# BioOntology MCP Server

> Use this tool when you need to search, annotate, and explore biological ontologies, and want a comprehensive API for accessing over 1,200 ontologies. It solves problems related to ontology-based data integration, annotation, and discovery, providing a standardized interface for querying and retrieving ontology data. The BioOntology MCP Server accepts API queries as input and returns relevant ontology data as output, ideal for use cases in bioinformatics, biomedical research, and data integration.

Canonical page: https://skillsregistry.net/skills/augmented-nature-bioontology-mcp-server  
JSON: https://api.skillsregistry.net/v1/skills/augmented-nature-bioontology-mcp-server

## Description

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

## Trust

- **Trust score (0–1):** 0.97
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** search
- **Updated:** 2026-09-28

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/m1f2kohszf)
- **Repository:** <https://github.com/Augmented-Nature/BioOntology-MCP-Server>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "augmented-nature-bioontology-mcp-server"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-bioontology-mcp-server` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-bioontology-mcp-server/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt