biodatafinder
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_EMAIL | No | Optional. Sent to NCBI with each request, as NCBI asks. | |
| NCBI_API_KEY | No | Optional. Raises the NCBI E-utilities limit from 3 to 10 requests/s (GEO). |
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
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_datasetsB | Search all registered open data sources at once and return ranked datasets. |
| get_datasetA | Fetch full metadata for one dataset, e.g. source='geo', accession='GSE123456'. |
| list_sourcesA | List the data sources this server can search, with the data types each covers. |
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 3 tools
Each tool has a clearly distinct purpose: search_datasets finds datasets, get_dataset retrieves metadata for a specific one, and list_sources enumerates available sources. No overlap or ambiguity between them.
All tool names follow the same verb_noun snake_case convention (search_datasets, get_dataset, list_sources). The naming pattern is consistent and predictable.
With 3 tools, the server is lean but well-scoped for its purpose of searching and retrieving biodata metadata. Each tool earns its place and the count falls within the ideal 3-15 range.
The tool set covers the core lifecycle of dataset discovery: listing sources, searching across them, and fetching full metadata. There are no obvious gaps or dead ends for the stated domain.