Omics AI MCP Server
A Model Context Protocol (MCP) server that enables AI agents to conversationally interact with Omics AI Explorer networks for genomics research and data analysis.
Overview
This MCP server wraps the functionality of the omics-ai-python-library to provide AI agents with seamless access to genomics data across multiple Omics AI Explorer networks including:
- HiFi Solves (hifisolves.org) - Long-read sequencing data
- Neuroscience AI (neuroscience.ai) - Neuroscience genomics data
- ASAP (cloud.parkinsonsroadmap.org) - Aligning Science Across Parkinson's
- Viral AI (viral.ai) - Viral genomics and surveillance data
- Target ALS (dataportal.targetals.org) - ALS research data
Features
The MCP server provides the following tools for AI agents:
list_collections- Discover available data collections in any networklist_tables- Browse tables within specific collectionsget_schema_fields- Examine table schemas and field typesquery_table- Query data with filters, pagination, and orderingcount_rows- Count rows matching specific criteriasql_search- Execute direct SQL queries using Trino syntax
Installation
git clone https://github.com/mfiume/omics-ai-mcp.git
cd omics-ai-mcp
npm install
Usage
Running the Server
npm start
Configuration for Claude Desktop
Add to your Claude Desktop configuration file:
{
"mcpServers": {
"omics-ai": {
"command": "node",
"args": ["src/index.js"],
"cwd": "/path/to/omics-ai-mcp"
}
}
}
Example AI Agent Interactions
Once configured, AI agents can conversationally query genomics data:
Agent: "What collections are available on the Viral AI network?"
User: "Show me the tables in the virusseq collection"
Agent: "List the first 10 variants from the variants table where chromosome equals chr1"
User: "How many total variants are in the VirusSeq database?"
Tool Reference
list_collections
Lists all available collections in a network.
Parameters:
network(required): Network name (hifisolves, viral, neuroscience, etc.) or full URLaccess_token(optional): Authentication token
list_tables
Lists all tables in a specific collection.
Parameters:
network(required): Network name or URLcollection_slug(required): Collection identifier (e.g., "virusseq", "gnomad")access_token(optional): Authentication token
get_schema_fields
Retrieves the schema and field definitions for a table.
Parameters:
network(required): Network name or URLcollection_slug(required): Collection identifiertable_name(required): Qualified table name (e.g., "collections.virusseq.variants")access_token(optional): Authentication token
query_table
Queries data from a table with optional filtering and pagination.
Parameters:
network(required): Network name or URLcollection_slug(required): Collection identifiertable_name(required): Qualified table namefilters(optional): Filter criteria objectlimit(optional): Max rows to return (default: 100)offset(optional): Rows to skip (default: 0)order_by(optional): Sort specificationaccess_token(optional): Authentication token
count_rows
Counts rows matching specified filters.
Parameters:
network(required): Network name or URLcollection_slug(required): Collection identifiertable_name(required): Qualified table namefilters(optional): Filter criteria objectaccess_token(optional): Authentication token
sql_search
Executes direct SQL queries against a collection using Trino syntax with enhanced result formatting.
Parameters:
network(required): Network name or URLcollection_slug(required): Collection identifiersql(required): SQL query string (use Trino syntax with double quotes for identifiers)max_polls(optional): Maximum number of polling attempts (default: 10)poll_interval(optional): Seconds to wait between polls (default: 2.0)access_token(optional): Authentication token
Features:
- Automatic async query polling with robust error handling
- Intelligent result formatting (table view for simple data, JSON for complex)
- Progress indicators and pagination info
- Timeout management for long-running queries
Example queries:
SELECT COUNT(*) FROM "schema"."table"SELECT * FROM "schema"."variants" WHERE chrom = 'chr1' LIMIT 10SELECT DISTINCT chrom FROM "schema"."variants" ORDER BY chrom
Supported Networks
The server supports these pre-configured networks (use short names for convenience):
| Short Name | Full URL | Description |
|---|---|---|
| hifisolves | hifisolves.org | Long-read sequencing data |
| neuroscience | neuroscience.ai | Neuroscience genomics |
| asap | cloud.parkinsonsroadmap.org | Parkinson's research |
| viral | viral.ai | Viral genomics |
| targetals | dataportal.targetals.org | ALS research |
Error Handling
The server includes robust error handling for:
- Network connectivity issues
- Authentication failures
- Invalid parameters
- API response parsing errors
- Timeout handling for long-running queries
Development
# Development mode with auto-restart
npm run dev
# Production mode
npm start
License
MIT License - see LICENSE file for details.
Related Projects
- omics-ai-python-library - Python client library
- Model Context Protocol - MCP specification and SDKs