Versioned security assessment

Report ID: SA-C4EAED94

6/30/2026, 5:22:21 AM

clinvar-database security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
clinvar-database
Version
v5
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.

Static analysis flagged many command execution and network patterns, but review shows they are Markdown examples for public NCBI ClinVar access rather than executable skill code. The main confirmed concern is that the documentation includes networked shell commands, including a remote installer pattern, so publication is acceptable with a warning about user approval before running commands.

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

5 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 5 evidence locations

Filesystem access

May read or write local files.

Not recorded by this audit

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Observed in 5 evidence locations

Capability review items (4)
Medium
SKILL.md:51-55SKILL.md:118-125SKILL.md:150-160references/data_formats.md:333-351
Networked Shell Commands in Documentation
The skill includes Markdown examples for curl, wget, bcftools, Entrez Direct, and FTP downloads. These are legitimate ClinVar workflows, but an assistant should not execute them without user approval because they contact external NCBI services and may download large files.
The commands are directly present in Markdown code blocks and perform public ClinVar data access. Context supports legitimate use, but external command execution and network downloads remain real operational risk.
Medium
references/api_reference.md:136-139
Remote Installer Command Example
The API reference shows a shell command that downloads an Entrez Direct installer and executes it with sh. This is a common installation pattern, but it is riskier than ordinary query examples because it executes remote script content.
The command substitution and shell execution pattern is explicit. The endpoint is NCBI and the use case is legitimate, so this is a cautionary finding rather than malicious behavior.
Low
SKILL.md:33references/api_reference.md:14-15references/data_formats.md:355-358
Public NCBI URLs Are Expected
The hardcoded URLs point to NCBI, ClinVar, ClinGen, Samtools, and related public documentation or data resources. No evidence found of credential exfiltration, tracking endpoints, or unrelated third-party callbacks.
The URLs match the stated ClinVar data-access purpose and are visible documentation links. I did not find evidence of hidden or suspicious network destinations.
Low
references/api_reference.md:169-172
API Key Placeholder Is Documentation Only
The API key reference uses a placeholder for NCBI rate limits and does not read environment variables or include a real secret. This dismisses the env_access static finding as a false positive.
The text instructs users to add a placeholder API key parameter. There is no code path that accesses environment variables or transmits stored credentials.

Risk findings

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

Confirmed security concerns (1)

RISK-001 Low
references/api_reference.md:125references/api_reference.md:167references/data_formats.md:244
Reconnaissance Alerts Are Benign Data Processing Examples
The system and network reconnaissance labels map to examples such as parsing JSON, filtering files, and listing public FTP content. No evidence found of host enumeration, port scanning, or local system profiling.
The surrounding context is ClinVar query and file-processing documentation. The flagged lines do not show reconnaissance intent or collection of local system details.

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.

Static false positives ignored (1)
Low
SKILL.md:3references/api_reference.md:5references/clinical_significance.md:5references/data_formats.md:5
Weak Cryptography Alerts Are False Positives
The weak cryptographic algorithm alerts appear on prose, headings, or biomedical terminology rather than cryptographic code. No evidence found of MD5, SHA1, DES, or other weak algorithms being used for security decisions.
Manual review found documentation text at these locations, not cryptographic operations. The pattern match is likely caused by domain terms or Markdown content.

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