linkml-term-validator

Validating LinkML schemas and datasets that depend on external ontology terms

A collection of LinkML ValidationPlugin implementations for validating ontology term references in schemas and data.

Key Features

✅ Three composable validation plugins for the LinkML validator framework
✅ Schema validation - Validates meaning fields in enum permissible values
✅ Dynamic enum validation - Validates data against reachable_from, matches, concepts
✅ Binding validation - Validates constraints on nested object fields
✅ Multi-level caching - In-memory + file-based for fast repeated validation
✅ Ontology Access Kit (OAK) integration - Supports multiple ontology sources
✅ AI hallucination prevention - Dual validation (ID + label) for AI-generated terms

pip install linkml-term-validator

Check that meaning fields reference valid ontology terms:

linkml-term-validator validate-schema schema.yaml

Validate data instances against dynamic enums and binding constraints:

linkml-term-validator validate-data data.yaml --schema schema.yaml

Schema Quality Assurance - Catch typos and mismatches in ontology term references before publishing
Data Validation - Ensure curated datasets only use valid, constrained ontology terms
AI-Generated Content - Prevent language models from hallucinating fake ontology identifiers
CI/CD Integration - Automated validation in continuous integration pipelines
Flexible Constraints - Define valid terms via ontology queries rather than hardcoded lists