pulsemcp Safe content atomic mcp-remote

BioPortal

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.

Cognium trust score

50%

Tier

Unverified

Composite of vulnerability cleanliness, spec conformance, provenance, stability, and usage signals — scanned and weighted by Cognium. Human and agent signals are tracked separately.

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Metadata

Version: 1.0.0
Skill type: atomic
Execution layer: mcp-remote
Category: data-analytics
Source: PulseMCP
Repository: github.com/augmented-nature/bioontology-mcp-server
Author type: human
Updated: 2026-04-25

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MCP

Resolve BioPortal from your agent

Streamable HTTP transport at https://api.skillsregistry.net/mcp. No auth for read tools. Discovery: .well-known/mcp.json.

One command in your shell — Claude Code wires it up and verifies the connection. Run /mcp in any session to confirm.

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

Swap --scope user for --scope project to commit it to .mcp.json.

Your client Same endpoint everywhere; only the config key differs. The full list is in the descriptor.

Claude Desktop · Settings → Connectors → Add custom connector

https://api.skillsregistry.net/mcp

Paste the URL as the connector endpoint. No authentication.

ChatGPT · Settings → Connectors → Create (developer mode) → MCP server URL

https://api.skillsregistry.net/mcp

Authentication: none. Works in chat and deep research — the server exposes the connector search and fetch tools.

Codex CLI · ~/.codex/config.toml

[mcp_servers.skillsregistry]
url = "https://api.skillsregistry.net/mcp"