geo-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| GEOMCP_EMAIL | Yes | Your email address (required by NCBI). | |
| GEOMCP_API_KEY | No | Optional API key for higher rate limits (get one from NCBI). | |
| GEOMCP_BASE_URL | No | Base URL for NCBI E-Utils API. | https://eutils.ncbi.nlm.nih.gov/entrez/eutils |
| GEOMCP_DOWNLOAD_DIR | No | Directory for downloaded GEO data. | ~/.local/share/geomcp/downloads |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_geoC | Search GEO for all types of records (GSE, GSM, GPL, GDS) |
| search_geo_profilesB | Search GEO Profiles database for gene expression profiles |
| search_geo_datasetsB | Search GEO Datasets (GDS) - curated gene expression datasets |
| search_geo_seriesC | Search GEO Series (GSE) - complete experiments |
| search_geo_samplesB | Search GEO Samples (GSM) - individual samples |
| search_geo_platformsC | Search GEO Platforms (GPL) - array/sequencing platforms |
| download_geo_dataC | Download GEO data files (SOFT format) |
| get_download_statusB | Check if a GEO dataset has been downloaded |
| list_downloaded_datasetsB | List all downloaded GEO datasets |
| get_download_statsB | Get download statistics and limits |
| cleanup_downloads_toolC | Clean up downloaded files |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 11 tools
Each tool targets a distinct resource or action: search tools are differentiated by GEO record type (series, samples, platforms, datasets, profiles) plus a general search; download and management tools are clearly distinct (download, stats, status, list, cleanup). No overlapping purposes.
Most tools follow a consistent verb_noun pattern (e.g., download_geo_data, search_geo_series). The outlier is cleanup_downloads_tool, which uses 'cleanup' instead of 'clean' and has a '_tool' suffix, breaking the pattern slightly.
11 tools is well-scoped for a GEO MCP server, covering search across key record types, download operations, and dataset management. The number feels appropriate—neither too few nor excessive.
The server provides comprehensive search, download, and management capabilities for GEO data. Potential gaps include the absence of an explicit delete operation for individual datasets (cleanup is a blanket operation) and lack of upload or update functionality, but these are peripheral to the primary purpose.