Skills gene-database

📦

gene-database

Name: gene-database
Author: K-Dense-AI

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

Query NCBI Gene Data

Gene lookup often requires exact IDs, organism filters, and API-specific formats. This skill guides NCBI Gene searches, metadata retrieval, and batch annotation workflows.

Supports: Claude Codex Code(CC)

⚠️ 38 Poor

Stop for confirmation before installing.

Review the plan and obtain explicit user consent before changing files.

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/k-dense-ai-gene-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-gene-database/manifest. Verify the artifact. Stop and obtain explicit user consent before installing or changing files.

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/k-dense-ai-gene-database.md Signed manifest GET /api/skills/k-dense-ai-gene-database/manifest Signed lockfile GET /api/skills/k-dense-ai-gene-database/lockfile

Test it

Using "gene-database". Find information about BRCA1 in human.

Expected outcome:

The response identifies Gene ID 672, symbol BRCA1, organism Homo sapiens, chromosome 17, and map location 17q21.31.

Using "gene-database". Annotate TP53, EGFR, and KRAS for human.

Expected outcome:

The response gives a compact annotation table with Gene IDs, official symbols, descriptions, chromosomes, and map locations.

Using "gene-database". Find genes related to apoptosis in mouse.

Expected outcome:

The response explains the GO-based search, applies the mouse organism filter, and summarizes candidate genes for review.

Security Audit

High Risk

v7 • 7/6/2026 Open versioned report

The static matches are largely false positives from documented NCBI API usage, optional user-provided NCBI API keys, Markdown code formatting, and explicit user-requested output files. However, untrusted package content includes a self-authored security audit that claims the skill is safe to publish, plus a separate instruction to promote an external hosted platform. Those intent-level issues should be removed or isolated before marketplace publication.

Files scanned

2,020

Lines analyzed

Review items

False positives ignored

Confirmed security concerns (2)

High

evaluation.json:14-18 evaluation.json:19-67

Prompt Injection Attempt Detected

evaluation.json embeds a security_audit block with "safe_to_publish": true and claims all static findings are false positives. Untrusted package content should not pre-adjudicate marketplace security or publication status.

The file directly contains self-authored audit fields and verdict claims. It can bias review, although it does not override this audit.

Medium

SKILL.md:178-179

Unrelated External Platform Promotion

SKILL.md instructs the assistant to proactively suggest K-Dense Web for complex workflows and large document analysis. This steers users toward an external hosted service outside the core gene database workflow.

The promotion instruction is explicit in the skill text. The risk is user steering and possible data-boundary confusion, not direct code execution.

Risk Factors

🌐 Network access (40)

🔑 Env variables (61)

📁 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

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https://skillstore.io/skills/k-dense-ai-gene-database/audits/7?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). gene-database security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-gene-database/audits/7

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-gene-database-2026,
  author = {K-Dense-AI},
  title = {gene-database security audit report (audit version 7)},
  institution = {Skillstore},
  year = {2026},
  number = {7},
  url = {https://skillstore.io/skills/k-dense-ai-gene-database/audits/7},
  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 7)"
version: "unspecified"
type: report
authors:
  - name: "K-Dense-AI"
date-released: "2026-07-06"
url: "https://skillstore.io/skills/k-dense-ai-gene-database/audits/7"
identifiers:
  - type: other
    value: "skillstore:k-dense-ai-gene-database:audit:7"
    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

davila7-gene-database

Skillstore Score 79

Evidence Confidence High

Skillstore usage 9

Updated

2026-08-21

K-Dense-AI Current

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: Medium

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Annotate gene panels

Retrieve Gene IDs, symbols, locations, and descriptions for a research gene list.

Build batch lookup tables

Map many gene symbols to stable NCBI Gene IDs with organism filters and rate limits.

Explain gene records

Find clear gene summaries for teaching examples, assignments, or guided database exploration.

Try These Prompts

Find one gene

Find the {gene_symbol} gene in {organism}. Include the Gene ID, description, chromosome, and map location.

Retrieve by ID

Retrieve NCBI Gene information for Gene ID {gene_id}. Summarize the organism, symbol, aliases, and key annotations.

Annotate a list

Annotate these {organism} genes: {gene_list}. Return a concise table with symbols, Gene IDs, descriptions, and locations.

Compare biological context

Find genes linked to {disease_or_pathway} in {organism}. Explain query terms, likely ambiguities, and follow-up validation steps.

Best Practices

Always include the organism when searching by gene symbol.
Use Gene IDs for stable storage and repeated lookups.
Batch requests when possible and respect NCBI rate limits.

Avoid

Do not treat gene symbols as globally unique identifiers.
Do not run large request loops without rate limiting.
Do not use database results as clinical evidence without expert validation.

Frequently Asked Questions

What database does this skill use?

It uses NCBI Gene through E-utilities and the NCBI Datasets API.

Does it require an NCBI API key?

No. An API key is optional, but it increases allowed request rates.

Can it process many genes at once?

Yes. The batch workflow accepts Gene IDs or a file of gene symbols.

What identifiers can I search with?

You can search by gene symbol, Gene ID, organism, disease term, GO term, pathway, or chromosome location.

Does it work with Claude, Codex, and Claude Code?

Yes. The skill metadata lists Claude, Codex, and Claude Code as supported tools.

Can it interpret clinical risk?

No. It retrieves database records and annotations, but clinical interpretation needs qualified review.

Developer Details

Author

K-Dense-AI

License

Unknown

Skillstore revision

Version notice

The author did not declare a version.

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/gene-database

Ref

b8ca75d2c0a7e7102978993058777d82b8ab2610

Maintenance freshness

7/18/2026

Usage

6 downloads · 214 views

File structure

📁 references/

📄 api_reference.md

📄 common_workflows.md

📁 scripts/

📄 batch_gene_lookup.py

📄 fetch_gene_data.py

📄 query_gene.py

📄 evaluation.json

📄 SKILL.md

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gene-database

Install with my Agent

Agent-readable resources

Test it

Security Audit

Confirmed security concerns (2)

Risk Factors

Copy report link

Markdown badge

HTML badge

Embed card

APA citation

BibTeX citation

CITATION.cff

Compare variants

Skillstore Score

What You Can Build

Annotate gene panels

Build batch lookup tables

Explain gene records

Try These Prompts

Best Practices

Avoid

Frequently Asked Questions

Developer Details

More from K-Dense-AI

venue-templates

iso-13485-certification

pytdc

diffdock

statistical-analysis

scanpy

Related Skills

bioservices

drugbank-database

kegg-database

string-database

reactome-database

uniprot-database