/geo-database

name: "geo-database"
description: "NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases."
license: "MIT"

GEO Gene Expression Omnibus Database

Overview

GEO (Gene Expression Omnibus) is NCBI's public repository for high-throughput functional genomics data, containing 200,000+ datasets (series) from microarrays, RNA-seq, ChIP-seq, methylation, and proteomics experiments. GEOparse provides a Python interface for downloading and parsing GEO records (GSE series, GPL platforms, GSM samples) while NCBI E-utilities enables programmatic search across GEO's metadata.

When to Use

• Searching for publicly available gene expression datasets by organism, tissue, disease, or experimental condition
• Downloading and parsing a specific GEO series (GSE) with its expression matrix and sample metadata
• Extracting sample annotation tables (e.g., treatment groups, clinical covariates) for meta-analysis
• Loading microarray expression data (GPL platform-annotated probes) into a tidy DataFrame
• Retrieving all GEO experiments associated with a gene or pathway of interest
• Building automated pipelines that download and process GEO datasets for downstream analysis
• For single-cell RNA-seq data at scale, use `cellxgene-census`; for aligned reads, download FASTQ from ENA/SRA instead

Prerequisites

• **Python packages**: `GEOparse`, `requests`, `pandas`
• **Data requirements**: GSE/GPL/GSM accession numbers, or search terms
• **Environment**: internet connection; write access to local directory for downloads
• **Rate limits**: E-utilities: 3 req/s unauthenticated, 10 req/s with API key; GEO FTP is unlimited

pip install GEOparse requests pandas

Quick Start

import GEOparse

# Download a GEO series (caches in current directory)
gse = GEOparse.get_GEO("GSE2553", destdir="./geo_data/")
print(f"Title: {gse.metadata['title'][0]}")
print(f"Samples: {len(gse.gsms)}")
print(f"Platform: {list(gse.gpls.keys())}")

# Sample metadata
meta = gse.phenotype_data
print(meta.head())

Core API

Query 1: Search GEO Datasets via E-utilities

Find GEO series (GSE) by keyword, organism, or dataset type.

import requests

EMAIL = "your@email.com"
BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

def geo_search(query, retmax=20):
    r = requests.get(f"{BASE}/esearch.fcgi",
                     params={"db": "gds", "term": query,
                             "retmax": retmax, "retmode": "json", "email": EMAIL})
    r.raise_for_status()
    return r.json()["esearchresult"]

# Search for human breast cancer RNA-seq datasets
result = geo_search(
    "breast cancer[title] AND Homo sapiens[organism] AND gse[entry type]",
    retmax=10
)
print(f"Found {result['count']} matching GEO datasets")
print(f"First accessions (UIDs): {result['idlist']}")

# Search for specific platform (e.g., Illumina HumanHT-12)
result = geo_search(
    "Illumina HumanHT-12[platform] AND Homo sapiens[organism] AND gse[entry type]",
    retmax=5
)
print(f"Illumina HumanHT-12 human datasets: {result['count']}")

Query 2: Fetch Dataset Summary Metadata

Retrieve title, accession, and organism for search results.

import requests

EMAIL = "your@email.com"
BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

def geo_summary(uids):
    r = requests.post(f"{BASE}/esummary.fcgi",
                      data={"db": "gds", "id": ",".join(uids),
                            "retmode": "json", "email": EMAIL})
    r.raise_for_status()
    return r.json()["result"]

# Get metadata for search results
result = geo_search_func = lambda q: requests.get(
    f"{BASE}/esearch.fcgi",
    params={"db": "gds", "term": q, "retmax": 3, "retmode": "json", "email": EMAIL}
).json()["esearchresult"]["idlist"]

uids = requests.get(
    f"{BASE}/esearch.fcgi",
    params={"db": "gds", "term": "lung cancer[title] AND gse[entry type]",
            "retmax": 3, "retmode": "json", "email": EMAIL}
).json()["esearchresult"]["idlist"]

summaries = geo_summary(uids)
for uid in summaries.get("uids", []):
    s = summaries[uid]
    print(f"\nAccession: {s.get('accession')} | {s.get('title')}")
    print(f"  Organism: {s.get('taxon')}")
    print(f"  Samples: {s.get('n_samples')}")
    print(f"  Type: {s.get('gdstype')}")

Query 3: Download and Parse a GEO Series

Use GEOparse to download a full GSE record with expression matrix and sample metadata.

import GEOparse

# Download GSE (auto-caches; skip download if already present)
gse = GEOparse.get_GEO("GSE2553", destdir="./geo_data/", silent=True)

# Series metadata
print(f"Title   : {gse.metadata['title'][0]}")
print(f"Summary : {gse.metadata['summary'][0][:200]}...")
print(f"Samples : {len(gse.gsms)} GSMs")
print(f"Platforms: {list(gse.gpls.keys())}")

# Sample metadata table (phenotype data)
meta = gse.phenotype_data
print(f"Metadata columns: {list(meta.columns)}")
print(meta.head())

Query 4: Extract Expression Matrix

Parse probe-level expression data and optionally merge with platform gene annotations.

import GEOparse, pandas as pd

gse = GEOparse.get_GEO("GSE2553", destdir="./geo_data/", silent=True)

# Pivot to gene expression matrix (probes × samples)
gpl_id = list(gse.gpls.keys())[0]
pivot = gse.pivot_samples("VALUE", gpl_id)
print(f"Expression matrix shape: {pivot.shape}")  # (probes, samples)
print(pivot.iloc[:5, :3])

# Annotate probes with gene symbols from the GPL platform
gpl = gse.gpls[gpl_id]
annot = gpl.table[["ID", "Gene Symbol", "Gene Title"]].copy()
annot.columns = ["ID", "gene_symbol", "gene_title"]
annot = annot.dropna(subset=["gene_symbol"])
annot = annot[annot["gene_symbol"] != ""]

expr_annotated = pivot.join(annot.set_index("ID"), how