큰 언어 모델은 병리학, 종종 복강 조건 또는 식별자와 작업에 악화됩니다. 이 서버는 접근 및 쿼리 ontologies에 대한 신뢰할 수있는 방법을 제공하며 정확한 최신 정보를 보장합니다.

이 저장소에는 Ontology Lookup Service (OLS) API에 대한 액세스를 제공하는 모델 Context Protocol (MCP) 서버가 포함되어 있습니다. 이 서버는 AI 조수가 다양한 생물학 및 의학 종양학에서 논리적인 용어, 개념 및 계층을 검색하고 검색 할 수 있습니다.

이 서버는 Claude Desktop과 같은 AI 조수와 원활하게 작동하도록 설계되어 자연 언어를 사용하여 ontologies를 쿼리 할 수 있습니다. Gene Ontology (GO), Human Phenotype Ontology (HP) 등 다양한 종양학을 지원합니다.

(아래 이미지의 상단 부분) 및 mcp 서버와 함께 참여 (아래 그림의 하단):

특징

OLS MCP Server는 다음과 같은 도구를 제공합니다.

• ** 숙련된 검색 조건**: 유연 필터링을 통해 ontologies의 조건을 검색
• ** 검색 Ontologies**: 사용 가능한 병리학 및 그들의 metadata
• i️ Ontology Information: 특정 종양에 대한 자세한 정보

OLS MCP Server

Large Language Models are notoriously bad at working with ontologies, often hallucinating terms or their identifiers. This server provides a reliable way to access and query ontologies, ensuring accurate and up-to-date information.

This repository contains a Model Context Protocol (MCP) server providing access to the Ontology Lookup Service (OLS) API. This server enables AI assistants to search for and retrieve ontological terms, concepts, and hierarchies from various biological and medical ontologies.

This server is designed to work seamlessly with AI assistants like Claude Desktop, allowing users to query ontologies using natural language. It supports a wide range of ontologies, including Gene Ontology (GO), Human Phenotype Ontology (HP), and many others.

Without (top part of image below) and with mcp server engaged (bottom of figure below):

Features

The OLS MCP Server provides the following tools:

• 🔍 Search Terms: Search for terms across ontologies with flexible filtering
• 📚 Search Ontologies: Discover available ontologies and their metadata
• ℹ️ Get Ontology Information: Retrieve detailed information about specific ontologies
• 🎯 Get Term Information: Get comprehensive details about specific terms
• 🌳 Get Term Children: Find direct child terms in ontological hierarchies
• 👨‍👩‍👧‍👦 Get Term Ancestors: Retrieve parent terms and ancestors
• 🤖 Find Similar Terms: Discover semantically similar terms using LLM embeddings

Supported Ontologies

The server works with any ontology available through the EBI Ontology Lookup Service, including:

• GO (Gene Ontology)
• EFO (Experimental Factor Ontology)
• HP (Human Phenotype Ontology)
• MONDO (Monarch Disease Ontology)
• ChEBI (Chemical Entities of Biological Interest)
• UBERON (Uber-anatomy ontology)
• And many more…

Installation

Prerequisites

• Python 3.12 or higher
• uv package manager

Install uv (if not already installed)

# macOS/Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows
powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Install the OLS MCP Server

# Clone the repository
git clone https://github.com/seandavi/ols-mcp-server.git
cd ols-mcp-server

# Install dependencies
uv sync

# Install as a tool (optional)
uv tool install .

Configuration

Claude Desktop Configuration

To use this server with Claude Desktop, add the following configuration to your Claude Desktop config file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {