Geneontology Mcp Server
About
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.
Details
- Author
- Augmented-Nature
- Downloads
- 304
- Categories
- Search, Database, Other, Knowledge Base
Jump to
- Search GO terms by keyword, name, or definition
- Retrieve detailed information for a specific GO term
- Validate GO identifiers and check term existence
- Navigate hierarchical relationships between ontology terms
- Access GO annotations for genes and proteins
- Obtain ontology statistics and metadata
Install with npm install && npm run build, then add the built index.js to your MCP client configuration as a command‑line server. Use the provided tools (search_go_terms, get_go_term, validate_go_id, get_ontology_stats) and resource templates (go://term/{id}, go://annotations/{gene}, go://search/{query}, go://hierarchy/{id}) to interact with GO data.
Access Gene Ontology (GO) data for ontology-based analysis, gene annotation research, and functional enrichment studies.
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
{ "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 }
Get detailed information about a GO term
# Using the get_go_term tool { "id": "GO:0006915" }
# Using the validate_go_id tool { "id": "GO:0008150" }
- 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}
Access PubMed articles through the Entrez API.
Fetch protein information from the UniProt database.
Access and interact with Allen Institute for Neural Dynamics (AIND) metadata directly within your IDE.
A high-performance JavaScript server for the Alliance of Genome Resources (AGR) MCP.
Access the AlphaFold Protein Structure Database for protein structure prediction and analysis.
Interface with Biomart, a biological data query tool, using the pybiomart Python package.
Agent-first rewrite of genomeoncology's BioMCP in TypeScript to provide next-gen biomedical data access for agents.
Perform complex queries on the DANDI Archive, a platform for neurophysiology data.
Interact with DROMA drug-omics association analysis databases using natural language.
A bridge to the Drug Gene Interaction Database (DGIdb) API, enabling AI clients to query drug-gene interaction data.
Sign in to leave a review
Use Google, GitHub, or an email account so ratings stay tied to real people.
No reviews posted yet.
