ontology-validator

name	ontology-validator
description	Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying that required properties are present, or validating that object property relationships have consistent domain and range. Catches unknown classes, unknown properties, domain mismatches, and missing required fields.
allowed-tools	Read, Bash

Ontology Validator

Goal

Validate that material sample annotations comply with ontology constraints: correct class names, valid properties, consistent domain/range relationships, and required fields present.

Requirements

• Python 3.8+
• No external dependencies (Python standard library only)
• Requires ontology-explorer's cmso_summary.json and ontology_registry.json

Inputs to Gather

Input	Description	Example
Annotation	JSON dict or list of annotation dicts	{"class":"UnitCell","properties":{"has Bravais lattice":"cF"}}
Class name	Class to check completeness for	Crystal Structure
Provided properties	Comma-separated property names	"has unit cell,has space group"
Relationships	JSON array of subject-property-object triples	[{"subject_class":"Material","property":"has structure","object_class":"Crystal Structure"}]

Decision Guidance

What do you need to validate?
├── An annotation (classes and properties are correct)
│   └── schema_checker.py --ontology cmso --annotation '<json>'
├── Completeness of a class annotation
│   └── completeness_checker.py --ontology cmso --class <name> --provided <props>
└── Object property relationships
    └── relationship_checker.py --ontology cmso --relationships '<json>'

Script Outputs (JSON Fields)

Script	Key Outputs
scripts/schema_checker.py	results.valid, results.errors, results.warnings, results.class_valid, results.properties_valid
scripts/completeness_checker.py	results.completeness_score, results.required_missing, results.recommended_missing, results.optional_missing, results.unrecognized
scripts/relationship_checker.py	results.valid, results.results, results.errors

Workflow

1. After mapping a sample with ontology-mapper, pass the annotations to schema_checker.py to verify correctness.
2. For a specific class, use completeness_checker.py to see what required/recommended properties are missing.
3. When building relationships between instances, use relationship_checker.py to ensure domain/range consistency.

Conversational Workflow Example

User: I annotated my sample as CrystalStructure with properties hasUnitCell and hasBasis.
      Is this correct and complete?

Agent: Let me validate your annotation and check completeness.

[Runs: completeness_checker.py --ontology cmso --class "Crystal Structure" --provided "has unit cell,has basis" --json]

Your annotation is partially complete:
- has unit cell: provided (required)
- has basis: not a direct property of Crystal Structure (it belongs to Unit Cell)
- **Missing required**: has space group

The "has basis" property belongs to the Unit Cell class, not Crystal Structure.
You should add "has space group" to Crystal Structure and move "has basis"
to the Unit Cell annotation.

CLI Examples

# Validate an annotation
python3 skills/ontology/ontology-validator/scripts/schema_checker.py \
  --ontology cmso \
  --annotation '{"class":"Unit Cell","properties":{"has Bravais lattice":"cF"}}' \
  --json

# Check completeness
python3 skills/ontology/ontology-validator/scripts/completeness_checker.py \
  --ontology cmso \
  --class "Crystal Structure" \
  --provided "has unit cell,has space group" \
  --json

# Validate relationships
python3 skills/ontology/ontology-validator/scripts/relationship_checker.py \
  --ontology cmso \
  --relationships '[{"subject_class":"Computational Sample","property":"has material","object_class":"Material"}]' \
  --json

Error Handling

Error	Cause	Resolution
Class 'X' not found	Invalid class name	Use ontology-explorer to find correct name
Property 'X' not found	Invalid property name	Use property_lookup.py to search
Annotation must be a dict	Wrong input format	Provide valid JSON dict
Relationships must be a non-empty list	Wrong input format	Provide JSON array of relationship dicts

Interpretation Guidance

• Errors indicate definite problems (unknown class/property, range mismatch)
• Warnings indicate potential issues (domain mismatch — may be intentional for subclasses)
• Completeness score: 0.0-1.0 ratio of provided vs. total tracked properties
• required_missing: must fix for valid annotation
• recommended_missing: should fix for quality
• unrecognized: may indicate typos or properties from a different ontology

Limitations

• Constraints file is manually curated, not derived from OWL axioms
• Does not validate data types (e.g., whether a value is actually a float vs string)
• Does not validate cardinality (e.g., exactly one space group per structure)
• Subclass checking uses simple parent traversal, not full OWL reasoning

References

• Validation Rules — what is validated and why
• CMSO Constraints — required/recommended properties per class
• CMSO Guide — CMSO ontology overview

Version History

Date	Version	Changes
2026-02-25	1.0	Initial release with CMSO validation support