for the ever-increasing volume and diversity of new datasets, with no reduction in community engagement. For 2026-27 and beyond, we project steady-state budgets of $5.3M/yr (a 38% reduction relative to 2023-24), to accommodate equipment upgrades, staff replacement, and appropriate institutional overhead.

Fiscal Host

Trustees of the University of Pennsylvania
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