Versioned security assessment

Report ID: SA-DE2A2FF0

6/30/2026, 6:04:55 AM

brenda-database security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
brenda-database
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/brenda-database
Coverage
6 Files scanned · 4,133 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

3 confirmed security findings require 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.

The static scan reported many high-risk patterns, but targeted review found most are false positives from Markdown code fences, EC numbers such as 1.1.1.1, biochemical cofactor names, and documented BRENDA SHA-256 authentication. Remaining concerns are legitimate but elevated operational risks: the skill uses API credentials, outbound network access, and user-controlled file exports.

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

6 Files scanned · 4,133 Lines analyzed

3 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.

Observed in 3 evidence locations

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 2 evidence locations

Env variables

May read values from the process environment.

Observed in 2 evidence locations

External commands

May invoke commands or programs outside the Skill.

Observed in 2 evidence locations

Risk findings

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

Confirmed security concerns (3)

RISK-001 Medium
SKILL.md:301-321references/api_reference.md:214-231
Credential-Based BRENDA API Access
The skill instructs users to store BRENDA_EMAIL and BRENDA_PASSWORD in a .env file or environment variables. This appears legitimate for BRENDA authentication, but it increases sensitivity because credentials are handled by the runtime environment.
Credential handling is directly documented and semantically required for the API. I did not find evidence of exfiltration, so the risk is operational rather than malicious.
RISK-002 Medium
references/api_reference.md:7-25scripts/brenda_queries.py:33-64
Outbound Network Access to BRENDA SOAP API
The skill is designed to query the BRENDA SOAP endpoint and related database methods. This is expected for the feature, but users should understand that prompts and query terms may result in outbound API requests.
The SOAP endpoint and client imports are explicit. The destination appears to be the official BRENDA service, and I did not find evidence of unrelated endpoints.
RISK-003 Medium
scripts/brenda_queries.py:732-777scripts/enzyme_pathway_builder.py:924-929
User-Controlled File Export Paths
Helper functions write CSV, JSON, Excel, and text reports to filenames supplied by the user or generated from input. This is normal export behavior, but it can overwrite local files if used with unsafe paths.
The write calls are direct and tied to export functionality. I did not find path validation or sandboxing in the reviewed code.

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 (5)
Low
SKILL.md:34-46references/api_reference.md:90-109scripts/brenda_queries.py:813-840
Static Analyzer False Positives from Scientific Identifiers
Many hardcoded IP and reconnaissance findings are EC numbers such as 1.1.1.1 or biochemical examples. These are enzyme identifiers and scientific data, not network addresses or reconnaissance behavior.
The flagged values occur in enzyme examples and EC number documentation. Their semantic context is biochemical classification, not networking.
Low
SKILL.md:295-299references/api_reference.md:9-12
Markdown Backticks Misclassified as Shell Execution
The external command findings in SKILL.md and references/api_reference.md are Markdown code spans or fenced examples. I did not find subprocess, os.system, or shell execution calls in the reviewed source files.
The evidence is documentation formatting, not executable shell invocation. A targeted search found no shell execution APIs in the cited Python files.
Low
scripts/enzyme_pathway_builder.py:140-149scripts/enzyme_pathway_builder.py:164-177
Biochemical Cofactors Misclassified as C2 Keywords
Terms such as NAD, NADH, ATP, ADP, and AMP are used as metabolic cofactors in pathway logic. They are not command-and-control indicators in this scientific context.
The flagged terms are embedded in metabolite and cofactor dictionaries. Their use aligns with enzyme pathway analysis.
Low
scripts/brenda_visualization.py:33-50scripts/enzyme_pathway_builder.py:32-63
Standard Imports Misclassified as Dynamic Imports
The reviewed import findings are ordinary Python import blocks for optional scientific dependencies and local helper modules. I did not find dynamic import() or __import__ execution in the cited source context.
The line context shows static imports inside try blocks. The analyzer appears to have generalized import syntax as dynamic import risk.
Low
references/api_reference.md:22-25references/api_reference.md:229-231
Weak Cryptography Finding Is Required API Hashing
The documentation describes SHA-256 password hashing for the BRENDA API. This is authentication protocol compatibility, not custom password storage or a downgrade attack in the skill itself.
The references describe the API-required password hash. No evidence found that the skill stores password hashes as a security boundary.

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