ontology-mapper agent skill by HeshamFS

At a glance

Before you install

Read from the skill's files at the directory's October 19, 2026 snapshot: what ships with it, what its code reads, and the terms it is published under.

• Bundled scripts: 3 script files (3 Python). Your agent may run them, so read them first.
• Tool permissions requested: Read, Grep, Glob (the allowed-tools field of SKILL.md).
• License: Apache-2.0, an open-source or open-content license.

Install ontology-mapper

The skills CLI works with Claude Code, Codex, Cursor and other agents; the other routes copy the folder by hand.

npx skills add https://github.com/HeshamFS/materials-simulation-skills/tree/main/skills/ontology/ontology-mapper

tmp="$(mktemp -d)"
git clone --depth 1 https://github.com/HeshamFS/materials-simulation-skills.git "$tmp/repo"
mkdir -p .claude/skills
cp -R "$tmp/repo/"skills/ontology/ontology-mapper .claude/skills/
rm -rf "$tmp"

python3 ~/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py \
    --repo HeshamFS/materials-simulation-skills \
    --path skills/ontology/ontology-mapper

HeshamFS/materials-simulation-skills is third-party code. Read SKILL.md and any bundled scripts before you install it.

How the author describes it

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."

From the description field of SKILL.md. Agents read this line to decide when to load the skill.

Sections in SKILL.md

• Goal
• Requirements
• Inputs to Gather
• Decision Guidance
• Script Outputs (JSON Fields)
• Workflow
• Conversational Workflow Example
• CLI Examples
• Adding a New Ontology
• Error Handling
• Interpretation Guidance
• Verification checklist
• Common pitfalls & rationalizations
• Security
• Input Validation
• File Access

Files in the skill folder

• CHANGELOG.md
• SKILL.md
• evals/evals.json
• references/asmo_mappings.json
• references/cmso_mappings.json
• references/crystal_systems.json
• references/element_data.json
• references/mapping_patterns.md
• scripts/concept_mapper.py
• scripts/crystal_mapper.py
• scripts/sample_annotator.py

Suede Skill Check: 82/100 · B

ontology-mapper passes the required frontmatter check and all seven graded checks, which cover the SKILL.md format, a declared license and a commit in the last year. Those checks earn 56 of the score’s points; the rest come from description quality, instruction depth, bundled files, maintenance and curated-list citations. How the score works.

Where this skill is cited

HeshamFS/materials-simulation-skills appears in 2 curated lists: BehiSecc/awesome-claude-skills, VoltAgent/awesome-agent-skills.

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