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.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-monarchgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-monarch)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-monarch"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-monarch/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.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-monarch"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-monarch.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Data Exfiltration · line 213 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00076 | $0.03663 |
| Opus 5 | $0.00038 | $0.01832 |
| Sonnet 5 | $0.00015 | $0.00733 |
| Haiku 4.5 | $0.00008 | $0.00366 |
Grade A, and why
alterlab-monarch 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 5d 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.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 374 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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.
Monarch enables:
- Mapping phenotypes across species to identify candidate disease genes
- Finding all genes associated with a disease or phenotype
- Discovering model organisms for human diseases
- Navigating the HPO hierarchy for phenotype ontology queries
Key resources:
- Monarch portal: https://monarchinitiative.org/
- API v3 base URL:
https://api-v3.monarchinitiative.org/v3/api(all endpoints live under/v3/api/...) - Interactive API docs (Swagger UI): https://api-v3.monarchinitiative.org/v3/docs
- HPO browser: https://hpo.jax.org/
Scripts
scripts/query_monarch.py — query the Monarch Initiative API v3 (stdlib only, JSON to stdout):
python scripts/query_monarch.py entity HP:0001250 # look up an entity (gene/disease/HPO)
python scripts/query_monarch.py search epilepsy # text search the knowledge graph
python scripts/query_monarch.py associations HGNC:1100 # associations for an entity
When to Use This Skill
Use Monarch when:
- Rare disease gene discovery: What genes are associated with my patient's phenotypes (HPO terms)?
- Phenotype similarity: Are two diseases similar based on their phenotypic profiles?
- Cross-species modeling: Are there mouse/zebrafish models for my disease of interest?
- HPO term lookup: Retrieve HPO term names, definitions, and ontology hierarchy
- Disease-phenotype mapping: List all HPO terms associated with a specific disease
- Gene-phenotype associations: What phenotypes are caused by variants in a gene?
- Ortholog-phenotype mapping: Use animal model phenotypes to infer human gene function
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 5d ago First seen · 374 lines · 76 tokens per session scan A 67a459f719a8
alterlab-monarch is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 6d ago), licensed MIT. It adds 76 tokens to every session and 3,663 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 2026-09-05.
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