Skip to content

/go-validate

Validate GO-CAM annotations against the official gocam-py/LinkML schema.

Usage

/go-validate [file-path]

If no file is specified, validates the most recent .json file in output/.

Examples

/go-validate output/gocam-20250101-120000.json

/go-validate

What It Checks

LinkML Schema Validation

Structural checks against the gocam LinkML schema:

  • Required fields are present
  • Field types are correct
  • Enum values are valid
  • Overall structure matches the schema

Pydantic Model Validation

Type and constraint checks by loading through the gocam-py Pydantic model:

  • Type coercion and validation
  • Field constraints
  • Model integrity

How It Reports

Passing validation: 

Validation Results for output/gocam-20250101-120000.json
────────────────────────────────────────────────────────
  LinkML schema validation:  PASSED
  Pydantic model validation: PASSED

Validation errors are translated to plain language with suggested fixes:

  • "Missing required field 'taxon'" becomes "Every GO-CAM model needs a species. Add a taxon like NCBITaxon:9606 (human)."
  • "Invalid enum value" becomes an explanation of the valid options

Schema Location

The schema is found automatically from the installed gocam package — no need to download or configure anything.

Next Steps

  • /go-check — Run deeper quality checks (term existence, evidence appropriateness)
  • /go-pr — Submit your validated annotation for review