Skills gwas-database

📦

gwas-database

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

Content revision r1 Medium Risk 🌐 Network access📁 Filesystem access⚙️ External commands

Query GWAS Catalog Associations

Genetic association searches often require many identifiers and endpoints. This skill guides Claude, Codex, and Claude Code through GWAS Catalog lookups with clear research outputs.

Supports: Claude Codex Code(CC)

⚠️ 50 Poor

Install with my Agent

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

Agent request

Review the Skillstore skill "gwas-database" from https://skillstore.io/skills/k-dense-ai-gwas-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-gwas-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/k-dense-ai-gwas-database.md Signed manifest GET /api/skills/k-dense-ai-gwas-database/manifest Signed lockfile GET /api/skills/k-dense-ai-gwas-database/lockfile

Test it

Using "gwas-database". rs7903146 association lookup

Expected outcome:

A concise association summary with traits, strongest allele, p-values, mapped genes, PMID, and GWAS Catalog study accession.

Using "gwas-database". Parkinson disease trait review

Expected outcome:

A grouped evidence summary listing top variants, reported traits, publication metadata, ancestry notes, and interpretation caveats.

Using "gwas-database". Summary statistics access plan

Expected outcome:

A documented access plan with source endpoint, file size concerns, integrity checks, license notes, and reproducibility fields.

Security Audit

Medium Risk

v7 • 7/5/2026 Open versioned report

Most static findings are false positives from Markdown backticks and intended examples accessing public NHGRI-EBI GWAS endpoints. Confirmed risks are limited to FTP or plain HTTP summary-statistics downloads and local file writing without integrity or path safeguards. No prompt injection or malicious exfiltration language was found.

Files scanned

1,402

Lines analyzed

Review items

False positives ignored

Confirmed security concerns (1)

Medium

SKILL.md:404-407 references/api_reference.md:758-774

Unverified Summary Statistics Download

The skill includes workflows that fetch summary statistics over FTP or plain HTTP and save them locally without checksum or signature validation.

The cited examples use wget over FTP or requests against an http://ftp.ebi.ac.uk URL, then write downloaded bytes locally. The endpoint is legitimate, but the workflow lacks integrity verification.

Capability review items (7)

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

references/api_reference.md:772

Python file write/append

with open(output_path, 'wb') as f:

The example writes streamed network content to a local path derived from parameters. Normal GCST IDs are structured, but the workflow lacks path validation, overwrite protection, and checksum checks.

Medium

SKILL.md:258

FTP protocol

# ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/

The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.

Medium

SKILL.md:407

FTP protocol

wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harm

The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.

Low

references/api_reference.md:769

Python HTTP libraries

response = requests.get(harmonised_url, stream=True)

This request streams a summary-statistics download built from a plain HTTP FTP mirror URL. The source is legitimate, but the example lacks secure transport and integrity validation.

Low

references/api_reference.md:761

Hardcoded URL

ftp_base = "http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics"

This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.

Low

SKILL.md:235

Hardcoded URL

1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/

This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.

Low

SKILL.md:602

Hardcoded URL

- **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/

This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.

Risk Factors

🌐 Network access (93)

📁 Filesystem access (1)

references/api_reference.md:772

⚙️ External commands (71)

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Audited by: codex View Audit History →

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Academic citations (APA · BibTeX · CFF)

APA citation

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

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-gwas-database-2026,
  author = {K-Dense-AI},
  title = {gwas-database security audit report (audit version 7)},
  institution = {Skillstore},
  year = {2026},
  number = {7},
  url = {https://skillstore.io/skills/k-dense-ai-gwas-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: "gwas-database security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
  - name: "K-Dense-AI"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/k-dense-ai-gwas-database/audits/7"
identifiers:
  - type: other
    value: "skillstore:k-dense-ai-gwas-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-gwas-database

Skillstore Score 74

Evidence Confidence High

Skillstore usage 8

Updated

2026-08-21

K-Dense-AI Current

k-dense-ai-gwas-database

Skillstore Score 50

Evidence Confidence High

Skillstore usage 13

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Variant Evidence Review

Look up a SNP and summarize traits, p-values, genes, and publication metadata from GWAS Catalog records.

Trait Association Search

Find genome-wide significant variants for a disease or phenotype and prepare a structured evidence summary.

Summary Statistics Planning

Identify studies with full summary statistics and plan secure, documented data access for downstream analysis.

Try These Prompts

Look Up a Variant

Use the GWAS Catalog skill to summarize known associations for rs7903146. Include traits, p-values, mapped genes, and study accessions.

Search a Trait

Find genome-wide significant associations for type 2 diabetes in the GWAS Catalog. Group results by variant and report study metadata.

Compare Gene Evidence

For APOE, identify nearby GWAS Catalog variants linked to Alzheimer disease. Include effect direction when available and note ancestry context.

Build a Reproducible Review

Create a reproducible GWAS Catalog search plan for body mass index. Include REST endpoints, pagination strategy, filters, and citation fields.

Best Practices

Record the GWAS Catalog access date and cite study accessions or PubMed IDs.
Use pagination, delays, and caching for broad API searches.
Check ancestry, sample size, genome build, and study design before interpreting associations.

Avoid

Do not treat GWAS associations as clinical recommendations.
Do not mix genome builds or coordinate systems without documenting conversion steps.
Do not download bulk summary statistics without checking license, size, and integrity.

Frequently Asked Questions

Does this skill need an API key?

No. The referenced GWAS Catalog APIs are open access, but users should respect service limits.

Can it search by rs ID?

Yes. It includes guidance for variant details and associations for specific rs identifiers.

Can it interpret personal disease risk?

No. It supports research lookup. Clinical interpretation requires qualified review and appropriate consent.

Does it cover summary statistics?

Yes. It explains API and bulk access patterns, including cautions for large files.

What sources does it use?

It focuses on the NHGRI-EBI GWAS Catalog, the Summary Statistics API, and official documentation.

Can results change over time?

Yes. The GWAS Catalog is updated, so reports should include the access date and identifiers.

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/gwas-database

Ref

a25199bc7d6b82598536822d1738eb5d5f54025b

Maintenance freshness

7/18/2026

Usage

8 downloads · 192 views

File structure

📁 references/

📄 api_reference.md

📄 SKILL.md