New: 97,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Reactome Database

by davila7 in davila7/claude-code-templates

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

MITAuto-check passedBackend & APIs

Install Reactome Database

skills CLI
$ npx skills add davila7/claude-code-templates --skill reactome-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install davila7/claude-code-templates reactome-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/davila7/claude-code-templates.git skills-src && mkdir -p .claude/skills && cp -r skills-src/cli-tool/components/skills/scientific/reactome-database .claude/skills/reactome-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
reactome-database
GitHub stars
32k
Used in
10 other repos
Token cost
~1.9k tokens
SKILL.md length
593 words
Files
3 (incl. scripts, references)
Skills in repo
477
Repo updated
First seen
Licence
MIT

At a glance

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

  • Works in 3 steps: Content Service - Data Retrieval → Analysis Service - Pathway Analysis → reactome2py Python Package
  • Tasks that involve REST APIs
  • SKILL.md covers Overview, When to Use This Skill, Core Capabilities and Querying Pathway Data, plus 7 more sections
  • Runs Python scripts from its folder; calls python and uv; reaches reactome.org

What it does

Reactome Database is an agent skill from davila7/claude-code-templates. Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts and reference files (for example `references/api_reference.md` and `scripts/reactome_query.py`).

It sits in Backend & APIs, covering REST APIs. It works with Python. The repository describes itself as: CLI tool for configuring and monitoring Claude Code. The licence is MIT.

When your agent uses it

  • Tasks that involve REST APIs

Example prompts

  • “/reactome-database”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Content Service - Data Retrieval
  2. Analysis Service - Pathway Analysis
  3. reactome2py Python Package

What it can do on your machine

Read from SKILL.md and the folder at commit 4c82aba. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • uv

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • reactome.org

    Also links to:

    • reactome.github.io

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Reactome Database loads about 1.9k tokens when it runs, and up to ~4.6k if it reads all its reference files. Until then it costs about 47 tokens; SKILL.md has 593 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~47
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~4.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from davila7/claude-code-templates at commit 4c82aba, republished under its MIT licence (© davila7). 593 words, ~1,945 tokens.

Download SKILL.mdSave it as .claude/skills/reactome-database/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
reactome-database
description
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Reactome Database

Overview

Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research.

When to Use This Skill

This skill should be used when:

  • Performing pathway enrichment analysis on gene or protein lists
  • Analyzing gene expression data to identify relevant biological pathways
  • Querying specific pathway information, reactions, or molecular interactions
  • Mapping genes or proteins to biological pathways and processes
  • Exploring disease-related pathways and mechanisms
  • Visualizing analysis results in the Reactome Pathway Browser
  • Conducting comparative pathway analysis across species

Core Capabilities

Reactome provides two main API services and a Python client library:

1. Content Service - Data Retrieval

Query and retrieve biological pathway data, molecular interactions, and entity information.

Common operations:

  • Retrieve pathway information and hierarchies
  • Query specific entities (proteins, reactions, complexes)
  • Get participating molecules in pathways
  • Access database version and metadata
  • Explore pathway compartments and locations

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

2. Analysis Service - Pathway Analysis

Perform computational analysis on gene lists and expression data.

Analysis types:

  • Overrepresentation Analysis: Identify statistically significant pathways from gene/protein lists
  • Expression Data Analysis: Analyze gene expression datasets to find relevant pathways
  • Species Comparison: Compare pathway data across different organisms

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

3. reactome2py Python Package

Python client library that wraps Reactome API calls for easier programmatic access.

Installation:

bash
uv pip install reactome2py

Note: The reactome2py package (version 3.0.0, released January 2021) is functional but not actively maintained. For the most up-to-date functionality, consider using direct REST API calls.

Querying Pathway Data

Using Content Service REST API

The Content Service uses REST protocol and returns data in JSON or plain text formats.

Get database version:

python
import requests

response = requests.get("https://reactome.org/ContentService/data/database/version")
version = response.text
print(f"Reactome version: {version}")

Query a specific entity:

python
import requests

entity_id = "R-HSA-69278"  # Example pathway ID
response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")
data = response.json()

Get participating molecules in a pathway:

python
import requests

event_id = "R-HSA-69278"
response = requests.get(
    f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities"
)
molecules = response.json()
Using reactome2py Package
python
import reactome2py
from reactome2py import content

# Query pathway information
pathway_info = content.query_by_id("R-HSA-69278")

# Get database version
version = content.get_database_version()

For detailed API endpoints and parameters, refer to references/api_reference.md in this skill.

Performing Pathway Analysis

Overrepresentation Analysis

Submit a list of gene/protein identifiers to find enriched pathways.

Using REST API:

python
import requests

# Prepare identifier list
identifiers = ["TP53", "BRCA1", "EGFR", "MYC"]
data = "\n".join(identifiers)

# Submit analysis
response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/",
    headers={"Content-Type": "text/plain"},
    data=data
)

result = response.json()
token = result["summary"]["token"]  # Save token to retrieve results later

# Access pathways
for pathway in result["pathways"]:
    print(f"{pathway['stId']}: {pathway['name']} (p-value: {pathway['entities']['pValue']})")

Retrieve analysis by token:

python
# Token is valid for 7 days
response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")
results = response.json()
Expression Data Analysis

Analyze gene expression datasets with quantitative values.

Input format (TSV with header starting with #):

#Gene	Sample1	Sample2	Sample3
TP53	2.5	3.1	2.8
BRCA1	1.2	1.5	1.3
EGFR	4.5	4.2	4.8

Submit expression data:

python
import requests

# Read TSV file
with open("expression_data.tsv", "r") as f:
    data = f.read()

response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/",
    headers={"Content-Type": "text/plain"},
    data=data
)

result = response.json()
Show full SKILL.md (243 more words)Show less
Species Projection

Map identifiers to human pathways exclusively using the /projection/ endpoint:

python
response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/projection/",
    headers={"Content-Type": "text/plain"},
    data=data
)

Visualizing Results

Analysis results can be visualized in the Reactome Pathway Browser by constructing URLs with the analysis token:

python
token = result["summary"]["token"]
pathway_id = "R-HSA-69278"
url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}"
print(f"View results: {url}")

Working with Analysis Tokens

  • Analysis tokens are valid for 7 days
  • Tokens allow retrieval of previously computed results without re-submission
  • Store tokens to access results across sessions
  • Use GET /token/{TOKEN} endpoint to retrieve results

Data Formats and Identifiers

Supported Identifier Types

Reactome accepts various identifier formats:

  • UniProt accessions (e.g., P04637)
  • Gene symbols (e.g., TP53)
  • Ensembl IDs (e.g., ENSG00000141510)
  • EntrezGene IDs (e.g., 7157)
  • ChEBI IDs for small molecules

The system automatically detects identifier types.

Input Format Requirements

For overrepresentation analysis:

  • Plain text list of identifiers (one per line)
  • OR single column in TSV format

For expression analysis:

  • TSV format with mandatory header row starting with "#"
  • Column 1: identifiers
  • Columns 2+: numeric expression values
  • Use period (.) as decimal separator
Output Format

All API responses return JSON containing:

  • pathways: Array of enriched pathways with statistical metrics
  • summary: Analysis metadata and token
  • entities: Matched and unmapped identifiers
  • Statistical values: pValue, FDR (false discovery rate)

Helper Scripts

This skill includes scripts/reactome_query.py, a helper script for common Reactome operations:

bash
# Query pathway information
python scripts/reactome_query.py query R-HSA-69278

# Perform overrepresentation analysis
python scripts/reactome_query.py analyze gene_list.txt

# Get database version
python scripts/reactome_query.py version

Additional Resources

For comprehensive API endpoint documentation, see references/api_reference.md in this skill.

Current Database Statistics (Version 94, September 2025)

  • 2,825 human pathways
  • 16,002 reactions
  • 11,630 proteins
  • 2,176 small molecules
  • 1,070 drugs
  • 41,373 literature references

© davila7, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 2 other files (scripts, references) in cli-tool/components/skills/scientific/reactome-database of davila7/claude-code-templates.

  • SKILL.md
  • references/api_reference.md
  • scripts/reactome_query.py

Open the folder on GitHubat commit 4c82aba

Used in 10 other repositories

We found 13 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 10 other GitHub owners. This page covers the copy in davila7/claude-code-templates, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Reactome Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Reactome Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Reactome Database this skilldavila7/claude-code-templates32k10 repos~1.9kAutomated safety check: PassMIT
Zhihu Searchitwanger/toBeBetterJavaer18k—~1.5kAutomated safety check: PassNone
Fastcrudbenavlabs/fastcrud1.6k—~5kAutomated safety check: PassMIT
Cloudflare Email Servicehodgef/apiker1273 repos~2kAutomated safety check: PassMIT
FastAPI Project Templateswshobson/agents40k11 repos~901Automated safety check: PassMIT
Starlettesimonw/research781—~8.6kAutomated safety check: NotesNone

Similar skills

  • Zhihu Search

    itwanger/toBeBetterJavaer

    Search Zhihu for content using the searchv3 API. An agent skill from itwanger/toBeBetterJavaer.

    18k GitHub stars~1.5k tokensUpdated today
    Backend & APIsAuto-check passed

  • Fastcrud

    benavlabs/fastcrud

    A skill your agent uses when building or modifying CRUD endpoints with FastCRUD (the fastcrud PyPI package) in a FastAPI project — covers FastCRUD, crudrouter, EndpointCreator, FilterConfig…

    1.6k GitHub stars~5k tokensUpdated 12 days ago
    Backend & APIsAuto-check passed

  • Cloudflare Email Service

    hodgef/apiker

    Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing).

    127 GitHub starsUsed in 3 repos~2k tokens
    Backend & APIsAuto-check passed

  • FastAPI Project Templates

    wshobson/agents

    Scaffolds FastAPI projects with a layered app layout, dependency injection through Depends, async handlers and database access, middleware and pytest setup.

    40k GitHub starsUsed in 11 repos~901 tokens
    Backend & APIsAuto-check passed

  • Starlette

    simonw/research

    Build async web applications and APIs with Starlette 1.0, the lightweight ASGI framework for Python.

    781 GitHub stars~8.6k tokensUpdated 2 days ago
    Backend & APIsAuto-check: notes

  • Build X402 Client

    coinbase/cdp-sdk

    Write code that pays for an HTTP API returning 402 Payment Required, using the x402 protocol and a CDP-managed wallet.

    204 GitHub stars~3k tokensUpdated yesterday
    Backend & APIsAuto-check passed

More from davila7/claude-code-templates

All 477 skills in this repo

  • Perplexity Web Search

    davila7/claude-code-templates

    Runs web-grounded searches through Perplexity's Sonar models over OpenRouter for current events, recent literature and cited facts beyond the model's training cutoff.

    32k GitHub starsUsed in 12 repos~3.5k tokens
    Auto-check: notes

  • Neuropixels Data Analysis

    davila7/claude-code-templates

    Analyzes Neuropixels recordings from SpikeGLX or Open Ephys through preprocessing, drift correction, Kilosort4 spike sorting, quality metrics and curation.

    32k GitHub starsUsed in 10 repos~2.8k tokens
    Auto-check passed

  • Scientific Venue Templates

    davila7/claude-code-templates

    Supplies LaTeX templates and formatting rules for journals, conferences, posters, and grant proposals, then can check a draft against them.

    32k GitHub starsUsed in 9 repos~5.1k tokens
    Auto-check: notes

  • Brand Voice Content Creator

    davila7/claude-code-templates

    Analyzes a brand's existing writing to lock in a consistent voice, then builds SEO blog posts and platform-specific social content around it.

    32k GitHub starsUsed in 2 repos~1.9k tokens
    Auto-check passed

  • CAPA Officer

    davila7/claude-code-templates

    Guides corrective and preventive action (CAPA) work in a quality management system, from initiation and root cause analysis through effectiveness verification.

    32k GitHub starsUsed in 1 repo~2k tokens
    Auto-check passed

  • Fda Consultant Specialist

    davila7/claude-code-templates

    Senior FDA consultant and specialist for medical device companies including HIPAA compliance and requirement management.

    32k GitHub starsUsed in 1 repo~2.7k tokens
    Auto-check passed

Works with

Categories

Questions about Reactome Database

What does Reactome Database do?

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies. Reactome Database is an agent skill from davila7/claude-code-templates. Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

When should I use Reactome Database?

Reactome Database fits situations like: tasks that involve REST APIs.

How do I install Reactome Database in Claude Code?

Run `npx skills add davila7/claude-code-templates --skill reactome-database -a claude-code`. Or copy the skill folder (cli-tool/components/skills/scientific/reactome-database in davila7/claude-code-templates) into .claude/skills/reactome-database in your project. Claude Code loads it when a task matches its description.

How do I install Reactome Database in Codex?

Run `npx skills add davila7/claude-code-templates --skill reactome-database -a codex`. Or copy the skill folder (cli-tool/components/skills/scientific/reactome-database in davila7/claude-code-templates) into .agents/skills/reactome-database in your project. Codex loads it when a task matches its description.

Can I use Reactome Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add davila7/claude-code-templates --skill reactome-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/reactome-database, .gemini/skills/reactome-database, .github/skills/reactome-database and .opencode/skills/reactome-database in your project.

What does Reactome Database need to run?

Going by SKILL.md and its folder, Reactome Database needs Python for the scripts in its folder and the command-line tools its instructions call (python and uv). Our summary lists: Python 3.

Does Reactome Database access the network?

SKILL.md names 2 domains. In commands or code: reactome.org; the agent is likely to contact it when it follows the instructions. As links in the text: reactome.github.io. This is read from the text; nothing was executed.

Is Reactome Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Reactome Database use?

Reactome Database is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Reactome Database use?

About 1.9k tokens (SKILL.md is roughly 7.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 2.6k tokens, read only when the agent opens those files.

What are the alternatives to Reactome Database?

Skills that share tags, products or a category with Reactome Database: Zhihu Search (itwanger/toBeBetterJavaer, 18k stars), Fastcrud (benavlabs/fastcrud, 1.6k stars), Cloudflare Email Service (hodgef/apiker, 127 stars) and FastAPI Project Templates (wshobson/agents, 40k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Reactome Database?

davila7 (a GitHub user) maintains it in davila7/claude-code-templates, which has 32,432 GitHub stars. The repository holds 477 skills in this directory. The repository was last updated on October 7, 2026.

Source: davila7/claude-code-templates on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.