Obsidian Literature Workflow
Galaxy-Dawn/claude-scholar
Runs a project literature review in an Obsidian vault: paper notes in Sources/Papers feed Knowledge synthesis, a Writing handoff and a default literature canvas.
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
Install Ontology Explorer
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorer --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ontology-explorer .claude/skills/ontology-explorer && rm -rf skills-srcUse ~/.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/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .claude/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorerType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorer --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/ontology-explorer .agents/skills/ontology-explorer && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .agents/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorer --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/ontology-explorer .cursor/skills/ontology-explorer && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .cursor/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/ontology-explorer--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorer --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/ontology-explorer .gemini/skills/ontology-explorer && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .gemini/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorerInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/ontology-explorer .github/skills/ontology-explorer && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .github/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills ontology-explorer --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/ontology-explorer .opencode/skills/ontology-explorer && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "ontology-explorer" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ontology-explorer into .opencode/skills/ontology-explorer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ontology-explorer", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
ontology-explorer- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 535 words
- Files
- 11 (incl. scripts, references)
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
- Works in 6 steps: Identify which ontology the user is… → Use class_browser.py --list-roots to see… → Drill into specific classes with… → …
- Exploring an ontology like CMSO
- SKILL.md covers Goal, Requirements, Inputs to Gather and Decision Guidance, plus 9 more sections
- Runs Python scripts from its folder; calls python3; reaches raw.githubusercontent.com
What it does
Ontology Explorer is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, understanding class relationships, finding properties for a given class, or searching for ontology terms related to a materials science concept. Supports OWL/XML format from the OCDO ecosystem (CMSO, ASMO, CDCO, PODO, PLDO, LDO).
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including scripts and reference files (for example `references/asmo_guide.md`, `references/asmo_summary.json` and `references/cmso_guide.md`).
It sits in Research & Science, covering Knowledge graphs and Physical and earth sciences. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Exploring an ontology like CMSO
- Understanding class relationships
- Finding properties for a given class
- Searching for ontology terms related to a materials science concept
Example prompts
- “/ontology-explorer”
Requirements
- Python 3
- Pre-approved tools (allowed-tools): Read, Bash
Workflow steps
6 steps, taken from the first numbered list in SKILL.md.
- Identify which ontology the user is working with (default: CMSO).
- Use class_browser.py --list-roots to see the top-level concepts.
- Drill into specific classes with class_browser.py --class to see hierarchy, children, and applicable properties.
- Look up individual properties with property_lookup.py --property .
- If the user mentions a concept but not its ontology name, use --search to find matching classes or properties.
- For a new or updated ontology, run owl_parser.py to parse the raw OWL, then ontology_summarizer.py to generate a summary JSON.
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:
ReadBash
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 4 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
Hosts in commands or code, which the agent is likely to contact:
raw.githubusercontent.com
Also links to:
ocdo.github.iogithub.com
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 Explorer loads about 2k tokens when it runs, and up to ~22k if it reads all its reference files. Until then it costs about 97 tokens; SKILL.md has 535 words of instructions outside code blocks.
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 535 words (~2,010 tokens).
“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.”
- name
- ontology-explorer
- allowed-tools
- Read, Bash
Files
SKILL.md and 10 other files (scripts, references) in skills/ontology-explorer of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- references/asmo_guide.md
- references/asmo_summary.json
- references/cmso_guide.md
- references/cmso_summary.json
- references/ontology_registry.json
- references/owl_primer.md
- scripts/class_browser.py
- scripts/ontology_summarizer.py
- scripts/owl_parser.py
- scripts/property_lookup.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 Explorer 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Ontology Explorer this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Notes | None | |
| Obsidian Literature WorkflowGalaxy-Dawn/claude-scholar | 5.7k | — | ~431 | Automated safety check: Pass | MIT | |
| Behive Researchqa10devteam/behive | 146 | — | ~838 | Automated safety check: Notes | MIT | |
| Scholar RAGjoshzyj/open-scholar-skill | 168 | — | ~7.4k | Automated safety check: Notes | Custom licence | |
| Torchdrugdavila7/claude-code-templates | 32k | 12 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Paper AnalyzerLigphiDonk/Oh-my--paper | 738 | 1 repos | ~973 | Automated safety check: Pass | MIT |
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Torchdrug
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Paper Analyzer
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Related
Categories
Questions about Ontology Explorer
What does Ontology Explorer do?
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Ontology Explorer is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
When should I use Ontology Explorer?
Ontology Explorer fits situations like: exploring an ontology like CMSO; understanding class relationships; finding properties for a given class; searching for ontology terms related to a materials science concept.
How do I install Ontology Explorer in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a claude-code`. Or copy the skill folder (skills/ontology-explorer in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/ontology-explorer in your project. Claude Code loads it when a task matches its description.
How do I install Ontology Explorer in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill ontology-explorer -a codex`. Or copy the skill folder (skills/ontology-explorer in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/ontology-explorer in your project. Codex loads it when a task matches its description.
Can I use Ontology Explorer 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-explorer -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-explorer, .gemini/skills/ontology-explorer, .github/skills/ontology-explorer and .opencode/skills/ontology-explorer in your project.
What does Ontology Explorer need to run?
Going by SKILL.md and its folder, Ontology Explorer 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 Explorer access the network?
SKILL.md names 3 domains. In commands or code: raw.githubusercontent.com; the agent is likely to contact it when it follows the instructions. As links in the text: ocdo.github.io and github.com. This is read from the text; nothing was executed.
Is Ontology Explorer 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 Explorer use?
No licence was found for Ontology Explorer or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Ontology Explorer use?
About 2k tokens (SKILL.md is roughly 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 20k tokens, read only when the agent opens those files.
What are the alternatives to Ontology Explorer?
Skills that share tags, products or a category with Ontology Explorer: Obsidian Literature Workflow (Galaxy-Dawn/claude-scholar, 5.7k stars), Behive Research (qa10devteam/behive, 146 stars), Scholar RAG (joshzyj/open-scholar-skill, 168 stars) and Torchdrug (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Ontology Explorer?
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.