The COPO-schemas repository contains a collection of schemas for various types of metadata used in the COPO project website, developed and maintained by the Collaborative OPen Omics (COPO) team at the Earlham Institute.
These schemas define metadata structures and checklists relevant to various omics data types and submission requirements. They serve as a reference for how metadata is structured across COPO's metadata workflows.
- JSON, YAML and XLSX schemas organised by metadata type or submission checklist
- Versioned files to track schema evolution over time
- Human-readable definitions and descriptions within each schema
- Schema files used for validation and rendering in the COPO web application
⚠️ This repository is maintained separately from the COPO project source code, but its schemas are integrated into the COPO platform and used for metadata validation and manifest rendering.
These schemas are used internally by the COPO platform to:
- Drive user-facing metadata manifests
- Validate user-submitted metadata
- Inform data submission to external repositories (e.g. European Nucleotide Archive (ENA), Zenodo and BioImage Archive (BIA))
They are not intended for direct use by external tools but may serve as references for integration or review.
Each schema aligns with a checklist or metadata category, such as:
- Single-cell submissions
- Spatial ranscriptomic datasets
- Sample metadata
- Image metadata
Checklists are sometimes referred to interchangeably as manifests. A manifest is essentially a spreadsheet (e.g., CSV or XLSX) that can be filled in with metadata relevant to a particular data type or submission workflow.
The repository is structured as follows:
COPO-schemas/
├── images/
│ └── image_schema_main.xlsx
├── sample/
│ ├── sample_checklist_dwc.xml
│ └── sample_checklist_faang.xml
├── single_cell/
│ ├── singlecell_schema_main.json
│ ├── singlecell_schema_main.yaml
│ └── singlecell_schema_main.xlsx
├── LICENSE
└── README.md
All schemas follow a versioning convention (e.g. v0.1, v1, v2, etc.) to track changes over time. Refer to the file names for the most recent version.
This repository is currently managed by the COPO project team. Contributions or suggestions may be considered via pull request or GitHub issues, especially regarding schema corrections or updates based on evolving standards.
Unless otherwise stated, all schema files are released under the MIT License.
- COPO web platform
- About COPO
- COPO Documentation
- Earlham Institute
- Single-cell schemas website
- Single-cell schemas documentation
Here are other COPO-related repositories you may find useful:
For questions, feedback or collaboration enquiries, please contact the COPO team at ei.copo@earlham.ac.uk.