Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.

No licenceAuto-check: notesResearch & Science

Install Ontology Mapper

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-mapper -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-mapper --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ontology-mapper .claude/skills/ontology-mapper && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
ontology-mapper
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.9k tokens
SKILL.md length
496 words
Files
9 (incl. scripts, references)
Skills in repo
170
Repo updated
First seen
Licence
None found

At a glance

Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.

  • Works in 5 steps: If the user provides natural-language… → If the user describes crystal structure… → For a complete sample description, use… → …
  • Translating natural-language material descriptions to ontology terms
  • SKILL.md covers Goal, Requirements, Inputs to Gather and Decision Guidance, plus 10 more sections
  • Runs Python scripts from its folder; calls python3

What it does

Ontology Mapper is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in ontologyregistry.json. Use when translating natural-language material descriptions to ontology terms, annotating simulation inputs with ontology metadata, or mapping crystal parameters (space group, Bravais lattice, lattice constants) to standardized ontology representations.

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including scripts and reference files (for example `references/asmo_mappings.json`, `references/cmso_mappings.json` and `references/crystal_systems.json`).

It sits in Research & Science, covering Physical and earth sciences and Translation. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Translating natural-language material descriptions to ontology terms
  • Annotating simulation inputs with ontology metadata
  • Mapping crystal parameters (space group
  • Bravais lattice

Example prompts

  • “/ontology-mapper”

Requirements

  • Python 3
  • Pre-approved tools (allowed-tools): Read, Bash

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. If the user provides natural-language terms, use concept_mapper.py to find matching ontology classes.
  2. If the user describes crystal structure parameters, use crystal_mapper.py to map them and validate constraints.
  3. For a complete sample description, use sample_annotator.py to produce full ontology annotations.
  4. Review any validation warnings (e.g., lattice parameter mismatches for the crystal system).
  5. Check unmapped_fields and suggested_properties for completeness.

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Bash

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 3 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python3

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Ontology Mapper loads about 1.9k tokens when it runs, and up to ~6.4k if it reads all its reference files. Until then it costs about 110 tokens; SKILL.md has 496 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~110
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~6.4k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Read, Bash

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 496 words (~1,949 tokens).

“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.”

— opening of SKILL.md by FreedomIntelligence
name
ontology-mapper
allowed-tools
Read, Bash

Read the full SKILL.md on GitHub

Files

SKILL.md and 8 other files (scripts, references) in skills/ontology-mapper of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • 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

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Ontology Mapper next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Ontology Mapper compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Ontology Mapper this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.9kAutomated safety check: NotesNone
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Cantera Ignition DelayK-Dense-AI/scientific-agent-skills48k2 repos~2.2kAutomated safety check: PassMIT
AstropyzLanqing/codex-claude-academic-skills4.6k14 repos~2.9kAutomated safety check: PassBSD-3-Clause
PymatgenzLanqing/codex-claude-academic-skills4.6k12 repos~5kAutomated safety check: PassMIT
Arxiv TranslatorLeey21/arxiv-translator497—~627Automated safety check: PassMIT

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Questions about Ontology Mapper

What does Ontology Mapper do?

Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Ontology Mapper is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.

When should I use Ontology Mapper?

Ontology Mapper fits situations like: translating natural-language material descriptions to ontology terms; annotating simulation inputs with ontology metadata; mapping crystal parameters (space group; bravais lattice.

How do I install Ontology Mapper in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-mapper -a claude-code`. Or copy the skill folder (skills/ontology-mapper in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/ontology-mapper in your project. Claude Code loads it when a task matches its description.

How do I install Ontology Mapper in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-mapper -a codex`. Or copy the skill folder (skills/ontology-mapper in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/ontology-mapper in your project. Codex loads it when a task matches its description.

Can I use Ontology Mapper in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-mapper -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ontology-mapper, .gemini/skills/ontology-mapper, .github/skills/ontology-mapper and .opencode/skills/ontology-mapper in your project.

What does Ontology Mapper need to run?

Going by SKILL.md and its folder, Ontology Mapper needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3. Its frontmatter pre-approves these tools: Read, Bash.

Does Ontology Mapper access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Ontology Mapper safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Ontology Mapper use?

No licence was found for Ontology Mapper or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Ontology Mapper use?

About 1.9k tokens (SKILL.md is roughly 7.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 4.5k tokens, read only when the agent opens those files.

What are the alternatives to Ontology Mapper?

Skills that share tags, products or a category with Ontology Mapper: Picture Book Wizard (aiskillstore/marketplace, 430 stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars), Astropy (zLanqing/codex-claude-academic-skills, 4.6k stars) and Pymatgen (zLanqing/codex-claude-academic-skills, 4.6k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Ontology Mapper?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 skills in this directory. The repository was last updated on July 21, 2026.

Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.