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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
PomBase Updates PMID:41518600 10.1093/genetics/iyag001
GO functionome PMID:40011791 10.1038/s41586-025-08592-0
GO consortium contributions PMID:41413728 10.1093/nar/gkaf1292
* Development of reusable tools and software for data hosting and curation
Canto Curation Tool PMID:24574118 DOI:10.1093/bioinformatics/btu103
JaponicusDB PMID:35380656 10.1093/genetics/iyab223
* Leaders in community (author led) curation of published biological molecular data
PMID:32353878 DOI:10.1093/database/baaa028

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

Policies & Governance

Governance Summary

The PomBase Scientific Advisory Board (SAB) provides strategic scientific advice to the PomBase resource covering current and future priorities related to curation, tools provided and outreach. They will advise how can we better align S. pombe knowledge to human genetics and health. The SAB is an independent body, made up of leading experts in both fission yeast biology and Model Organism Databases from around the world. The SAB meets annually, but are also the first point of contact for intermittent feedback on resource reallocation that may affect the wider community.

Policies

Privacy Policy

Implemented
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Governance Records

Implemented
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Governance Structure & Processes

Implemented
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Policy Statements

Access Conditions

  • Open without restrictions

Board Structure

  • Advisory board or steering committee

Board Level

  • Other
Scientific oversight

Community Governance

  • Formal

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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