GeneOntology MCP Server
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
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_go_termsC | Search across Gene Ontology terms by keyword, name, or definition |
| get_go_termC | Get detailed information for a specific GO term |
| validate_go_idB | Validate GO identifier format and check if term exists |
| get_ontology_statsC | Get statistics about GO ontologies (term counts, recent updates) |
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 4 tools
Each tool has a clearly distinct purpose with no overlap: get_go_term retrieves specific term details, get_ontology_stats provides statistical summaries, search_go_terms enables keyword-based discovery, and validate_go_id handles identifier validation. The descriptions clearly differentiate between retrieving, searching, validating, and statistical analysis functions.
All tools follow a consistent verb_noun pattern with snake_case formatting: get_go_term, get_ontology_stats, search_go_terms, validate_go_id. The naming convention is perfectly uniform throughout the set, making the tools predictable and easy to understand.
Four tools is reasonable for a GeneOntology server, covering core operations like retrieval, search, validation, and statistics. While slightly minimal, each tool serves a distinct purpose and the count aligns well with the domain's typical query patterns. A few additional tools for relationships or annotations could enhance completeness but aren't essential.
The tools cover basic query operations well but have notable gaps for a GeneOntology domain. Missing are tools for term relationships (e.g., get_parents, get_children), annotations (e.g., get_annotations_for_term), or ontology traversal. While agents can work with the provided tools, they cannot perform common GO analysis tasks like exploring term hierarchies or retrieving associated genes.