Skills gene-database

📦

gene-database

Name: gene-database
Author: davila7

Content revision r1 Safe 🌐 Network access🔑 Env variables📁 Filesystem access⚙️ External commands

Query NCBI Gene Data

Gene lookup often requires several NCBI endpoints and careful query formatting. This skill gives Claude, Codex, and Claude Code reusable workflows for gene search, retrieval, and batch annotation.

Supports: Claude Codex Code(CC)

🥉 79 Bronze

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "gene-database" from https://skillstore.io/skills/davila7-gene-database.md and its manifest at https://skillstore.io/api/skills/davila7-gene-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/davila7-gene-database.md Signed manifest GET /api/skills/davila7-gene-database/manifest Signed lockfile GET /api/skills/davila7-gene-database/lockfile

Test it

Using "gene-database". Search for BRCA1 in human.

Expected outcome:

A concise result with Gene ID 672, symbol BRCA1, the official description, human organism details, chromosome 17, and map location.

Using "gene-database". Annotate a list of four cancer genes.

Expected outcome:

A table-style summary showing each query symbol, matched Gene ID, description, organism, chromosome, map location, and not-found status when needed.

Using "gene-database". Plan a pathway gene search for apoptosis.

Expected outcome:

A workflow that searches by Gene Ontology term, limits results by organism, retrieves summaries in batches, and records the exact query terms used.

Security Audit

Safe

v14 • 7/9/2026 Open versioned report

The executable scripts make intended outbound requests to NCBI Gene APIs and one batch workflow can write results to a user-selected file. API-key and command-execution alerts are false positives from parameter names, placeholders, and Markdown examples; no hardcoded secrets, environment access, prompt injection, or hidden system reconnaissance was found.

Files scanned

1,837

Lines analyzed

Review items

False positives ignored

Capability review items (19)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

Medium

scripts/batch_gene_lookup.py:287

Python file write/append

with open(args.output, 'w') as f:

batch_gene_lookup.py writes JSON results to args.output supplied on the command line. This is intended output behavior, but an unsafe path could overwrite an arbitrary local file.

Low

scripts/batch_gene_lookup.py:14

Python HTTP libraries

import urllib.request

This executable script performs outbound HTTPS requests to NCBI public gene APIs using user-provided gene IDs or search terms. The behavior is intended, but it can disclose queries and optional API keys to an external service.

Low

scripts/batch_gene_lookup.py:78

Python HTTP libraries

with urllib.request.urlopen(url) as response:

Low

scripts/batch_gene_lookup.py:131

Python HTTP libraries

with urllib.request.urlopen(url) as response:

Low

scripts/batch_gene_lookup.py:53

Hardcoded URL

base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

Low

scripts/batch_gene_lookup.py:109

Hardcoded URL

base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

Low

scripts/fetch_gene_data.py:13

Python HTTP libraries

import urllib.request

Low

scripts/fetch_gene_data.py:74

Python HTTP libraries

req = urllib.request.Request(url, headers=headers)

Low

scripts/fetch_gene_data.py:75

Python HTTP libraries

with urllib.request.urlopen(req) as response:

Low

scripts/fetch_gene_data.py:112

Python HTTP libraries

req = urllib.request.Request(url, headers=headers)

Low

scripts/fetch_gene_data.py:113

Python HTTP libraries

with urllib.request.urlopen(req) as response:

Low

scripts/fetch_gene_data.py:146

Python HTTP libraries

req = urllib.request.Request(url, data=data, headers=headers, method='POST')

Low

scripts/fetch_gene_data.py:147

Python HTTP libraries

with urllib.request.urlopen(req) as response:

Low

scripts/fetch_gene_data.py:17

Hardcoded URL

DATASETS_API_BASE = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene"

Low

scripts/query_gene.py:14

Python HTTP libraries

import urllib.request

Low

scripts/query_gene.py:48

Python HTTP libraries

with urllib.request.urlopen(url) as response:

Low

scripts/query_gene.py:88

Python HTTP libraries

with urllib.request.urlopen(url) as response:

Low

scripts/query_gene.py:123

Python HTTP libraries

with urllib.request.urlopen(url) as response:

Low

scripts/query_gene.py:19

Hardcoded URL

BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

Risk Factors

🌐 Network access (39)

🔑 Env variables (50)

📁 Filesystem access (1)

scripts/batch_gene_lookup.py:287

⚙️ External commands (22)

Audited by: codex View Audit History →

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Open versioned report

Copy report link

https://skillstore.io/skills/davila7-gene-database/audits/14?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

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Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). gene-database security audit report (audit version 14) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-gene-database/audits/14

BibTeX citation

@techreport{davila7-davila7-gene-database-2026,
  author = {davila7},
  title = {gene-database security audit report (audit version 14)},
  institution = {Skillstore},
  year = {2026},
  number = {14},
  url = {https://skillstore.io/skills/davila7-gene-database/audits/14},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "gene-database security audit report (audit version 14)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/davila7-gene-database/audits/14"
identifiers:
  - type: other
    value: "skillstore:davila7-gene-database:audit:14"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended Current

davila7-gene-database

Skillstore Score 79

Evidence Confidence High

Skillstore usage 9

Updated

2026-08-21

K-Dense-AI

k-dense-ai-gene-database

Skillstore Score 38

Evidence Confidence Medium

Skillstore usage 8

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Annotate a Gene Panel

Map a list of gene symbols to Gene IDs, descriptions, organisms, chromosomes, and map locations.

Prepare Research Queries

Build precise NCBI Gene searches for diseases, pathways, phenotypes, publications, and model organisms.

Check Gene Metadata

Retrieve current NCBI summaries for single genes before writing reports, tickets, or documentation.

Try These Prompts

Find a Gene by Symbol

Use the gene-database skill to search NCBI Gene for BRCA1 in human. Return the Gene ID, official symbol, description, organism, chromosome, and map location.

Retrieve Gene Details

Use the gene-database skill to fetch NCBI Gene ID 672. Summarize nomenclature, aliases, organism, genomic location, transcripts, and available output formats.

Batch Annotate Genes

Use the gene-database skill to annotate BRCA1, TP53, EGFR, and KRAS for human. Produce a concise table with Gene ID, description, chromosome, and status.

Design a Disease Workflow

Use the gene-database skill to design an NCBI Gene workflow for finding human genes linked to diabetes, retrieving summaries, checking publications, and avoiding rate-limit problems.

Best Practices

Always include an organism or taxon filter when searching by gene symbol.
Use Gene IDs for exact retrieval when a trusted identifier is available.
Batch requests and respect NCBI rate limits to avoid failed lookups.

Avoid

Do not assume a gene symbol is unique across species.
Do not paste real API keys into shared prompts, logs, or examples.
Do not use returned gene annotations as clinical guidance without expert review.