geo-database

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• SKILL.md
• geo_reference.md · references/
• query.cpython-313.pyc · scripts/__pycache__/
• query.py · scripts/

SKILL.md (first lines)

# GEO Database

## Overview

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.

## When to Use This Skill

This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.

## Core Capabilities

### 1. Understanding GEO Data Organization

GEO organizes data hierarchically using different accession types:

**Series (GSE):** A complete experiment with a set of related samples
- Example: GSE123456
- Contains experimental design, samples, and overall study information
- Largest organizational unit in GEO
- Current count: 264,928+ series

**Sample (GSM):** A single experimental sample or biological replicate
- Example: GSM987654
- Contains individual sample data, protocols, and metadata
- Linked to platforms and series
- Current count: 8,068,632+ samples

**Platform (GPL):** The microarray or sequencing platform used
- Example: GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array)
- Describes the technology and probe/feature annotations
- Shared across multiple experiments
- Current count: 27,739+ platforms

**DataSet (GDS):** Curated collections with consistent formatting
- Example: GDS5678
- Experimentally-comparable samples organized by study design
- Processed for differential analysis
- Subset of GEO data (4,348 curated datasets)
- Ideal for quick comparative analyses

**Profiles:** Gene-specific expression data linked to sequence features
- Queryable by gene name or annotation
- Cross-references to Entrez Gene
- Enables gene-centric searches across all studies

### 2. Searching GEO Data

**GEO DataSets Search:**

Search for studies by keywords, organism, or experimental conditions:

```python
from Bio import Entrez

# Configure Entrez (required)
Entrez.email = "your.email@example.com"

# Search for datasets
def search_geo_datasets(query, retmax=20):
    """Search GEO DataSets database"""
    handle = Entrez.esearch(
        db="gds",
        term=query,
        retmax=retmax,
        usehistory="y"
    )
    results = Entrez.read(handle)
    handle.close()
    return results

# Example searches
results = search_geo_datasets("breast cancer[MeSH] AND Homo sapiens[Organism]")
print(f"Found {results['Count']} datasets")

# Search by specific platform
results = search_geo_datasets("GPL570[Accession]")

# Search by study type
results = search_geo_datasets("expression profiling by array[DataSet Type]")
```

**GEO Profiles Search:**

Find gene-specific expression patterns:

```python
# Search for gene expression profiles
def search_geo_profiles(gene_name, organism="Homo sapiens", retmax=100):
    """Search GEO Profiles for a specific gene"""
    query = f"{gene_name}[Gene Name] AND {organism}[Organism]"
    handle = Entrez.esearch(
        db="geoprofiles",
        term=query,
        retmax=retmax
    )
    results = Entrez.read(handle)
    handle.close()
    return results

# Find TP53 expression across studies
tp53_results = search_geo_profiles("TP53", organism="Homo sapiens")
print(f"Found {tp53_results['Count']} expression profiles for TP53")
```

**Advanced Search Patterns:**

```python
# Combine multiple search terms
def advanced_geo_search(terms, operator="AND"):
    """Build complex search queries"""
    query = f" {operator} ".join(terms)
    return search_geo_datasets(query)

# Find recent high-throughput studies
search_terms = [
    "RNA-seq[DataSet Type]",
    "Homo sapiens[Organism]",
    "2024[Publication Date]"

From lamm-mit/scienceclaw, Apache-2.0.

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