Borrowing it
Nothing to install: this file belongs to nickzren/mygene-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/nickzren/mygene-mcp/main/AGENTS.mdgit clone --depth 1 https://github.com/nickzren/mygene-mcpWrote 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/instructions/nickzren/mygene-mcp/agents-md)<a href="https://agentmods.dev/instructions/nickzren/mygene-mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/nickzren/mygene-mcp/agents-md/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/instructions/nickzren/mygene-mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/nickzren/mygene-mcp/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00585 | $0.00585 |
| Opus 5 | $0.00293 | $0.00293 |
| Sonnet 5 | $0.00117 | $0.00117 |
| Haiku 4.5 | $0.00059 | $0.00059 |
Grade A, and why
mygene-mcp AGENTS.md scanned grade A with 0 findings 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 8d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 52 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Agent Guide — mygene-mcp
Brief for AI coding agents (Claude Code, Codex) working in this repo or routing biomedical questions through it.
What this server is
MCP server wrapping the MyGene.info API. Aggregates gene-centric annotations from NCBI, Ensembl, UniProt, HPA, GTEx, KEGG, Reactome, GO, DisGeNET, ClinVar, OMIM, PharmGKB, DrugBank, ChEMBL, InterPro, Pfam, PANTHER, …
Run locally (stdio)
uv sync
uv run python -m mygene_mcp.server # stdio (default)
HTTP/SSE: append --transport http --host 127.0.0.1 --port 8000.
Use this server for
- Gene lookup by symbol, name, Entrez/Ensembl/UniProt/RefSeq IDs
- Comprehensive gene annotations from many sources in one record
- Tissue expression (HPA, GTEx, BioGPS), pathways (KEGG, Reactome, WikiPathways)
- GO term annotations with evidence codes
- Orthologs / homologs across species; genomic interval queries
- Batch operations (up to 1000 genes per request)
- Boolean / faceted advanced queries; export to TSV/CSV/JSON/XML
Prefer over other servers when the question is gene-centric annotation aggregation rather than scored target–disease evidence (use opentargets-mcp for that).
Triage hints
- Symbol → ID resolution is built into the gene query; no separate resolver call needed.
- Use batch queries before iterating gene-by-gene.
- For "genes in pathway X" or "genes expressed in tissue Y", prefer the dedicated tool over building a boolean query.
Pitfalls
- MyGene returns large nested records; ask only for the fields you need (the API supports field projection).
- Some species' annotations are sparser; empty fields are common, not errors.
- Variant data here is pointer-level (rsIDs, ClinVar links); use mydisease-mcp or opentargets-mcp for variant biology.
Source layout
src/mygene_mcp/server.py— FastMCP entrypointsrc/mygene_mcp/client.py— HTTP client to MyGene.infosrc/mygene_mcp/tools/— tool implementations
Dev
uv sync --extra dev
uv run pytest tests/ -v
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.
- 8d ago First seen · 52 lines · 585 tokens per session scan A 3d7cbbeec595
mygene-mcp AGENTS.md is an instructions file published in the GitHub repository nickzren/mygene-mcp (0 stars, last pushed 4mo ago), licensed MIT. It adds 585 tokens to every session, about $0.0029 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.