Bio Geo Data

Version Compatibility

Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

GEO Data

Query and access Gene Expression Omnibus datasets using Biopython's Entrez module.

"Find expression datasets in GEO" → Search GEO for microarray/RNA-seq datasets by organism, tissue, or condition, then download expression matrices or link to SRA runs.

• Python: Entrez.esearch(db='gds', term=...) (BioPython)
• CLI: esearch -db gds -query "term" (Entrez Direct)

Required Setup

from Bio import Entrez

Entrez.email = 'your.email@example.com'  # Required by NCBI
Entrez.api_key = 'your_api_key'          # Optional

GEO Database Types

GEO Record Types:

Searching GEO

Search GEO DataSets (GDS)

from Bio import Entrez

Entrez.email = 'your.email@example.com'

# Search curated datasets
handle = Entrez.esearch(db='gds', term='breast cancer AND Homo sapiens[orgn]', retmax=10)
record = Entrez.read(handle)
handle.close()

print(f"Found {record['Count']} datasets")
print(f"IDs: {record['IdList']}")

Search GEO Series (GSE)

# Search GEO Series via gds database
# Use entry_type filter
handle = Entrez.esearch(db='gds', term='RNA-seq[title] AND human[orgn] AND gse[entry_type]', retmax=10)
record = Entrez.read(handle)
handle.close()

Common Search Fields

GDS Types

# Expression profiling by array
term = 'expression profiling by array[gdstype] AND cancer'

# RNA-seq expression
term = 'expression profiling by high throughput sequencing[gdstype]'

# ChIP-seq
term = 'genome binding/occupancy profiling[gdstype]'

Fetching GEO Information

Get GEO DataSet Summary

# Fetch summary for GDS records
handle = Entrez.esummary(db='gds', id='200024320')
record = Entrez.read(handle)
handle.close()

summary = record[0]
print(f"Accession: {summary['Accession']}")
print(f"Title: {summary['title']}")
print(f"Summary: {summary['summary'][:200]}...")
print(f"Organism: {summary['taxon']}")
print(f"Platform: {summary['GPL']}")
print(f"Samples: {summary['n_samples']}")

Summary Fields

summary['Accession']     # GSE/GDS accession
summary['title']         # Dataset title
summary['summary']       # Description
summary['taxon']         # Organism
summary['GPL']           # Platform ID
summary['n_samples']     # Number of samples
summary['FTPLink']       # FTP download link
summary['PubMedIds']     # Associated publications
summary['gdsType']       # Dataset type
summary['ptechType']     # Platform technology

Code Patterns

Search and List GEO Series

Goal: Find GEO experiment series matching a query and retrieve their metadata summaries.

Approach: Search the gds database with entry_type filtering, then fetch summaries for matched IDs to extract accessions, titles, organisms, and sample counts.

from Bio import Entrez

Entrez.email = 'your.email@example.com'

def search_geo(term, entry_type='gse', max_results=20):
    full_term = f'{term} AND {entry_type}[entry_type]'
    handle = Entrez.esearch(db='gds', term=full_term, retmax=max_results)
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return []

    handle = Entrez.esummary(db='gds', id=','.join(search['IdList']))
    summaries = Entrez.read(handle)
    handle.close()

    results = []
    for s in summaries:
        results.append({
            'accession': s['Accession'],
            'title': s['title'],
            'organism': s['taxon'],
            'samples': s['n_samples'],
            'platform': s['GPL']
        })
    return results

datasets = search_geo('breast cancer RNA-seq AND human[orgn]')
for ds in datasets:
    print(f"{ds['accession']}: {ds['title'][:60]}... ({ds['samples']} samples)")

Find RNA-Seq Datasets

def find_rnaseq_datasets(organism, keywords, max_results=20):
    term = f'{keywords} AND {organism}[orgn] AND expression profiling by high throughput sequencing[gdstype] AND gse[entry_type]'

    handle = Entrez.esearch(db='gds', term=term, retmax=max_results)
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return []

    handle = Entrez.esummary(db='gds', id=','.join(search['IdList']))
    summaries = Entrez.read(handle)
    handle.close()

    return summaries

datasets = find_rnaseq_datasets('Homo sapiens', 'COVID-19')
for ds in datasets:
    print(f"{ds['Accession']}: {ds['n_samples']} samples - {ds['title'][:50]}...")

Get GSE Download Link

def get_geo_ftp(gse_accession):
    '''Get FTP download link for a GSE'''
    handle = Entrez.esearch(db='gds', term=f'{gse_accession}[accn]')
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return None

    handle = Entrez.esummary(db='gds', id=search['IdList'][0])
    summary = Entrez.read(handle)[0]
    handle.close()

    return summary.get('FTPLink')

ftp_link = get_geo_ftp('GSE123456')
print(f"Download from: {ftp_link}")

Link GEO to SRA

Goal: Find the raw sequencing runs (SRA accessions) associated with a GEO series for downloading FASTQ files.

Approach: Search for the GSE accession in the gds database, use ELink to cross-reference to SRA, then fetch SRA summaries to extract run metadata.

def geo_to_sra(gse_accession):
    '''Find SRA runs associated with a GEO series'''
    # Search GEO
    handle = Entrez.esearch(db='gds', term=f'{gse_accession}[accn]')
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return []

    # Link to SRA
    handle = Entrez.elink(dbfrom='gds', db='sra', id=search['IdList'][0])
    links = Entrez.read(handle)
    handle.close()

    if not links[0]['LinkSetDb']:
        return []

    sra_ids = [link['Id'] for link in links[0]['LinkSetDb'][0]['Link']]

    # Get SRA accessions
    handle = Entrez.esummary(db='sra', id=','.join(sra_ids[:50]))
    summaries = Entrez.read(handle)
    handle.close()

    runs = []
    for s in summaries:
        expxml = s.get('ExpXml', '')
        if 'SRR' in str(expxml) or 'SRX' in str(expxml):
            runs.append(s)
    return runs

sra_data = geo_to_sra('GSE123456')
print(f"Found {len(sra_data)} SRA records")

Search by PubMed ID

def geo_from_pubmed(pmid):
    '''Find GEO datasets associated with a publication'''
    handle = Entrez.elink(dbfrom='pubmed', db='gds', id=pmid)
    links = Entrez.read(handle)
    handle.close()

    if not links[0]['LinkSetDb']:
        return []

    gds_ids = [link['Id'] for link in links[0]['LinkSetDb'][0]['Link']]

    handle = Entrez.esummary(db='gds', id=','.join(gds_ids))
    summaries = Entrez.read(handle)
    handle.close()

    return summaries

datasets = geo_from_pubmed('35412348')
for ds in datasets:
    print(f"{ds['Accession']}: {ds['title']}")

Download GEO Data (GEOparse)

Goal: Download a complete GEO series including sample metadata and expression data for local analysis.

Approach: Use GEOparse to fetch and parse the GSE record, then access sample metadata via the gsms dictionary and expression values via pivot_samples.

# pip install GEOparse
import GEOparse

# Download and parse GSE
gse = GEOparse.get_GEO('GSE123456')

# Access metadata
print(f"Title: {gse.metadata['title'][0]}")
print(f"Samples: {len(gse.gsms)}")

# Get sample metadata
for gsm_name, gsm in gse.gsms.items():
    print(f"{gsm_name}: {gsm.metadata['title'][0]}")

# Get expression table
if gse.gpls:
    gpl_name = list(gse.gpls.keys())[0]
    expression_table = gse.pivot_samples('VALUE')

Download Options

Direct FTP Download

# Download entire GSE
wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/

# Download specific file types
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/*counts*.txt.gz

Series Matrix Files

import gzip
import urllib.request

def download_series_matrix(gse):
    '''Download series matrix file'''
    gse_prefix = gse[:len(gse)-3] + 'nnn'
    url = f'https://ftp.ncbi.nlm.nih.gov/geo/series/{gse_prefix}/{gse}/matrix/{gse}_series_matrix.txt.gz'

    filename = f'{gse}_series_matrix.txt.gz'
    urllib.request.urlretrieve(url, filename)
    return filename

Common Errors

Decision Tree

Need GEO expression data?
├── Looking for curated datasets?
│   └── Search gds with [entry_type]=gds
├── Looking for any experiment?
│   └── Search gds with [entry_type]=gse
├── Want RNA-seq specifically?
│   └── Add 'expression profiling by high throughput sequencing[gdstype]'
├── Have a publication?
│   └── Link pubmed -> gds
├── Need raw sequencing data?
│   └── Link gds -> sra, then use sra-data skill
├── Need processed expression matrix?
│   └── Download series matrix or use GEOparse
└── Need full metadata?
    └── Use GEOparse library

Related Skills

• entrez-search - General database searching
• entrez-link - Link GEO to SRA and other databases
• sra-data - Download raw sequencing data from linked SRA
• batch-downloads - Download multiple GEO records