# ontology-mapper

Maps materials-science terms and crystal data to ontology classes and properties. Use it to prepare sample annotations or add structured metadata to simulation inputs.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · ★ 83
- Author: HeshamFS
- License: Apache-2.0 · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/HeshamFS/materials-simulation-skills/tree/HEAD/skills/ontology/ontology-mapper/SKILL.md
- Updated: 2026-10-21
- HTML: https://affpapa.org/en/nevibecode/skills/ontology-mapper

## What it does

Ask the skill to resolve a term such as “space group” to an ontology class, or to turn lattice parameters into ontology-ready annotations. It can also build sample metadata from structured input. Results include matches, unmapped terms or fields, and validation warnings.

The skill uses separate scripts for concept lookup, crystal mapping, and sample annotation. It requires Python 3.10+, a summary JSON from ontology-explorer, `ontology_registry.json`, and a `<name>_mappings.json` file for the chosen ontology. It uses Python’s standard library, so no external Python packages are needed.

Crystal and sample annotations use CMSO vocabulary. ASMO covers simulation methods, so use concept mapping for ASMO terms instead. If the sample or crystal mapper runs against ASMO, unresolved terms receive confidence 0.0 and validation warnings; that distinction matters when preparing metadata for reuse.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add HeshamFS/materials-simulation-skills --skill ontology-mapper -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/ontology-mapper/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/ontology-mapper/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add HeshamFS/materials-simulation-skills --skill ontology-mapper -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/ontology-mapper/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add HeshamFS/materials-simulation-skills --skill ontology-mapper -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/ontology-mapper/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install HeshamFS/materials-simulation-skills ontology-mapper
```

2. **Manually: put the files in place**
- File: `.github/skills/ontology-mapper/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add HeshamFS/materials-simulation-skills --skill ontology-mapper -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/HeshamFS/materials-simulation-skills --path skills/ontology/ontology-mapper
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/ontology-mapper/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add HeshamFS/materials-simulation-skills --skill ontology-mapper -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/HeshamFS/materials-simulation-skills/tree/HEAD/skills/ontology/ontology-mapper/SKILL.md

## When to use it
- resolve a materials-science term to an ontology class
- map a Bravais lattice and space group to ontology properties
- create ontology annotations from structured sample data
- identify unmapped fields and validation warnings

## Example prompts
- Find CMSO classes for “unit cell” and “space group”.
- Map a BCC lattice, space group 229, and a=2.87 to CMSO terms.
- Create ontology annotations for a copper sample with FCC structure and lattice parameter 3.615.

## Source text · SKILL.md · Apache-2.0

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: 437fcaea3a387703.

BEGIN THIRD-PARTY FILE 437fcaea3a387703
```text
---
name: ontology-mapper
description: >
  Map materials science terms, crystal structures, and sample descriptions to
  standardized ontology classes and properties — resolve natural-language
  concepts to ontology entries with confidence scores, translate Bravais
  lattice types, space groups, and lattice constants into ontology-compliant
  annotations, and produce full sample metadata from structured descriptions.
  Supports any ontology in ontology_registry.json (CMSO, ASMO, etc.). Use
  when annotating simulation inputs with FAIR metadata, translating "BCC
  iron" or "FCC copper" into formal ontology terms, preparing machine-
  readable sample descriptions, or bridging between lab vocabulary and
  ontology vocabulary, even if the user only says "what CMSO terms describe
  my material" or "annotate this sample for me."
allowed-tools: Read, Grep, Glob
metadata:
  last_deterministic_eval: "2026-10-20"
  agent_evaluation_status: "not_revalidated"
  author: HeshamFS
  version: "1.2.3"
  security_tier: low
  security_reviewed: true
  tested_with:
    - claude-code
  last_evaluated: "2026-06-24"
  eval_cases: 8
  last_reviewed: "2026-10-19"
  standards:
    - "CMSO (Computational Material Sample Ontology)"
    - "ASMO (Atomistic Simulation Methods Ontology)"
    - "International Tables for Crystallography (7 crystal systems, 14 Bravais lattices via Pearson symbols, 230 space groups)"
    - "FAIR data principles (Wilkinson et al. 2016)"
---

# Ontology Mapper

## Goal

Translate real-world materials science descriptions into standardized ontology annotations. Given terms like "FCC copper" or structured data like `{"material": "iron", "structure": "BCC", "lattice_a": 2.87}`, produce the corresponding ontology classes and properties for any registered ontology.

## Requirements

- Python 3.10+
- No external dependencies (Python standard library only)
- Requires ontology-explorer's summary JSON and `ontology_registry.json`
- Per-ontology mapping config (`<name>_mappings.json`) for ontology-specific synonyms and labels

## Inputs to Gather

| Input | Description | Example |
|-------|-------------|---------|
| Ontology | Ontology name from registry | `cmso`, `asmo` |
| Term(s) | Natural-language materials concept(s) | `"unit cell"`, `"FCC,copper,lattice"` |
| Crystal system | One of the 7 crystal systems | `cubic`, `hexagonal` |
| Bravais lattice | Lattice type (symbol or common name) | `FCC`, `cF`, `BCC` |
| Space group | Space group number (1-230) | `225` |
| Lattice parameters | a, b, c in angstroms; alpha, beta, gamma in degrees | `a=3.615` |
```
END THIRD-PARTY FILE 437fcaea3a387703

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