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PomBase

University of Cambridge
United Kingdom of Great Britain and Northern Ireland
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Mission

PomBase accelerates discovery in fundamental biology as the comprehensive knowledgebase for the fission yeast Schizosaccharomyces pombe. Building on FAIR principles, we deliver expert literature curation, high-quality genome annotation, and access to large-scale experimental datasets, complemented by intuitive analysis tools. Through community engagement and integration with global resources, PomBase empowers researchers to interrogate gene function, generate new insights, and connect discoveries in S. pombe to broader questions in health, disease, and evolution.

Key Achievements

* Awarded Global Biodata Coalition "Global Core Biodata Resource" status (2022) and Elixir "Core BioData Resource" status (2023)
* Major contributors to the Gene Ontology (curation, ontology development and annotation QC), including the highest proteome coverage of GO-CAM (pathway models) of any species
Recent paper
GO functionome
GO paper
* Development of reusable tools and software for data hosting and curation
Canto
Japonicus
* Leaders in community (author led) curation of published biological molecular data, and associated tools C

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

  • html
  • perl
  • python
  • rust
  • typescript

Technology Readiness Level

  • Actual system proven in operational environment

Code Licenses Used

  • GNU General Public License (GPL)
  • MIT License

Content Licensing

  • Creative commons licenses

Standards

Metadata

  • JSON
  • Web Ontology Language (OWL)
Other:
XML, GO-GAF, GO-GPAD, GO-GPI, gocam-py, EMBL, obo

Persistent Identifier

  • ORCiD

Integrations

  • Europe PMC
  • Zenodo

Community Engagement

Community Engagement

Implemented
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Community Statements

User Contribution Pathways

  • Contribute funds
  • Contribute to code
  • Contribute to documentation
  • Contribute to education or training
  • Contribute to governance
  • Contribute to peer reviews
  • Contribute to user research or user testing

Community Engagement Activities

  • Conference participation
  • Mailing lists and discussion forums (including Slack)
  • Social media
  • Staff roles with responsibility for community engagement
  • Volunteer or ambassador network
  • Webinars and training

Engagement with Values Frameworks

  • FAIR Guiding Principles for Scientific Data Management and Stewardship

More About Community Engagement

User Contribution Pathways:

Community curation

Additional Information

Organizational History

PomBase was launched in 2012

Organizational Structure

Business or Ownership Model

Fiscal sponsorship (academic institution)

Full-time Staff

1-5

Volunteers

More than 20

Current Affiliations

University of Cambridge
University College London
Babraham Institute

Funding

Primary Funding Source

  • Contributions

Revenue Sources

  • Grants (public)

Funding Needs

The achievement of all goals is dependent on grant funding because the project is fully grant-funded. Institutional support is provided only for overhead costs.

Fiscal Host

University of Cambridge
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