HeshamFS/ontology-explorer

Ontology Explorer

Goal

Enable an agent to understand, navigate, and query the structure of materials science ontologies without loading verbose OWL/XML files directly. Provides fast access to class hierarchies, property definitions, and domain-range relationships through pre-processed JSON summaries.

Requirements

• Python 3.10+
• No external dependencies (Python standard library only)
• Internet access required only for owl_parser.py and ontology_summarizer.py when fetching remote OWL files

Inputs to Gather

| Input | Description | Example | |-------|-------------|---------| | Ontology name | Registered ontology to query | cmso | | Class name | A specific class to inspect | Material, UnitCell | | Property name | A specific property to look up | hasMaterial, hasSpaceGroupNumber | | Search term | Keyword to search across labels | crystal, lattice | | OWL source | Path or URL to an OWL/XML file (for parsing/summarizing) | https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl |

Decision Guidance

What do you need?
├── Understand overall ontology structure
│   └── class_browser.py --ontology cmso --list-roots
├── Inspect a specific class
│   └── class_browser.py --ontology cmso --class <name>
├── Find properties for a class
│   └── property_lookup.py --ontology cmso --class <name>
├── Look up a specific property
│   └── property_lookup.py --ontology cmso --property <name>
├── Search for a concept
│   ├── class_browser.py --ontology cmso --search <term>
│   └── property_lookup.py --ontology cmso --search <term>
├── Parse a new/updated OWL file
│   └── owl_parser.py --source <path-or-url>
└── Generate/refresh a summary JSON
    └── ontology_summarizer.py --source <url> --output <path>

Script Outputs (JSON Fields)

| Script | Key Outputs | |--------|-------------| | scripts/owl_parser.py | results.metadata, results.classes, results.object_properties, results.data_properties, results.class_hierarchy | | scripts/ontology_summarizer.py | results.output_file, results.statistics | | scripts/class_browser.py | results.class_info, results.subtree, results.properties, results.path_to_root, results.roots, results.search_results | | scripts/property_lookup.py | results.property_info, results.class_properties, results.search_results |

Workflow

1. Identify which ontology the user is working with (default: CMSO).
2. Use class_browser.py --list-roots to see the top-level concepts.
3. Drill into specific classes with class_browser.py --class <name> to see hierarchy, children, and applicable properties.
4. Look up individual properties with property_lookup.py --property <name>.
5. If the user mentions a concept but not its ontology name, use --search to find matching classes or properties.
6. For a new or updated ontology, run owl_parser.py to parse the raw OWL, then ontology_summarizer.py to generate a summary JSON.

Conversational Workflow Example

User: I have an FCC copper simulation. What CMSO classes should I use to describe it?

Agent: Let me explore the CMSO ontology to find the relevant classes.

[Runs: class_browser.py --ontology cmso --search "crystal" --json]

For an FCC copper simulation, the relevant CMSO classes are:

- **Computational Sample** → **Atomic Scale Sample**: your simulation is an atomic-scale sample
- **Material** → **Crystalline Material**: copper is crystalline
- **Crystal Structure**: describes the FCC arrangement
- **Unit Cell**: the repeating FCC unit cell (a=b=c=3.615 Å, α=β=γ=90°)
- **Space Group**: FCC copper is space group 225 (Fm-3m)
- **Chemical Element**: Cu

The key relationships:
  AtomicScaleSample → hasMaterial → CrystallineMaterial → hasStructure → CrystalStructure → hasUnitCell → UnitCell

Shall I look up the specific properties for any of these classes?

CLI Examples

# List root classes in CMSO
python3 skills/ontology/ontology-explorer/scripts/class_browser.py \
  --ontology cmso --list-roots --json

# Inspect the Material class hierarchy
python3 skills/ontology/ontology-explorer/scripts/class_browser.py \
  --ontology cmso --class Material --json

# Search for crystal-related classes
python3 skills/ontology/ontology-explorer/scripts/class_browser.py \
  --ontology cmso --search crystal --json

# Find all properties for UnitCell
python3 skills/ontology/ontology-explorer/scripts/property_lookup.py \
  --ontology cmso --class UnitCell --json

# Look up a specific property
python3 skills/ontology/ontology-explorer/scripts/property_lookup.py \
  --ontology cmso --property "has space group" --json

# Parse a remote OWL file
python3 skills/ontology/ontology-explorer/scripts/owl_parser.py \
  --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl --json

# Generate a summary JSON from an OWL file
python3 skills/ontology/ontology-explorer/scripts/ontology_summarizer.py \
  --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl \
  --output summary.json --json

Error Handling

| Error | Cause | Resolution | |-------|-------|------------| | Ontology 'X' not in registry | Ontology name not registered | Check references/ontology_registry.json for available names | | Class 'X' not found | Class label doesn't match any entry | Use --search to find similar names, or --list-roots to see available classes | | Property 'X' not found | Property label doesn't match | Use --search to find similar properties | | Cannot parse OWL source | Invalid XML or unreachable URL | Check file path or URL; ensure the file is valid OWL/XML | | Summary file not found | Summary JSON hasn't been generated | Run ontology_summarizer.py first |

Interpretation Guidance

• Class hierarchy: root classes are the broadest concepts; leaf classes are the most specific. A class inherits all properties from its ancestors.
• Object properties: show how classes relate to each other (domain → range). A property with domain UnitCell and range Basis means a unit cell has a basis.
• Data properties: show what literal values a class carries. A property with domain ChemicalElement and range xsd:string means an element has a string-valued attribute.
• Union domains: some properties apply to multiple classes (e.g., hasVector applies to both SimulationCell and UnitCell), shown as SimulationCell | UnitCell.
• Search relevance: 1.0 = label match, 0.5 = description match only.

Security

Input Validation

• --ontology is validated against registered ontology names in ontology_registry.json (fixed allowlist)
• --class and --property names are validated against a safe-character pattern to prevent injection
• --search terms are length-limited and used only for substring matching against pre-processed labels (never interpolated into queries or code)
• --source for owl_parser.py accepts file paths or URLs; URLs are validated against https:// scheme only

File Access

• class_browser.py and property_lookup.py read pre-processed JSON summary files from the references/ directory (read-only)
• owl_parser.py reads a single OWL/XML file from a local path or HTTPS URL; remote fetches have a 30-second timeout
• ontology_summarizer.py writes a single JSON summary file to the path specified by --output
• No scripts modify or delete existing files

Tool Restrictions

• Read: Used to inspect script source, reference files, and ontology summaries
• Bash: Used to execute the four Python scripts (owl_parser.py, ontology_summarizer.py, class_browser.py, property_lookup.py) with explicit argument lists; URL fetching is contained within the Python scripts with timeout limits

Safety Measures

• No eval(), exec(), or dynamic code generation
• All subprocess calls use explicit argument lists (no shell=True)
• OWL/XML parsing uses Python's xml.etree.ElementTree which does not resolve external entities by default, mitigating XXE attacks
• Remote URL fetching is limited to HTTPS with a 30-second timeout to prevent abuse
• Search results are capped in count to prevent output flooding

Limitations

• Only supports OWL/XML format (not Turtle, JSON-LD, or N-Triples)
• Does not support OWL reasoning or inference (e.g., does not compute transitive closures)
• Class hierarchy extraction handles simple rdfs:subClassOf only (not complex OWL restrictions)
• Descriptions may be missing for classes that lack rdfs:comment, skos:definition, or IAO annotations
• URL fetching requires internet access and may time out (30-second limit)

References

• OWL/RDF Primer — brief introduction to OWL concepts
• CMSO Guide — narrative guide to the CMSO ontology
• Ontology Registry — registered ontologies and their metadata
• CMSO Summary — pre-processed CMSO structure
• CMSO Documentation — official CMSO docs
• CMSO Repository — source OWL file and development

Version History

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