Agent Skills › Runchuan-BU/BioClaw › query-reactome

query-reactome

GitHub

通过调用 Reactome API 查询生物通路、反应机制及信号级联，支持按关键词搜索通路详情、获取参与者信息以及基于基因列表进行富集分析。

container/skills/query-reactome/SKILL.md Runchuan-BU/BioClaw

触发场景

用户询问生物通路或信号级联细节需要获取通路图谱或反应机制对基因列表进行通路富集分析

安装

npx skills add Runchuan-BU/BioClaw --skill query-reactome -g -y

更多选项

非标准路径

npx skills add https://github.com/Runchuan-BU/BioClaw/tree/main/container/skills/query-reactome -g -y

不安装直接使用

npx skills use Runchuan-BU/BioClaw@query-reactome

指定 Agent (Claude Code)

npx skills add Runchuan-BU/BioClaw --skill query-reactome -a claude-code -g -y

安装 repo 全部 skill

npx skills add Runchuan-BU/BioClaw --all -g -y

预览 repo 内 skill

npx skills add Runchuan-BU/BioClaw --list

SKILL.md

Frontmatter

{
    "name": "query-reactome",
    "description": "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\"."
}

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

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 pathway_enrichment(gene_list):
    url = f"{ANALYSIS_URL}/identifiers/projection"
    genes_text = "\n".join(gene_list)
    headers = {"Content-Type": "text/plain"}
    r = requests.post(url, data=genes_text, headers=headers)
    r.raise_for_status()
    return r.json()

# 5. Look up a gene in Reactome
def query_gene(gene_symbol):
    url = f"{CONTENT_URL}/data/query/{gene_symbol}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# Example: DNA repair pathways
results = search_pathways("DNA repair")
entries = results.get("results", [])
for entry in entries[:5]:
    for e in entry.get("entries", []):
        print(f"{e.get('stId', 'N/A')}: {e.get('name', 'N/A')}")

# Pathway enrichment
enrichment = pathway_enrichment(["BRCA1", "BRCA2", "TP53", "ATM", "CHEK2"])
for p in enrichment.get("pathways", [])[:5]:
    name = p.get("name", "N/A")
    pval = p.get("entities", {}).get("pValue", "N/A")
    found = p.get("entities", {}).get("found", 0)
    print(f"{name} — p={pval:.2e}, {found} genes found")