query-reactome
Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".
npx skills add BioTender-max/awesome-bio-agent-skills --skill query-reactome --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Reactome Pathway Database Query the Reactome ContentService and AnalysisService APIs. ## When to Use - User asks about detailed biological pathways - User wants pathway diagrams - User asks about specific reactions in a pathway - User wants to do pathway enrichment with a gene list ## How to Execute ```python import requests import json CONTENT_URL = "https://reactome.org/ContentService" ANALYSIS_URL = "https://reactome.org/AnalysisService" # 1. Search pathways by keyword def search_pathways(keyword, species="Homo sapiens"): url = f"{CONTENT_URL}/search/query" params = {"query": keyword, "species": species, "types": "Pathway", "cluster": True} r = requests.get(url, params=params) r.raise_for_status() return r.json() # 2. Get pathway details def get_pathway(pathway_id): url = f"{CONTENT_URL}/data/query/{pathway_id}" r = requests.get(url, headers={"Accept": "application/json"}) r.raise_for_status() return r.json() # 3. Get genes/proteins in a pathway def get_pathway_participants(pathway_id): url = f"{CONTENT_URL}/data/participants/{pathway_id}" r = requests.get(url, headers={"Accept": "application/json"}) r.raise_for_status() return r.json() # 4. Gene list pathway enrichment def pa
- When to Use
- How to Execute
- Common Pathway IDs
- Follow-up Suggestions
What does the query-reactome skill do?
Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill query-reactome --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.