Biosamples - MCP

A Model Context Protocol (MCP) server for biological sample checklist validation and recommendation.

Built as part of GSoC 2026 proposal preparation for EMBL-EBI (Project: Expose BioSamples Submission and Search Capabilities as MCP Tools for AI-Assisted Metadata Interaction).

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What it does

Exposes 3 MCP tools that an LLM (e.g. Claude) can call:

Tool	Description
validate_sample	Validates sample metadata against a specific ENA checklist via BioValidator API
get_checklist_info	Returns all mandatory and optional fields for a given checklist ID
recommend_checklist	Scores sample metadata against 15 checklists and returns ranked recommendations with confidence scores

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Architecture

<img width="807" height="461" alt="image" src="https://github.com/user-attachments/assets/5fff6c8a-98c6-44d6-99bb-9e5834f00698" />

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Key findings from API research

• BioValidator (/biosamples/validate) validates JSON structure but does not enforce checklist mandatory fields — the MCP server's scoring engine fills this gap independently
• ENA Browser XML API (/ena/browser/api/xml/{id}) is the reliable public source for checklist field definitions
• BioSamples JSON Schema Store (internal MongoDB) is not publicly accessible — flagged as a risk in the GSoC proposal with ENA XML as a confirmed working alternative
• Validation errors return as structured {dataPath, errors} arrays — machine-parseable and LLM-friendly

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Setup

git clone https://github.com/rithvik318/biosamples-mcp
cd biosamples-mcp
python -m venv venv
venv\Scripts\activate        # Windows
# source venv/bin/activate   # Mac/Linux
pip install -r requirements.txt

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Run

python server.py

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Test with MCP Inspector

npx @modelcontextprotocol/inspector python D:\biosamples-mcp\server.py

Open http://localhost:6274 and connect using:

• Command: D:\biosamples-mcp\venv\Scripts\python.exe
• Arguments: D:\biosamples-mcp\server.py

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Example tool calls

validate_sample

{
  "sample_name": "soil sample from Delhi",
  "characteristics": "{\"organism\": [{\"text\": \"soil metagenome\"}], \"collection_date\": [{\"text\": \"2024-01-01\"}], \"geographic_location_country_andor_sea\": [{\"text\": \"India\"}]}",
  "checklist_id": "ERC000011"
}

recommend_checklist

{
  "sample_name": "soil metagenome sample",
  "characteristics": "{\"organism\": [{\"text\": \"soil metagenome\"}], \"collection_date\": [{\"text\": \"2024-01-01\"}]}",
  "top_n": 3
}

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Technologies

• Python 3.10+
• MCP Python SDK
• httpx (async HTTP)
• xml.etree.ElementTree (XML parsing)
• Tested with MCP Inspector v0.21.1