SDRF Templates

Versioned templates and validation rules for SDRF-Proteomics.

Structure

{template-name}/
  {version}/
    {template-name}.yaml      # Validation rules and column definitions
    {template-name}.sdrf.tsv  # Example template file

Manifest

The templates.yaml manifest is auto-generated on merge to master. It contains:

• All available templates
• Latest version for each template
• Version history
• Inheritance relationships (extends)

Usage

Finding the latest version

import yaml

with open('templates.yaml') as f:
    manifest = yaml.safe_load(f)

# Get latest human template version
latest = manifest['templates']['human']['latest']  # e.g., "1.1.0"

Loading a template

from pathlib import Path
import yaml

def load_template(name: str, version: str = None) -> dict:
    if version is None:
        with open('templates.yaml') as f:
            manifest = yaml.safe_load(f)
        version = manifest['templates'][name]['latest']

    template_path = Path(name) / version / f'{name}.yaml'
    with open(template_path) as f:
        return yaml.safe_load(f)

Template Inheritance

Templates use an extends field to inherit columns from parent templates:

• base - Core columns shared by all templates
• ms-proteomics extends base - Mass spectrometry columns
• affinity-proteomics extends base - Affinity assay columns
• human extends base - Human sample columns
• dda-acquisition extends ms-proteomics - DDA-specific columns

Adding a New Version

1. Create a new version directory: {template-name}/{new-version}/
2. Add {template-name}.yaml with updated version field
3. Add {template-name}.sdrf.tsv example file
4. Submit PR to master
5. Manifest will auto-update on merge

Repositories Using This

• proteomics-metadata-standard - Specification
• sdrf-pipelines - Validator