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 
├── Find properties for a class
│   └── property_lookup.py --ontology cmso --class 
├── Look up a specific property
│   └── property_lookup.py --ontology cmso --property 
├── Search for a concept
│   ├── class_browser.py --ontology cmso --search 
│   └── property_lookup.py --ontology cmso --search 
├── Parse a new/updated OWL file
│   └── owl_parser.py --source 
└── Generate/refresh a summary JSON
    └── ontology_summarizer.py --source  --output 

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 to see hierarchy, children, and applicable properties.
4. Look up individual properties with property_lookup.py --property .
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

# 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: a property can apply to more than one class. When it does, the domain is shown as the classes joined with a pipe, e.g. A | B. (The bundled CMSO/ASMO summaries currently contain no union-domain properties.)
• Search relevance: 1.0 = label match, 0.5 = description match only.

Verification checklist

Before presenting any class, property, or relationship as fact, confirm and record:

• [ ] Resolved the target via class_browser.py --class (or property_lookup.py) and recorded the exact canonical label returned in results.class_info.label / results.property_info.name — do not quote a name the agent typed; quote the label the tool resolved (e.g. UnitCell → Unit Cell).
• [ ] For every relationship chain stated, cited the actual domain and range from a property_lookup.py --property call (recorded results.property_info.domain and .range), rather than inferring the link from class names.
• [ ] When a property's domain contains a pipe (A | B), reported it as a union (applies to each listed class) and confirmed the class in question matches one normalized member — did not silently assume single-class domain.
• [ ] For --search results, recorded each match's relevance and stated whether it was a label match (1.0) or description-only match (0.5); did not present a 0.5 description hit as a confirmed term match.
• [ ] Identified the ontology by its registry key (cmso or asmo) and confirmed it exists in references/ontology_registry.json; did not query an unregistered ontology or conflate CMSO and ASMO terms.
• [ ] When relying on a generated/refreshed summary, recorded its metadata.source_url and metadata.generated_at and the statistics (num_classes, num_object_properties, num_data_properties) so the result is traceable to a specific OWL source.
• [ ] Treated absent parents, descriptions, or domain/range as missing data (not as "no such relationship"), since the parser extracts only simple rdfs:subClassOf and declared domains/ranges and does no reasoning.

Common pitfalls & rationalizations

| Tempting shortcut | Why it's wrong / what to do | |-------------------|-----------------------------| | "The class name UnitCell returned nothing, so the term doesn't exist." | Labels carry spaces (Unit Cell). The tools resolve exact → case-insensitive → space-normalized; if a direct guess fails, run --search and use the canonical label the tool returns, not the typed string. | | "These two classes are obviously related, so I'll state the link." | Relationships exist only where an object property declares them. Verify with property_lookup.py --property and quote the recorded domain → range; never infer a triple from class names alone. | | "The script ran and printed results, so the answer is complete." | Run success ≠ completeness. A missing parent, description, or domain/range means the OWL lacked that annotation — the parser does no inference and ignores complex OWL restrictions. State what is absent. | | "--search crystal matched it, so it's the right term." | A match may be relevance 0.5 (description-only), not a label match. Check the relevance field and prefer 1.0 label matches; report 0.5 hits as "mentioned in the description," not as the canonical term. | | "A property has one domain class." | Domains can be unions (A | B). Split on | and check each normalized member; a property may legitimately apply to several classes. The bundled CMSO/ASMO summaries currently have none, but parsed/refreshed ones can. | | "Any OCDO ontology will work / CMSO and ASMO are interchangeable." | Only cmso and asmo are registered; CDCO/PODO/PLDO/LDO are planned, not available. Pick the correct registry key and don't mix terms across ontologies. | | "I'll point the parser at this http:// OWL URL." | owl_parser.py/ontology_summarizer.py reject non-https:// URLs by design. Use an https:// source or a local file path. |

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](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 — official CMSO docs
• CMSO Repository — source OWL file and development

Version History

| Date | Version | Changes | |------|---------|---------| | 2026-06-24 | 1.2.2 | Added a Verification checklist (evidence-based, tied to canonical-label resolution, recorded domain/range, union domains, search relevance, registry keys, and summary provenance) and a Common pitfalls & rationalizations table. | | 2026-06-23 | 1.2.0 | Fixed property_lookup --class to resolve canonical labels (spaceless names like UnitCell now match), made class/property domain matching consistent across tools, enforced documented security controls (safe-character pattern, length caps, search-result caps, HTTPS-only URLs), corrected union-domain doc example and eval assertions, scoped description to CMSO/ASMO. | | 2026-02-25 | 1.0 | Initial release with CMSO support |

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: HeshamFS
• Source: HeshamFS/materials-simulation-skills
• License: Apache-2.0

Install and usage instructions live in the source repository linked above.