ontology-explorer

Files (14)

• CHANGELOG.md
• SKILL.md
• evals.json · evals/
• mini_ontology.owl · evals/files/
• asmo_guide.md · references/
• asmo_summary.json · references/
• cmso_guide.md · references/
• cmso_summary.json · references/
• ontology_registry.json · references/
• owl_primer.md · references/
• class_browser.py · scripts/
• ontology_summarizer.py · scripts/
• owl_parser.py · scripts/
• property_lookup.py · scripts/

SKILL.md (first lines)

# 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. I'll run
a few targeted searches and property lookups (the answer below is synthesized
from several commands, per the Workflow section).

[Runs: class_browser.py --ontology cmso --search "crystal" --json]
  → Crystalline Material, Crystal Structure (among others)
[Runs: class_browser.py --ontology cmso --search "sample" --json]
  → Computational Sample, Atomic Scale Sample
[Runs: class_browser.py --ontology cmso --search "unit cell" --json]
  → Unit Cell
[Runs: class_browser.py --ontology cmso --search "space group" --json]
  → Space Group
[Runs: class_browser.py --ontology cmso --search "element" --json]
  → Chemical Element
[Runs: property_lookup.py --ontology cmso --property "has material" --json]
  → domain Computational Sample → range Material
[Runs: property_lookup.py --ontology cmso --property "has structure" --json]
  → domain Material → range Structure
[Runs: property_lookup.py --ontology cmso --property "has unit cell" --json]
  → domain Crystal Structure → range Unit Cell

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 relationship chain (from the property domains/ranges above):
  Computational Sample → has material → Material → has structure → Structure
  → (Crystal Structure) → has unit cell → Unit Cell

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

From HeshamFS/materials-simulation-skills, Apache-2.0.

More from HeshamFS/materials-simulation-skills