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 |
Capabilities
Features and capabilities supported by this server
| 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 | |
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