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Run npx skillmds@latest add runchuan-bu/query-geo in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Query Geo free to use?

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Who published Query Geo?

Runchuan-BU (@runchuan-bu) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Query Geo by runchuan-bu — Agent Skill

Name: Query Geo
Rating: 4.2 (5 reviews)
Author: Runchuan-BU

Query Geo

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".

Runchuan-BU Updated Sep 9, 2026

File contents

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]

Follow-up Suggestions

"Want me to download the expression matrix for this dataset?"
"Should I do differential expression analysis?"
"Want me to check what genes are differentially expressed?"

---name: query-geodescription: 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 ```python 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]` ## Follow-up Suggestions - "Want me to download the expression matrix for this dataset?" - "Should I do differential expression analysis?" - "Want me to check what genes are differentially expressed?"

Frequently asked questions