monarch-database

monarch-database is a skill for Claude Code from jaechang-hits/SciAgent-Skills. It costs 78 tokens per session (6,904 once invoked), scanned A, original, no licence file.

A connection to the Monarch Initiative knowledge graph, which links diseases, genes, and observable traits across species. It helps compare disease and phenotype information when studying rare conditions.

In plain words
What is it for?
Use it to find disease-to-gene and disease-to-phenotype links, compare phenotypes between species, and rank possible rare-disease genes from observed traits.
Why use it?
It removes the need to gather disease, gene, phenotype, and cross-species relationships from separate sources. The results can narrow down which genes are worth investigating.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the sciagent-skills plugin — 146 skills shipped together

Good fit Use it to find disease-to-gene and disease-to-phenotype links, compare phenotypes between species, and rank possible rare-disease genes from observed traits.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/monarch-database
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add jaechang-hits/SciAgent-Skills --skill monarch-database
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 146 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for monarch-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/monarch-database/github.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/monarch-database)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/monarch-database"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/monarch-database/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for monarch-database

Your own site · 80×15
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/monarch-database"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/monarch-database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 78 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 6,904 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00078 $0.06904
Opus 5 $0.00039 $0.03452
Sonnet 5 $0.00016 $0.01381
Haiku 4.5 $0.00008 $0.00690

Measured 9d ago against content hash aff1e11cbb45, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

monarch-database scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

r = requests.get(f"{MONARCH_API}{endpoint}", params=params, timeout=30)
skills/genomics-bioinformatics/databases/monarch-database/SKILL.md · 645 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 645 lines · 78 tokens per session scan A aff1e11cbb45

Subscribe to this mod's changes

monarch-database is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (361 stars, last pushed 11d ago), with no licence file. It adds 78 tokens to every session and 6,904 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.