uniprot-mcp-server

Name: uniprot-mcp-server
Availability: InStock
Author: QuentinCody

このMCPサーバーは、UniProtおよびEBIのプロテインAPIへの統一されたアクセスを提供します。データのステージング機能を備え、SQLiteを使用して複雑なクエリを効率的に処理します。Cloudflare Workers上に構築されており、スケーラブルなアーキテクチャを持っています。

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UniProt & Proteins API MCP Server

A comprehensive Model Context Protocol server for UniProt and EBI Proteins APIs, built on Cloudflare Workers with advanced data staging capabilities using Durable Objects and SQLite.

Overview

This MCP server provides unified access to:

UniProtKB: Search and retrieve protein sequence and functional information
EBI Proteins API: Detailed protein features, variations, and structural data

Key Features

🚀 Unified Interface: Single tool for searching UniProt and fetching detailed protein data
📊 Advanced Data Staging: Large datasets automatically staged in SQLite for complex queries
🔍 Smart Query Generation: Automatic suggestions for exploring staged data
📈 Intelligent Bypassing: Small datasets returned directly for efficiency
🏗️ Scalable Architecture: Built on Cloudflare Workers with Durable Objects
⚡ Rate Limit Aware: Intelligent handling of API rate limits

Tools Available

UniProt Database Tools

`uniprot_search`

Advanced UniProtKB search with comprehensive filtering and pagination:

Query: Complex search queries with UniProt syntax
Formats: JSON, TSV, FASTA, XML
Features: Sorting, facets, compression, isoforms
Pagination: Up to 500 results per page with automatic staging for large datasets

{
  "query": "organism_id:9606 AND reviewed:true",
  "format": "json",
  "fields": "accession,protein_name,gene_names,organism_name",
  "size": 100,
  "sort": "score desc",
  "compressed": true
}

`uniprot_stream`

Bulk download tool for large datasets with automatic staging:

Purpose: Stream large datasets efficiently
Auto-staging: Always stages responses for SQL querying
Compression: Built-in compression support
Formats: JSON, TSV, FASTA, XML

{
  "query": "organism_id:9606 AND reviewed:true",
  "format": "fasta",
  "compressed": true
}

`uniprot_entry`

Retrieve individual UniProtKB entries by accession:

Direct Access: Get specific protein entries
Multiple Formats: JSON, TSV, FASTA, XML
Isoforms: Include protein isoforms
Field Selection: Choose specific data fields

{
  "accession": "P04637",
  "format": "json",
  "fields": "accession,protein_name,sequence,organism_name",
  "include_isoforms": true
}

`uniprot_id_mapping`

Map IDs between different database systems:

Batch Processing: Up to 100,000 IDs per job
Cross-Database: Map between UniProt, Ensembl, PDB, etc.
Job-Based: Asynchronous processing with status tracking
Filtering: Taxonomy-based filtering

{
  "from_db": "Gene_Name",
  "to_db": "UniProtKB",
  "ids": ["TP53", "BRCA1", "BRCA2"],
  "taxon_id": "9606"
}

`uniprot_blast`

Perform BLAST searches against UniProtKB:

Programs: BLASTP, BLASTX, TBLASTN
Databases: UniProtKB, UniRef90, UniRef50
Parameters: E-value, matrix, hit limits
Async Processing: Job-based with polling

{
  "program": "blastp",
  "sequence": "MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN",
  "database": "uniprotkb",
  "threshold": 0.001,
  "hits": 50
}

EBI Proteins API Tools

`proteins_api_details`

Detailed protein information from EBI Proteins API:

Rich Data: Sequence, functional annotations, isoforms
Formats: JSON, XML
Isoforms: Include protein variants

{
  "accession": "P04637",
  "format": "json",
  "include_isoforms": true
}

`proteins_api_features`

Protein sequence features and annotations:

Categories: Domains, sites, regions, PTMs
Formats: JSON, XML, GFF
Filtering: Specific feature categories

{
  "accession": "P04637",
  "categories": ["DOMAINS_AND_SITES", "PTM"],
  "format": "json"
}

`proteins_api_variation`

Protein sequence variations and disease variants:

Sources: UniProt, large-scale studies
Consequences: Missense, nonsense, synonymous
Disease Filter: Disease-associated variants only
Clinical Data: ClinVar, COSMIC integration

{
  "accession": "P04637",
  "sources": ["uniprot", "large_scale_studies"],
  "consequences": ["missense", "nonsense"],
  "disease_filter": true
}

`proteins_api_proteomics`

Proteomics data from various studies:

Studies: PeptideAtlas, MaxQB, ProteomicsDB
Tissues: Brain, liver, heart, etc.
Quantitative: Expression levels and modifications

{
  "accession": "P04637",
  "tissues": ["brain", "liver"],
  "format": "json"
}

`proteins_api_genome`

Genome coordinate mappings:

Assemblies: GRCh38, GRCh37
Coordinates: Protein to genomic position mapping
Exon Structure: Gene structure information

{
  "accession": "P04637",
  "assembly": "GRCh38",
  "format": "json"
}

Data Management Tools

`data_manager`

Query, analyze, and manage staged datasets:

Operations: Query, schema, cleanup, export
SQL Interface: Full SQLite support
Export: JSON, CSV, TSV formats
Analytics: Built-in query suggestions

{
  "operation": "query",
  "data_access_id": "uniprot_1234567890_abc123",
  "sql": "SELECT * FROM protein WHERE JSON_EXTRACT(data, '$.organism.scientificName') = 'Homo sapiens' LIMIT 10"
}

Quick Start

1. Setup

npm install

2. Development

npm run dev

The server will be available at:

MCP Endpoint: http://localhost:8787/mcp
SSE Endpoint: http://localhost:8787/sse

3. Testing Examples

Search for Human Proteins

{
  "method": "tools/call",
  "params": {
    "name": "uniprot_query",
    "arguments": {
      "operation": "search",
      "query": "organism_id:9606 AND reviewed:true",
      "limit": 10
    }
  }
}

Get Protein Details

{
  "method": "tools/call", 
  "params": {
    "name": "uniprot_query",
    "arguments": {
      "operation": "protein_details",
      "accession": "P04637"
    }
  }
}

Stage and Query Multiple Proteins

{
  "method": "tools/call",
  "params": {
    "name": "data_manager", 
    "arguments": {
      "operation": "fetch_and_stage",
      "accessions": "P04637,Q92793",
      "fields": "accession,protein_name,gene_names,organism_name"
    }
  }
}

Data Staging & SQL Querying

For large datasets, the server automatically stages data in SQLite tables within Durable Objects, enabling complex analytical queries:

Automatic Table Creation

Data is normalized into tables like:

proteins: Core protein information
gene_names: Gene names and synonyms
features: Protein sequence features
keywords: Functional keywords
references: Literature references

Example SQL Queries

-- Query staged JSON using SQLite JSON1
SELECT 
  json_extract(data, '$.primaryAccession') as accession,
  json_extract(data, '$.genes[0].geneName.value') as gene_name,
  json_extract(data, '$.sequence.length') as length
FROM protein
WHERE json_extract(data, '$.organism.scientificName') = 'Homo sapiens'
LIMIT 10;

API Endpoints and Rate Limits

UniProtKB REST API

Base URL: https://rest.uniprot.org/uniprotkb/
Rate Limits: IP-based, ~3 requests/second recommended
Formats: JSON, TSV, FASTA, GFF, XML

EBI Proteins API

Base URL: https://www.ebi.ac.uk/proteins/api/
Rate Limits: ~10 requests/second per IP
Authentication: None required for public data

Architecture

Components

UniProtMCP: Main MCP agent implementing ToolContext interface
ToolRegistry: Manages and registers all available tools
JsonToSqlDO: Durable Object for data staging and SQL operations
ChunkingEngine: Handles large dataset chunking for efficient processing
DataInsertionEngine: Optimized bulk data insertion with conflict resolution
SchemaInferenceEngine: Automatic schema discovery and documentation

Data Flow

Request: Tool receives search/fetch request
API Call: Fetches data from UniProt/Proteins APIs
Parsing: Normalizes JSON responses into structured entities
Staging Decision: Determines if staging is beneficial
Storage: Creates optimized SQLite tables in Durable Objects
Querying: Enables complex SQL analysis of staged data

Deployment

Cloudflare Workers

npm run deploy

Configuration

Ensure wrangler.jsonc includes:

Durable Object bindings for UniProtMCP and JsonToSqlDO
Node.js compatibility flags
Proper migration configuration

Environment Variables

No API keys required - both UniProt and EBI Proteins APIs are open access.

Connect to Claude Desktop

You can connect to your remote MCP server from Claude Desktop using the mcp-remote proxy.

Update your Claude Desktop configuration:

{
  "mcpServers": {
    "uniprot": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "http://localhost:8787/sse"  // or your-uniprot-server.workers.dev/sse
      ]
    }
  }
}

Rate Limiting Strategy

See RATE_LIMITING.md for detailed information about:

API-specific rate limits and best practices
Intelligent request throttling and retry logic
Monitoring and optimization strategies
Bulk operation handling

Examples

Research Workflow: Cancer-related Proteins

Search for cancer-related proteins:

{
  "operation": "search",
  "query": "keyword:Cancer AND organism_id:9606",
  "limit": 100
}

Stage for analysis:

{
  "operation": "fetch_and_stage",
  "accessions": "P04637,P53_HUMAN,BRCA1_HUMAN,BRCA2_HUMAN"
}

Analyze with SQL:

SELECT 
  p.accession,
  p.protein_name,
  COUNT(f.feature_id) as feature_count,
  GROUP_CONCAT(DISTINCT k.keyword) as keywords
FROM proteins p
LEFT JOIN features f ON p.accession = f.accession  
LEFT JOIN keywords k ON p.accession = k.accession
WHERE k.keyword LIKE '%cancer%'
GROUP BY p.accession
ORDER BY feature_count DESC;

Protein Family Analysis

Search protein family:

{
  "operation": "search", 
  "query": "family:\"protein kinase\" AND reviewed:true",
  "fields": "accession,protein_name,gene_names,ec"
}

Get detailed features:

{
  "operation": "protein_features",
  "accession": "P06493",
  "features": "DOMAIN,BINDING,ACT_SITE"
}

Contributing

Fork the repository
Create a feature branch
Make your changes
Test thoroughly with both APIs
Submit a pull request

License

MIT License - see LICENSE file for details.

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QuentinCody

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