LLM Wiki Knowledge Graph
Egonex-AI/Understand-Anything
Detects a Karpathy-pattern LLM wiki and builds an interactive knowledge graph with entities, implicit relationships and topic clusters.
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species.
Install Monarch Database
$ npx skills add lamm-mit/scienceclaw --skill monarch-database -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install lamm-mit/scienceclaw monarch-database --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/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/monarch-database .claude/skills/monarch-database && 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 "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .claude/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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/lamm-mit/scienceclaw/tree/main/skills/monarch-databaseType 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 lamm-mit/scienceclaw --skill monarch-database -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install lamm-mit/scienceclaw monarch-database --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/monarch-database .agents/skills/monarch-database && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .agents/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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 lamm-mit/scienceclaw --skill monarch-database -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install lamm-mit/scienceclaw monarch-database --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/monarch-database .cursor/skills/monarch-database && 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 "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .cursor/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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/lamm-mit/scienceclaw.git --path skills/monarch-database--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 lamm-mit/scienceclaw --skill monarch-database -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install lamm-mit/scienceclaw monarch-database --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/monarch-database .gemini/skills/monarch-database && 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 "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .gemini/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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 lamm-mit/scienceclaw monarch-databaseInstalls 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 lamm-mit/scienceclaw --skill monarch-database -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/monarch-database .github/skills/monarch-database && 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 "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .github/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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 lamm-mit/scienceclaw --skill monarch-database -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install lamm-mit/scienceclaw monarch-database --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/monarch-database .opencode/skills/monarch-database && 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 "monarch-database" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/monarch-database into .opencode/skills/monarch-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "monarch-database", 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
monarch-database- GitHub stars
- 244
- Used in
- 2 other repos
- Token cost
- ~453 tokens
- SKILL.md length
- 168 words
- Files
- 1
- Skills in repo
- 85
- Repo updated
- First seen
- Licence
- CC0-1.0
At a glance
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species.
- Works in 5 steps: Phenotype-to-gene mapping - Find genes… → Disease-to-gene associations - Discover… → Cross-species ortholog discovery -… → …
- Rare disease gene discovery
- SKILL.md covers Overview, Core Capabilities, Key Workflows and Best Practices
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Monarch Database is an agent skill from lamm-mit/scienceclaw. Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.
Its SKILL.md is about 450 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Knowledge Management, covering Knowledge graphs. The licence is CC0-1.0.
When your agent uses it
- Rare disease gene discovery
- Phenotype-to-gene mapping
- Cross-species disease modeling
- HPO term lookup
Example prompts
- “/monarch-database”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Phenotype-to-gene mapping - Find genes associated with human phenotype terms
- Disease-to-gene associations - Discover disease-causing genes using MONDO disease identifiers
- Cross-species ortholog discovery - Identify model organism orthologs for human genes
- HPO semantic similarity - Compare phenotype profiles between individuals/organisms
- Automated disease diagnosis - Build diagnostic algorithms from phenotype to gene lists
What it can do on your machine
Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
monarchinitiative.org
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
Monarch Database loads about 453 tokens when it runs. Until then it costs about 76 tokens; SKILL.md has 168 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 passed
The automated check found no risky patterns in SKILL.md.
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); files beside SKILL.md are not scanned.
SKILL.md
The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its CC0-1.0 licence (© lamm-mit). 168 words, ~453 tokens.
Download SKILL.mdSave it as
.claude/skills/monarch-database/SKILL.md (or your agent's skills folder).- name
- monarch-database
- description
- Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.
- license
- CC0-1.0
- metadata.skill-author
- Kuan-lin Huang
Monarch Initiative Database
Overview
The Monarch Initiative (https://monarchinitiative.org/) is a multi-species integrated knowledgebase that links genes, diseases, and phenotypes across humans and model organisms. It integrates data from over 40 sources including OMIM, ORPHANET, HPO (Human Phenotype Ontology), ClinVar, MGI (Mouse Genome Informatics), ZFIN (Zebrafish), RGD (Rat), FlyBase, and WormBase.
Core Capabilities
The skill provides REST API v3 access for:
- Phenotype-to-gene mapping - Find genes associated with human phenotype terms
- Disease-to-gene associations - Discover disease-causing genes using MONDO disease identifiers
- Cross-species ortholog discovery - Identify model organism orthologs for human genes
- HPO semantic similarity - Compare phenotype profiles between individuals/organisms
- Automated disease diagnosis - Build diagnostic algorithms from phenotype to gene lists
Key Workflows
- Rare disease gene discovery using patient phenotypes (HP terms)
- Model organism selection for disease research
- Phenotype-based patient stratification
- Cross-species disease mechanism studies
- Regulatory variant functional consequence prediction
Best Practices
Use standardized identifiers: MONDO for diseases, HP for phenotypes, HGNC for human genes. Leverage the integrated data from multiple curated sources for robust evidence accumulation.
© lamm-mit, CC0-1.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/monarch-database of lamm-mit/scienceclaw.
Open the folder on GitHubat commit ab9aba1
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in lamm-mit/scienceclaw, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Monarch Database 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 |
|---|---|---|---|---|---|---|
| Monarch Database this skilllamm-mit/scienceclaw | 244 | 2 repos | ~453 | Automated safety check: Pass | CC0-1.0 | |
| LLM Wiki Knowledge GraphEgonex-AI/Understand-Anything | 85k | 1 repos | ~1.5k | Automated safety check: Pass | MIT | |
| Obsidian Canvas BoardsAgriciDaniel/claude-obsidian | 15k | — | ~1.4k | Automated safety check: Pass | MIT | |
| Ontology1mancompany/OneManCompany | 438 | 2 repos | ~1.5k | Automated safety check: Pass | Apache-2.0 | |
| Graphagenticnotetaking/arscontexta | 3.5k | 1 repos | ~4.9k | Automated safety check: Notes | MIT | |
| Knowledge Graphgnomeria/usbtree | 688 | — | ~1.5k | Automated safety check: Pass | MIT |
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Categories
Questions about Monarch Database
What does Monarch Database do?
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Monarch Database is an agent skill from lamm-mit/scienceclaw. Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species.
When should I use Monarch Database?
Monarch Database fits situations like: rare disease gene discovery; phenotype-to-gene mapping; cross-species disease modeling; HPO term lookup.
How do I install Monarch Database in Claude Code?
Run `npx skills add lamm-mit/scienceclaw --skill monarch-database -a claude-code`. Or copy the skill folder (skills/monarch-database in lamm-mit/scienceclaw) into .claude/skills/monarch-database in your project. Claude Code loads it when a task matches its description.
How do I install Monarch Database in Codex?
Run `npx skills add lamm-mit/scienceclaw --skill monarch-database -a codex`. Or copy the skill folder (skills/monarch-database in lamm-mit/scienceclaw) into .agents/skills/monarch-database in your project. Codex loads it when a task matches its description.
Can I use Monarch Database 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 lamm-mit/scienceclaw --skill monarch-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/monarch-database, .gemini/skills/monarch-database, .github/skills/monarch-database and .opencode/skills/monarch-database in your project.
What does Monarch Database need to run?
SKILL.md names no scripts, command-line tools or credentials: Monarch Database is instructions for the agent only.
Does Monarch Database access the network?
SKILL.md names 1 domain. As links in the text: monarchinitiative.org. This is read from the text; nothing was executed.
Is Monarch Database safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Monarch Database use?
Monarch Database is published under the CC0-1.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Monarch Database use?
About 453 tokens (SKILL.md is roughly 1.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Monarch Database?
Skills that share tags, products or a category with Monarch Database: LLM Wiki Knowledge Graph (Egonex-AI/Understand-Anything, 85k stars), Obsidian Canvas Boards (AgriciDaniel/claude-obsidian, 15k stars), Ontology (1mancompany/OneManCompany, 438 stars) and Graph (agenticnotetaking/arscontexta, 3.5k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Monarch Database?
lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.
Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.