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YAML Templates for Neuroshapes

Human-readable templates for manual data entry. These templates can be filled out and converted to JSON-LD for validation.

Usage

  1. Copy the relevant template file
  2. Fill in your experimental data
  3. Convert to JSON-LD using scripts/yaml_to_jsonld.py
  4. Validate against Neuroshapes schemas

Available Templates

  • subject.yaml - Subject/animal information
  • slice.yaml - Brain slice preparation
  • patched_slice.yaml - Electrophysiology recording
  • reconstructed_cell.yaml - Complete neuron reconstruction workflow

Example

# Copy a template
cp templates/yaml/subject.yaml my_experiment.yaml

# Edit with your data
nano my_experiment.yaml

# Convert to JSON-LD
python scripts/yaml_to_jsonld.py my_experiment.yaml my_experiment.json

# Validate (optional)
python scripts/yaml_to_jsonld.py my_experiment.yaml my_experiment.json --validate

Why YAML?

  • Human-readable: Cleaner syntax than JSON
  • Less error-prone: No bracket matching issues
  • Compact: Uses indentation instead of separators
  • JSON-compatible: YAML is a superset of JSON
  • Better for manual editing: Easier to see hierarchy

Contributing

When creating new templates:

  1. Follow the existing naming convention
  2. Include helpful comments for each field
  3. Provide example values where appropriate
  4. Test conversion to JSON-LD