gnn-ontology - SKILL.md Agent Skill

name: gnn-ontology description: GNN Active Inference ontology processing and validation. Use when working with ActInfOntologyAnnotation sections, mapping GNN variables to ontology terms, validating semantic annotations, or exploring Active Inference concept hierarchies.

GNN Ontology Processing (Step 10)

Purpose

Processes Active Inference ontology annotations in GNN models. Maps GNN variables to standardized Active Inference concepts and validates semantic consistency.

Key Commands

# Run ontology processing
python src/10_ontology.py --target-dir input/gnn_files --output-dir output --verbose

# As part of pipeline
python src/main.py --only-steps 10 --verbose

Ontology Term Mapping

GNN Annotation	Ontology Concept	Description
`LikelihoodMatrix`	A matrix	Observation model
`TransitionMatrix`	B matrix	State dynamics
`HiddenState`	s vector	Latent state beliefs
`Observation`	o vector	Sensory observations
`Policy`	π	Action sequences
`Preference`	C matrix	Preferred observations

API

from ontology import (
    process_ontology, parse_gnn_ontology_section, process_gnn_ontology,
    load_defined_ontology_terms, validate_annotations,
    generate_ontology_report_for_file, parse_annotation,
    OntologyProcessor, OntologyValidator
)

# Process ontology section from GNN content
parsed = parse_gnn_ontology_section(gnn_content)

# Load defined ontology terms
terms = load_defined_ontology_terms()

# Validate annotations against defined terms
result = validate_annotations(annotations_list, terms)

# Use OntologyProcessor class
processor = OntologyProcessor()
result = processor.process_ontology(data)

# Use OntologyValidator class
validator = OntologyValidator()
is_valid = validator.validate_ontology(content)

Key Exports

process_ontology — main pipeline processing function
parse_gnn_ontology_section — extract ontology from GNN content
validate_annotations — validate against known terms
OntologyProcessor — class with process_ontology(), validate_terms()
OntologyValidator — class with validate_ontology(), check_consistency()

Output

Ontology mappings in output/10_ontology_output/
Validation reports for annotation consistency

MCP Tools

This module registers tools with the GNN MCP server (see mcp.py):

extract_ontology_annotations
list_standard_ontology_terms
process_ontology
validate_ontology_terms

References

AGENTS.md — Module documentation
README.md — Usage guide
SPEC.md — Module specification

Documentation

README: Module Overview
AGENTS: Agentic Workflows
SPEC: Architectural Specification
SKILL: Capability API