ontology-explorer

by FreedomIntelligence

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SKILL.md About

---
name: ontology-explorer
description: >
  Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
  Use when exploring an ontology like CMSO, understanding class relationships, finding properties
  for a given class, or searching for ontology terms related to a materials science concept.
  Supports OWL/XML format from the OCDO ecosystem (CMSO, ASMO, CDCO, PODO, PLDO, LDO).
allowed-tools: Read, Bash
---

# 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 3.8+
- 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

```bash
# 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.

## 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](references/owl_primer.md) — brief introduction to OWL concepts
- [CMSO Guide](references/cmso_guide.md) — narrative guide to the CMSO ontology
- [Ontology Registry](references/ontology_registry.json) — registered ontologies and their metadata
- [CMSO Summary](references/cmso_summary.json) — pre-processed CMSO structure
- [CMSO Documentation](https://ocdo.github.io/cmso/) — official CMSO docs
- [CMSO Repository](https://github.com/OCDO/cmso) — source OWL file and development

## Version History

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