bioportal-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
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": true
} |
| logging | {} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| extensions | {
"io.modelcontextprotocol/ui": {}
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_ontology_termsB | Search for ontology terms in BioPortal. This function searches across BioPortal ontologies for terms matching the given query. It returns a list of tuples containing the term ID, preferred label, ontology, and ontology URL. |
| search_ontology_propertiesA | Search for ontology properties in BioPortal. This function searches for ontology properties (object properties, annotation properties, datatype properties) by their labels and IDs across BioPortal ontologies. |
| get_ontology_analyticsA | Get visitor analytics for BioPortal ontologies. This function retrieves Google Analytics data for ontology visits. You can get analytics for all ontologies, filter by month/year, or get detailed analytics for a specific ontology. |
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 targets a different aspect of BioPortal: analytics for usage data, properties search for ontology properties, and term search for ontology terms. There is no overlap in functionality.
All tool names follow a consistent verb_noun (snake_case) pattern: get_ontology_analytics, search_ontology_properties, search_ontology_terms.
Three tools is on the lower end but reasonable for a focused search and analytics server. The number is appropriate given the scope, though additional tools could be justified.
The server lacks essential operations for ontology management: no tool to list or retrieve ontologies, no term details beyond search, no mappings or annotations. This leaves significant gaps for typical BioPortal use cases.