Query Geo Agent Skill
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".
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill query-geoThe instruction itself
5 sections, as written by the authorNCBI 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 = "[email protected]"
# 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?"
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How to use it
Take biotender-max/query-geo from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.