miEAA3_MCP

An MCP (Model Context Protocol) server that integrates the miEAA 3.x REST API with Claude Desktop, exposing miEAA functionality as callable tools for microRNA and precursor enrichment analysis.

---

Introduction

miEAA3_MCP provides a clean integration layer between Claude Desktop and the miEAA bioinformatics platform.
The server is implemented in TypeScript, bundled as a single Node.js ESM entry point, and registered with Claude via MCP.

The project focuses on:

• Correct MCP protocol integration
• Robust request/response normalization
• Reliable execution of miEAA tools inside Claude Desktop

No biological logic is reimplemented; all analysis is performed by the official miEAA API.

---

Repository Structure

miEAA3_mcp/
├── README.md
├── manifest.json
├── package.json
├── package-lock.json
├── tsconfig.json
├── dist/
│ ├── server.js
│ └── handlers/
│ ├── mieaa_categories_handler.js
│ ├── mieaa_mirna_precursor_converter_handler.js
│ ├── mieaa_mirbase_converter_handler.js
│ └── over_representation_analysis_handler.js
├── src/
│ ├── server.ts
│ ├── handlers/
│ │ ├── mieaa_categories_handler.ts
│ │ ├── mieaa_mirna_precursor_converter_handler.ts
│ │ ├── mieaa_mirbase_converter_handler.ts
│ │ └── over_representation_analysis_handler.ts
│ └── utils/
│ └── mieaa.ts
├── test.mjs
└── miEAA3_mcp.dxt

---

Integrated Tools (Claude MCP)

The following four miEAA tools are integrated, registered, and visible in Claude Desktop:

1. Over-Representation Analysis (ORA)

Tool: over_representation_analysis

• Runs miEAA ORA for miRNA or precursor inputs
• Handles job submission, polling, and result retrieval
• Supports category-based enrichment analysis

---

2. List Enrichment Categories

Tool: list_enrichment_categories

• Queries available enrichment categories from miEAA
• Intended to guide category selection for ORA

---

3. miRNA ↔ Precursor Converter

Tool: mirna_precursor_converter

• Converts between miRNA and precursor identifiers
• Handles miEAA rate limits
• Normalizes plain-text API responses into structured output

---

4. miRBase Version Converter

Tool: mirbase_version_converter

• Converts miRNA identifiers between miRBase versions
• Explicitly reports converted, unchanged, and unmappable entries

---

Environment Setup

Prerequisites

• Node.js ≥ 18
• npm

Install dependencies:

npm install

---

Build Process

The MCP server must be bundled into a single ESM-compatible file for Claude Desktop.

npx esbuild src/server.ts   --bundle   --platform=node   --format=esm   --target=node18   --outfile=dist/server.js   --log-level=debug

Why this build step is required

• Bundles all handlers and utilities into one file
• Ensures compatibility with Claude’s Node runtime
• Resolves MCP SDK and module resolution issues

---

Claude Desktop Integration

• The MCP server is correctly discovered and launched by Claude Desktop
• Extension folder detection issues are resolved
• MCP SDK resolution issues are resolved by the current build setup
• All four tools appear as callable tools inside Claude

No manual server startup is required when using Claude Desktop.

---

Local Testing

node test.mjs

All tools execute correctly in a local Node.js environment.

---

MCP Inspector

For protocol-level inspection and debugging:

npm install @modelcontextprotocol/inspector --save-dev
npx @modelcontextprotocol/inspector

Using in Claude as .dxt

• Install prerequisites: Node.js ≥ 18, npm, and Claude Desktop

• Clone or open the miEAA3_mcp project directory

• Install dependencies:

  npm install
  

Build the MCP server into a single ESM file:

npx esbuild src/server.ts \
  --bundle \
  --platform=node \
  --format=esm \
  --target=node18 \
  --outfile=dist/server.js

npx esbuild src/server.ts `
  --bundle `
  --platform=node `
  --format=esm `
  --target=node18 `
  --outfile=dist/server.js

Create the Claude extension package (.dxt)

(or use the existing .dxt file from the repository):

zip -r miEAA3_mcp.dxt \
  manifest.json \
  package.json \
  package-lock.json \
  tsconfig.json \
  dist \
  -x "*.ts" "*.map" "*.log"

• Open Claude Desktop → Settings → Advanced → Install Extension
• Select the miEAA3_mcp.dxt file (from your Windows or local folder)
• Open a new Claude chat and use the miEAA tools directly
• (no manual server start required)

---

Current Issue

At the moment, I am refining the result formatting, so the outputs are more structured and easier to use by user, while remaining MCP-compatible. The miEAA server was temporarily down during testing, but I expect to complete this today once it is reachable again.

One issue I encountered is that GSEA analysis has API endpoints but expects a different input format that is not documented on the miEAA website, which currently prevents successful execution. All other API-based tools are working as expected.

---