Skills reactome-database

📦

reactome-database

Name: reactome-database
Author: davila7

Content revision r1 Safe 🌐 Network access📁 Filesystem access⚙️ External commands

Analyze Reactome Pathways

Biology teams need fast access to curated pathway data without memorizing Reactome endpoints. This skill guides Claude, Codex, and Claude Code through pathway queries, enrichment analysis, and result interpretation.

Supports: Claude Codex Code(CC)

🥉 79 Bronze

Install with my Agent

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

Agent request

Review the Skillstore skill "reactome-database" from https://skillstore.io/skills/davila7-reactome-database.md and its manifest at https://skillstore.io/api/skills/davila7-reactome-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/davila7-reactome-database.md Signed manifest GET /api/skills/davila7-reactome-database/manifest Signed lockfile GET /api/skills/davila7-reactome-database/lockfile

Test it

Using "reactome-database". Summarize Reactome pathway R-HSA-69278.

Expected outcome:

A concise pathway summary with the Reactome stable identifier, species, pathway type, biological description, and related participants.

Using "reactome-database". Analyze TP53, BRCA1, EGFR, and MYC for pathway enrichment.

Expected outcome:

Top enriched pathways ranked by significance.
Matched entity counts and FDR values for each pathway.
A Reactome Pathway Browser link when an analysis token is available.

Using "reactome-database". Prepare a workflow for expression analysis in Reactome.

Expected outcome:

A step-by-step analysis plan covering TSV formatting, submission, token retrieval, significance filtering, and result export.

Security Audit

Safe

v14 • 7/9/2026 Open versioned report

Confirmed findings are limited to expected Reactome network access and controlled result-file writes. The high device-file alerts are false positives from Reactome documentation URLs, and the command-execution alerts are Markdown formatting matches. No prompt injection or malicious intent was found in the reviewed files.

Files scanned

1,026

Lines analyzed

Review items

False positives ignored

Capability review items (49)

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:439

Python file write/append

with open(output_file, "w") as f:

The API reference includes a runnable example that writes analysis results to an output file. It is legitimate documentation, but it still models filesystem write behavior.

Medium

scripts/reactome_query.py:227

Python file write/append

with open(output_file, 'w') as f:

The helper script writes full analysis results to a path derived from the input filename. This is intentional output, but it can overwrite files if the derived path collides.

Low

references/api_reference.md:26

Python HTTP libraries

response = requests.get("https://reactome.org/ContentService/data/database/version")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:57

Python HTTP libraries

response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:76

Python HTTP libraries

response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278/displayName")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:94

Python HTTP libraries

response = requests.get(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:126

Python HTTP libraries

response = requests.get(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:207

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:258

Python HTTP libraries

response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:372

Python HTTP libraries

result = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:391

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:420

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

references/api_reference.md:26

Hardcoded URL

response = requests.get("https://reactome.org/ContentService/data/database/version")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:57

Hardcoded URL

response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:76

Hardcoded URL

response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278/displayName")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:95

Hardcoded URL

"https://reactome.org/ContentService/data/event/R-HSA-69278/participatingPhysicalEntities"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:127

Hardcoded URL

"https://reactome.org/ContentService/data/query",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:208

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:258

Hardcoded URL

response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:372

Hardcoded URL

result = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:392

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/projection/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:421

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

references/api_reference.md:450

Hardcoded URL

url = f"https://reactome.org/PathwayBrowser/#{top_pathway['stId']}&DTAB=AN&ANALYSIS={token}"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

scripts/reactome_query.py:36

Python HTTP libraries

response = requests.get(f"{self.CONTENT_BASE}/data/database/version")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:42

Python HTTP libraries

response = requests.get(f"{self.CONTENT_BASE}/data/query/{pathway_id}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:48

Python HTTP libraries

response = requests.get(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:56

Python HTTP libraries

response = requests.get(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:66

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:76

Python HTTP libraries

response = requests.get(f"{self.ANALYSIS_BASE}/token/{token}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

scripts/reactome_query.py:31

Hardcoded URL

CONTENT_BASE = "https://reactome.org/ContentService"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

scripts/reactome_query.py:32

Hardcoded URL

ANALYSIS_BASE = "https://reactome.org/AnalysisService"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

scripts/reactome_query.py:221

Hardcoded URL

url = f"https://reactome.org/PathwayBrowser/#{top_pathway}&DTAB=AN&ANALYSIS={token}"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:72

Python HTTP libraries

response = requests.get("https://reactome.org/ContentService/data/database/version")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:82

Python HTTP libraries

response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:91

Python HTTP libraries

response = requests.get(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:127

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:144

Python HTTP libraries

response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:168

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:182

Python HTTP libraries

response = requests.post(

This is intentional Reactome API access for pathway lookup or analysis. It is a real low-severity network risk because identifiers or analysis data may leave the workspace for reactome.org.

Low

SKILL.md:38

Hardcoded URL

**API Base URL:** `https://reactome.org/ContentService`

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:49

Hardcoded URL

**API Base URL:** `https://reactome.org/AnalysisService`

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:72

Hardcoded URL

response = requests.get("https://reactome.org/ContentService/data/database/version")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:82

Hardcoded URL

response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:92

Hardcoded URL

f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:128

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:144

Hardcoded URL

response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:169

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:183

Hardcoded URL

"https://reactome.org/AnalysisService/identifiers/projection/",

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Low

SKILL.md:196

Hardcoded URL

url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}"

This hardcoded URL points to Reactome API or Pathway Browser services used by the skill. It is expected behavior, but still confirms an external network dependency.

Risk Factors

🌐 Network access (50)

📁 Filesystem access (4)

references/api_reference.md:462 references/api_reference.md:463 references/api_reference.md:439 scripts/reactome_query.py:227

⚙️ External commands (33)

Audited by: codex View Audit History →

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Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). reactome-database security audit report (audit version 14) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-reactome-database/audits/14

BibTeX citation

@techreport{davila7-davila7-reactome-database-2026,
  author = {davila7},
  title = {reactome-database security audit report (audit version 14)},
  institution = {Skillstore},
  year = {2026},
  number = {14},
  url = {https://skillstore.io/skills/davila7-reactome-database/audits/14},
  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: "reactome-database security audit report (audit version 14)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/davila7-reactome-database/audits/14"
identifiers:
  - type: other
    value: "skillstore:davila7-reactome-database:audit:14"
    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 Current

davila7-reactome-database

Skillstore Score 79

Evidence Confidence High

Skillstore usage 10

Updated

2026-08-21

K-Dense-AI

k-dense-ai-reactome-database

Skillstore Score 50

Evidence Confidence High

Skillstore usage 12

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Find enriched pathways from a gene list

Submit identifiers and review significant Reactome pathways with p-values, FDR values, and matched entity counts.

Inspect pathway participants

Retrieve proteins, complexes, and small molecules that participate in a selected Reactome pathway.

Create reproducible pathway summaries

Use documented API calls and helper commands to create consistent pathway reports for teams.

Try These Prompts

Look up one pathway

Use the Reactome skill to summarize pathway R-HSA-69278. Include its name, species, type, and a short biological description.

Analyze a gene list

Use the Reactome Analysis Service for these identifiers: TP53, BRCA1, EGFR, MYC. Summarize the top enriched pathways and FDR values.

Compare pathway entities

For pathway R-HSA-69278, retrieve participating physical entities. Group the first results by entity type and explain their roles.

Build a reproducible workflow

Design a Reactome workflow for a differential expression file. Include input validation, analysis submission, token handling, result filtering, and reporting steps.

Best Practices

Confirm that gene identifiers use supported formats before submitting analysis requests.
Tell users when identifiers or expression values will be sent to Reactome services.
Store analysis tokens only when users need to retrieve results within seven days.

Avoid

Do not submit private clinical or unpublished expression data without user approval.
Do not treat Reactome enrichment results as proof of biological causality.
Do not overwrite input files when saving helper script output.