activeinferenceinstitute/gnn-ontology

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):

• process_ontology
• validate_ontology_terms
• extract_ontology_annotations

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