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ncbi-gene-search

ncbi-gene-search is a skill for Claude Code, Codex from ma-compbio-lab/SkillFoundry. It costs 46 tokens per session (534 once invoked), scanned A, original, Apache-2.0.

A lookup workflow for NCBI Gene, a public database of official information about genes, using a gene symbol and organism. It returns matching gene identifiers and short summaries.

In plain words
What is it for?
Use it for quick single-gene searches, checking the organism, description, genomic location, and Entrez Gene identifier.
Why use it?
It helps resolve ambiguous gene names and obtain an official identifier before using a gene in a larger genomics or literature workflow.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 39repo +1 4mo ago A scan 46 tokens original Apache-2.0

Good fit Use it for quick single-gene searches, checking the organism, description, genomic location, and Entrez Gene identifier.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/ma-compbio-lab/skillfoundry/ncbi-gene-search
View source ↗ ma-compbio-lab/SkillFoundry ma-compbio-lab.github.io
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 ma-compbio-lab/SkillFoundry --skill ncbi-gene-search
Clone the repo
git clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundry

Made for: Claude Code, Codex.

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 ncbi-gene-search

README.md
[![agentmods](https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search/github.svg)](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search)
Your own site
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search/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 ncbi-gene-search

Your own site · 80×15
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/ncbi-gene-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 534 The whole file, excluding the scripts and references it only reads on demand.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00046 $0.00534
Opus 5 $0.00023 $0.00267
Sonnet 5 $0.00009 $0.00107
Haiku 4.5 $0.00005 $0.00053

Measured 6d ago against content hash c3077c56f12e, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

ncbi-gene-search 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 6d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/search_ncbi_gene.py, tests/test_ncbi_gene_search.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/genomics/ncbi-gene-search/SKILL.md · 58 lines

What it actually says

Purpose

Resolve a gene symbol through NCBI E-utilities and return concise Gene database summaries.

When to use

  • You need an official Entrez Gene identifier for a symbol and species.
  • You want a quick NCBI summary before a larger genomics workflow.

When not to use

  • You need transcript-level coordinates or large-batch annotation.
  • You need clinical interpretation or variant effect prediction.
  • You need offline execution.

Inputs

  • Gene symbol
  • Optional species, maximum result count, email, and output path

Outputs

  • JSON payload containing the query, matched Gene IDs, and compact gene summaries

Requirements

  • Python 3.10+
  • Network access to eutils.ncbi.nlm.nih.gov

Procedure

  1. Run python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol BRCA1 --species "homo sapiens" --retmax 1 --out skills/genomics/ncbi-gene-search/assets/brca1_gene_summary.json.
  2. Inspect the genes list for gene_id, symbol, description, organism, and map_location.
  3. Use the NCBI gene ID in downstream lookup or literature workflows when needed.

Validation

  • Command exits successfully.
  • search.ids contains at least one Gene ID for a known symbol.
  • The first result has a non-empty symbol and organism.

Failure modes and fixes

  • No hits: confirm the symbol and organism spelling.
  • Unexpected species: make the organism explicit with --species.
  • Too many matches: lower --retmax and review the returned summaries.

Safety and limits

  • Metadata lookup only.
  • This skill does not perform variant interpretation or clinical classification.

Example

  • python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol TP53 --species "homo sapiens" --retmax 1

Provenance

  • ensembl-gene-lookup
  • ncbi-pubmed-search
Files

What ships with it

8 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.

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. 6d ago First seen · 58 lines · 46 tokens per session scan A c3077c56f12e

Subscribe to this mod's changes

ncbi-gene-search is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (39 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 46 tokens to every session and 534 once invoked, about $0.0002 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 2026-09-03.

ResearchScientificagent-skillsai-for-scienceautomationcomputational-biologygenomicsllm-agents
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