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GE
Expression datasetsNCBI E-utilities (gds)

NCBI GEO database

GEO, the Gene Expression Omnibus, is the NCBI repository where researchers deposit expression and other functional genomics data sets. Through ScholarMuse, an agent calls search_expression_data with keywords and an optional organism and gets matching GEO series (GSE records) with their accession, title, organism, sample count, platform, data type, date and linked PubMed ids.

ScholarMuse tools: search_expression_data. Each successful call uses credits.

Use in my agent

Ask your agent

Find GEO datasets on single cell RNA-seq of lung fibrosis in mouse.
Which GEO series cover glioblastoma temozolomide resistance, and how many samples does each have?
List 20 GEO series on Arabidopsis drought stress with their platforms and dates.

What your agent gets back

Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from NCBI GEO.

search_expression_data

One record per GEO series, returned when the `query` input is given.

accession
GEO series accession (GSE number)
organism
Organism or organisms of the series
samples
Number of samples
platform
Platform accessions (GPL), up to 5
dataType
Study type as recorded in GEO
date
Publication date of the series
supplementaryFiles
Supplementary file information from GEO
pubmedIds
Linked PubMed ids, up to 5
summary
Series summary, cut at 600 characters

What it covers

  • GEO series (GSE) records found through the Entrez gds database, with the total number of matches reported in the tool's summary.
  • Keyword search, with an optional organism filter that takes a scientific name or a common name such as mouse.
  • Each series links to its GEO accession page.

Limits

  • Up to 25 series per call (10 by default), sorted by relevance. There is no paging beyond that.
  • Series only. Individual samples (GSM), platforms (GPL) and curated DataSets (GDS) are not returned as records.
  • Metadata only. The tool does not download or parse expression matrices or raw files.
  • Quotes, brackets, parentheses and colons are stripped from the query, so Entrez field tags such as [Title] cannot be used. There is no date filter.

How ScholarMuse reaches NCBI GEO

The connector calls NCBI E-utilities directly: esearch on the Entrez gds database, limited to series (GSE) and sorted by relevance, then esummary for the records. An NCBI API key is sent when one is configured. Without it the same data comes back, with requests spaced further apart (680 ms instead of 210 ms).

Search results are cached for up to 6 hours and series records for up to 1 day, so a newly released series can take that long to appear.

API key: the upstream API can be called without one, so you do not add one.

Licence and attribution

Licence: Public domain database (NCBI/NLM policies); individual submitters may hold rights in their data

Dataset records from NCBI Gene Expression Omnibus (ncbi.nlm.nih.gov/geo).

Records that come from NCBI GEO carry this licence and attribution. When you cite the data in a paper, follow NCBI GEO's own citation guidance.

Capabilities that use NCBI GEO

Gene & protein lookupNew

Gene & protein lookup

Life sciences & medicine · NCBI Gene, Ensembl, UniProt +5

Related sources

NCBI GeneEnsemblUniProtInterProReactomeGTExSTRING

FAQ

ScholarMuse is not an official NCBI GEO product. It is one MCP server for academic data, and its search_expression_data tool queries NCBI GEO. An agent connected to ScholarMuse can use NCBI GEO without a separate server.

No. The NCBI GEO API can be called without a key, and ScholarMuse does not ask you for one. You sign in to ScholarMuse once and your agent calls the tool.

The connector calls NCBI E-utilities directly: esearch on the Entrez gds database, limited to series (GSE) and sorted by relevance, then esummary for the records. An NCBI API key is sent when one is configured. Without it the same data comes back, with requests spaced further apart (680 ms instead of 210 ms). Search results are cached for up to 6 hours and series records for up to 1 day, so a newly released series can take that long to appear.

Public domain database (NCBI/NLM policies); individual submitters may hold rights in their data. Attribution: Dataset records from NCBI Gene Expression Omnibus (ncbi.nlm.nih.gov/geo). Records that come from NCBI GEO carry this licence and attribution.

Yes. Each successful call to search_expression_data uses credits, and a call that fails is not charged. Current price: Gene & protein lookup, 1 credit / call.