# BioPortal

> Use this tool when you need to search, annotate, and explore biological ontologies and medical terminologies. BioPortal solves problems in bioinformatics research, clinical text annotation, and application development by providing access to over 1,200 ontologies through a robust API with advanced filtering and customizable parameters. It takes in search queries, text, and configuration parameters as input and outputs annotated data, ontology recommendations, and analytics, making it a valuable resource in contexts where semantic understanding of biological and medical terminology is required.

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

## Description

Provides access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies including medical terminologies like NCIT, DOID, and MESH. Built by Moudather Chelbi from Augmented Nature using TypeScript and the Model Context Protocol SDK, the implementation offers nine specialized tools covering term search with advanced filtering, text annotation with configurable parameters, ontology recommendations with customizable weights, batch processing capabilities, and analytics data retrieval. Features comprehensive input validation, robust error handling, resource templates for direct data access, and support for all ontologies available in BioPortal, making it valuable for bioinformatics researchers analyzing biological data, medical professionals annotating clinical texts, and developers building applications that require semantic understanding of biological and medical terminology.

## Trust

- **Trust score (0–1):** 0.50
- **Verification tier:** unverified

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** data-analytics
- **Updated:** 2026-04-25

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/augmented-nature-bioontology)
- **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"
    }
  }
}
```

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

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