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>'

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.

# 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