Used for version control, contribution, and distribution of the Gene Ontology MCP server codebase.
Used for installation and package management of the Gene Ontology MCP server.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@GeneOntology MCP Server search for apoptosis-related biological processes"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
A comprehensive Model Context Protocol server for accessing Gene Ontology (GO) data, enabling AI systems to perform ontology-based analysis, gene annotation research, and functional enrichment studies.
Term Search & Lookup: Search GO terms by keyword, name, or definition
Ontology Navigation: Explore hierarchical relationships between terms
Gene Annotations: Access GO annotations for genes and proteins
Validation: Validate GO identifiers and check term existence
Statistics: Get comprehensive ontology statistics and metadata
Related MCP server: OWL-MCP
npm install
npm run buildAdd to your MCP client configuration:
{
"mcpServers": {
"go-server": {
"command": "node",
"args": ["/path/to/go-server/build/index.js"]
}
}
}Search across Gene Ontology terms by keyword, name, or definition.
{
"query": "apoptosis",
"ontology": "biological_process",
"size": 10
}Get detailed information for a specific GO term.
{
"id": "GO:0006915"
}Validate GO identifier format and check if term exists.
{
"id": "GO:0008150"
}Get statistics about GO ontologies (term counts, recent updates).
{
"ontology": "all"
}go://term/{id} - Complete GO term information
go://annotations/{gene} - Gene annotations
go://search/{query} - Search results
go://hierarchy/{id} - Term hierarchy relationships
# Using the search_go_terms tool
{
"query": "apoptosis",
"ontology": "biological_process",
"size": 5,
"include_obsolete": false
}# Using the get_go_term tool
{
"id": "GO:0006915"
}# Using the validate_go_id tool
{
"id": "GO:0008150"
}This server integrates with:
QuickGO API (https://www.ebi.ac.uk/QuickGO/) - Primary data source
GO Consortium (https://geneontology.org/) - Official Gene Ontology
AmiGO (http://amigo.geneontology.org/) - Additional browsing interface
The server includes comprehensive error handling for:
Invalid GO identifiers
Missing terms
API timeouts
Network errors
Malformed requests
Fork the repository
Create a feature branch
Make your changes
Add tests if applicable
Submit a pull request
If you use this project in your research or publications, please cite it as follows:
author = {Moudather Chelbi},
title = {GeneOntology MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/GeneOntology-MCP-Server},
note = {Accessed: 2025-06-29}Get detailed information for a specific GO term
Inputs: id (required).
Get statistics about GO ontologies (term counts, recent updates)
Inputs: ontology.
Search across Gene Ontology terms by keyword, name, or definition
Inputs: query (required), ontology, size, exact, +1 more.
Validate GO identifier format and check if term exists
Inputs: id (required).
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
Loading tool schema changelog…
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.
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