What is mygene-mcp AGENTS.md?

Instructions for using an MCP server that looks up gene information through the MyGene.info API. Genes are units of biological information, and the server combines annotations from many biomedical databases.

Use it for gene lookups, gene annotations, tissue expression, pathways, gene relationships across species, genomic regions, batch queries, and data exports.

It tells coding assistants which biomedical questions the server handles, how to run it, and when to choose it over another server.

How nickzren/mygene-mcp configures Codex and OpenCode

Reuse

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.

Copy the file

curl -O https://raw.githubusercontent.com/nickzren/mygene-mcp/main/AGENTS.md

Clone the repo

git clone --depth 1 https://github.com/nickzren/mygene-mcp

Made for: Codex, OpenCode.

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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/nickzren/mygene-mcp/agents-md/github.svg)](https://agentmods.dev/instructions/nickzren/mygene-mcp/agents-md)

Your own site

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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.

Your own site · 80×15

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Per session 585 This file is loaded in full into every session.

When invoked 585 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original 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.

Model	Per session	Once invoked
Fable 5.1	$0.00585	$0.00585
Opus 5.5	$0.00234	$0.00234
Sonnet 5.5	$0.00117	$0.00117
Haiku 4.5	$0.00059	$0.00059

Measured 2mo ago against content hash 3d7cbbeec595, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 2mo 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.

AGENTS.md · 52 lines

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 entrypoint
src/mygene_mcp/client.py — HTTP client to MyGene.info
src/mygene_mcp/tools/ — tool implementations

Dev

uv sync --extra dev
uv run pytest tests/ -v

Read the full file on GitHub · 52 lines

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.

2mo ago First seen · 52 lines · 585 tokens per session scan A 3d7cbbeec595

Subscribe to this mod's changes

mygene-mcp AGENTS.md is an instructions file published in the GitHub repository nickzren/mygene-mcp (0 stars, last pushed 6mo ago), licensed MIT. It adds 585 tokens to every session, about $0.0023 per session on Opus 5.5. 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.

Scientific bioinformatics fastmcp gene-annotation gene-expression gene-ontology genomics

mygene-mcp AGENTS.md next to 6 instructions from other repositories
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mygene-mcp AGENTS.mdnickzren/mygene-mcp	Instructions file	0	6mo ago	MIT	A	585	Codex, OpenCode
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mygene-mcp: Instructions file for Codex