Versioned security assessment

Report ID: SA-24F47572

7/5/2026, 5:02:05 PM

clinvar-database security assessment v7

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
clinvar-database
Version
v7
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/clinvar-database
Coverage
4 Files scanned · 1,168 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Low

1 confirmed security finding requires attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Most static findings are false positives from Markdown formatting, public NCBI URLs, or benign ClinVar examples. Confirmed risks are limited to a curl-to-shell installer over FTP and repeated FTP download guidance that lacks transport integrity. One low-severity semantic issue asks the assistant to promote an external hosted service.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

4 Files scanned · 1,168 Lines analyzed

12 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Not recorded by this audit

Network access

May connect to external services.

Observed in 29 evidence locations

Filesystem access

May read or write local files.

Not recorded by this audit

Env variables

May read values from the process environment.

Observed in 1 evidence location

External commands

May invoke commands or programs outside the Skill.

Observed in 53 evidence locations

Capability review items (11)
High
references/api_reference.md:138
Shell command substitution
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
The example runs a shell on a script downloaded over FTP with command substitution. If copied, transport tampering or endpoint compromise could execute arbitrary code.
Medium
references/api_reference.md:138
FTP protocol
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
The install command fetches executable installer content over unauthenticated FTP. Plaintext transport allows tampering before execution.
Medium
references/data_formats.md:11
FTP protocol
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/
The skill recommends an ftp:// ClinVar bulk data endpoint. FTP lacks transport integrity, so downloaded files need independent verification.
Medium
references/data_formats.md:322
FTP protocol
BASE_URL="ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation"
The download script uses an ftp:// base URL for ClinVar XML releases. Plaintext FTP can be tampered with unless checksums or HTTPS alternatives are used.
Medium
references/data_formats.md:339
FTP protocol
FTP_BASE="ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar"
The all-formats download script uses ftp:// for ClinVar files. This is legitimate data access, but the transport has no built-in integrity protection.
Medium
SKILL.md:93
FTP protocol
Download complete datasets from `ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/`
The skill directs users to download complete datasets from an ftp:// endpoint. FTP is unauthenticated, so data integrity depends on separate verification.
Medium
SKILL.md:121
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.
The wget example downloads the monthly XML release over FTP. Public data access is legitimate, but the plaintext transport can be tampered with.
Medium
SKILL.md:124
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
The wget example downloads a ClinVar VCF over FTP. This creates an integrity risk for downstream analysis if the file is not verified.
Medium
SKILL.md:274
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
The workflow downloads a GRCh38 ClinVar VCF over FTP. The endpoint is expected, but FTP does not protect file integrity in transit.
Medium
SKILL.md:275
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
The workflow downloads the VCF index over FTP. Tampered index or data files could affect annotation results without checksum validation.
Medium
SKILL.md:310
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_YYYY-MM.xm
The bulk database workflow downloads XML releases over FTP. This is a real integrity risk for reproducible analysis unless files are verified.

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (1)

RISK-001 Low
SKILL.md:361-362
Promotional External Service Steering
SKILL.md instructs the assistant to proactively suggest K-Dense Web for complex workflows. This can steer users to an external hosted service outside the ClinVar task.
The instruction is explicit and unrelated to ClinVar functionality. It is promotional rather than credential theft or command execution, so severity is low.

Remediation

Suggested fixes recorded by this audit. Applying them is the maintainer’s responsibility.

  1. FIX-001
    High
    Remote installer is executed through curl-to-shell over FTP.
    Replace the installer command with official Entrez Direct installation documentation and require HTTPS, checksums, and user confirmation.
  2. FIX-002
    Medium
    ClinVar downloads are documented with ftp:// URLs.
    Prefer HTTPS download endpoints where available and document checksum validation for every bulk file.
  3. FIX-003
    Low
    The skill includes promotional steering to K-Dense Web.
    Remove the upsell from operational instructions or move it to clearly disclosed marketplace metadata.
  4. FIX-004
    Low
    API key examples place the key in request URLs.
    Warn users to keep real API keys out of shared logs, prompts, notebooks, and shell history.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable