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

query-geo

GitHub

查询NCBI GEO数据库以获取公开的基因表达数据集，支持RNA-seq和微阵列数据搜索、GEO编号检索及摘要获取。

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

Trigger Scenarios

用户询问RNA-seq或微阵列数据集提供GEO登录号(GSE/GDS)进行查找需要下载表达数据提及geo, gene expression omnibus, GSE等关键词

Install

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

More Options

Non-standard path

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

Use without installing

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

指定 Agent (Claude Code)

npx skills add Runchuan-BU/BioClaw --skill query-geo -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-geo",
    "description": "Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on \"geo\", \"gene expression omnibus\", \"expression dataset\", \"RNA-seq dataset\", \"microarray dataset\", \"GSE\", \"GDS\"."
}

NCBI GEO Database Query

Query Gene Expression Omnibus for public expression datasets.

When to Use

User wants to find RNA-seq or microarray datasets
User asks about gene expression studies for a disease/tissue
User provides a GEO accession (GSE/GDS) to look up
User wants to download expression data

How to Execute

from Bio import Entrez
import json

Entrez.email = "bioclaw@example.com"

# 1. Search GEO datasets
def search_geo(query, max_results=10, db="gds"):
    handle = Entrez.esearch(db=db, term=query, retmax=max_results, sort="relevance")
    record = Entrez.read(handle)
    handle.close()
    return record

# 2. Get dataset summaries
def geo_summary(id_list, db="gds"):
    ids = ",".join(str(i) for i in id_list)
    handle = Entrez.esummary(db=db, id=ids, retmode="json")
    result = json.loads(handle.read())
    handle.close()
    return result

# 3. Search for Series (GSE)
def search_gse(keyword, organism="Homo sapiens", max_results=10):
    query = f'"{keyword}" AND "{organism}"[Organism] AND gse[ETYP]'
    return search_geo(query, max_results)

# Example: Find breast cancer RNA-seq datasets
search = search_gse("breast cancer RNA-seq", max_results=5)
print(f"Found {search['Count']} datasets")

if search['IdList']:
    summaries = geo_summary(search['IdList'])
    for uid in search['IdList']:
        info = summaries['result'].get(str(uid), {})
        title = info.get('title', 'N/A')
        gse = info.get('accession', 'N/A')
        gpl = info.get('gpl', 'N/A')
        n_samples = info.get('n_samples', 'N/A')
        summary = info.get('summary', 'N/A')[:200]
        print(f"\n{gse}: {title}")
        print(f"  Platform: {gpl}, Samples: {n_samples}")
        print(f"  Summary: {summary}...")
        print(f"  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={gse}")

Search Syntax

By keyword: "CRISPR" AND gse[ETYP]
By organism: "Homo sapiens"[Organism]
By platform: "Illumina"[Platform]
By date: "2024/01:2026/12"[PDAT]
Combine: "breast cancer" AND "RNA-seq" AND "Homo sapiens"[Organism] AND gse[ETYP]