GWAS Catalog MCP Server

🚀 GWAS Analysis Server (MCP Server) Documentation

The MCP server offers a powerful toolbox for genetic researchers to conduct large-scale GWAS (Genome-Wide Association Studies) analyses. By integrating the GWAS Catalog REST API and GWAS Summary Statistics API from EBRL-EBI, the MCP server can efficiently analyze the relationships between multiple SNPs (Single Nucleotide Polymorphisms) and disease phenotypes.

✨ Features

1. Obtain significant associations in genomic regions

   • Perform multi-SNP association test (MCP) analysis.
   • Support input of genomic regions of any size.
   • Automatically exclude low-quality or QC-failed SNPs.

2. Query GWAS Catalog data

   • Rapidly retrieve association analysis results through pre-stored GWAS data.

3. Integrate Summary Statistics API

   • Conduct secondary analyses using GWAS summary statistics provided by EBRL-EBI.
   • Support flexible data input formats, including statistical values extracted directly from literature.

4. Advanced data processing capabilities

   • Provide automated memory management when processing large-scale GWAS data.
   • Automatically save and manage intermediate result files.

📚 Documentation

Basic API Parameters

All API requests must include the following common parameters:

Functional API Parameters

Single SNP Significance Test

curl -X POST http://mcp_server/api/single-snp-significance \
  -H "Content-Type: application/json" \
  -d '{"snp_id":"rs123456", "phenotype":"disease"}'

Region Significance Test

curl -X POST http://mcp_server/api/region-significance \
  -H "Content-Type: application/json" \
  -d '{"chromosome":"1", "start":10000, "end":20000}'

Transcription Factor Enrichment Analysis

curl -X POST http://mcp_server/api/transcription-factor-enrichment \
  -H "Content-Type: application/json" \
  -d '{"snp_id":"rs123456", "phenotype":"disease"}'

💻 Usage Examples

Basic Usage

Request Example: Single SNP Significance Test

curl -X POST http://mcp_server/api/single-snp-significance \
  -H "Content-Type: application/json" \
  -d '{"snp_id":"rs123456", "phenotype":"disease", "api_key":"your_api_key"}'

Response Example:

{
  "status": {
    "code": 0,
    "message": "Success"
  },
  "result": {
    "p_value": 0.001234,
    "q_value": 0.005678,
    "odds_ratio": 1.23
  }
}

📦 Output Format

JSON Response Structure

All API requests will return the following unified JSON format:

{
  "status": {
    "code": integer,   // Status code, 0 indicates success
    "message": string   // Status description information
  },
  "result": {
    // Specific function-related analysis results
  }
}

Result Field Explanation

For single SNP significance test:

{
  "p_value": float,       // One-sided p-value
  "q_value": float,       // Multiple-corrected q-value
  "odds_ratio": float     // Odds ratio
}

For region significance test:

{
  "region_scores": [
    {
      "position": integer,
      "score": float
    }
  ],
  "top_hit": {
    "position": integer,
    "p_value": float
  }
}

⚠️ Important Note

1. API access limits

   • Each API key allows a maximum of 100 calls per day.
   • For high-frequency users, it is recommended to upgrade to the paid service.

2. Data input specifications

   • All SNP IDs must comply with the dbSNP format specification.
   • It is recommended to perform QC processing in advance to improve analysis efficiency.

3. Result file management

   • Automatically saved intermediate result files are retained for 7 days by default and will be automatically deleted after the expiration date.
   • If long-term storage is required, please download the result files in a timely manner.

4. Memory limit settings

   • It is recommended to set the memory_limit parameter to 80% of the available memory when processing large-scale data.
   • Overloading the memory may cause the analysis process to interrupt. It is recommended to allocate resources reasonably.

5. Error handling mechanism

   • The system automatically captures and records all runtime error information.
   • You can query the specific error cause and solution suggestions through the logs.

📧 Contact Information

For more technical support or to report issues, please contact: support@mcp-server.com