MCP server

Bioportal

io.github.pipeworx-io/bioportal

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

BioPortal — NCBO's biomedical ontology repository (data.bioontology.org).

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,569 tokens per request once connected46 tools

https://gateway.pipeworx.io/bioportal/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 46
Token cost: About 27,569 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http bioportal https://gateway.pipeworx.io/bioportal/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.bioportal]
url = "https://gateway.pipeworx.io/bioportal/mcp"

Gemini CLI

{"mcpServers":{"bioportal":{"httpUrl":"https://gateway.pipeworx.io/bioportal/mcp"}}}

Cursor

{"mcpServers":{"bioportal":{"url":"https://gateway.pipeworx.io/bioportal/mcp"}}}

VS Code

{"servers":{"bioportal":{"type":"http","url":"https://gateway.pipeworx.io/bioportal/mcp"}}}

Antigravity

agy mcp add bioportal https://gateway.pipeworx.io/bioportal/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"bioportal","server_url":"https://gateway.pipeworx.io/bioportal/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"bioportal","server_url":"https://gateway.pipeworx.io/bioportal/mcp"}

bioportal_class ~288 tokens
Full record for one ontology class by its IRI — preferred label, every synonym, the curated definition, semantic types, obsolescence flag, and links to parents and children. AUTHORITATIVE for the canonical meaning of a coded concept. Pass the ontology acronym and the class IRI exactly as bioportal_s
bioportal_mappings ~348 tokens
Cross-ontology mappings for one class — the equivalent concepts in every other BioPortal ontology, with the mapping source (SAME_URI, LOOM, CUI, REST). AUTHORITATIVE for translating a code between terminologies, e.g. an NCIT concept to its SNOMEDCT, MESH and ICD10CM equivalents. Pass the ontology ac
bioportal_ontologies ~248 tokens
List the biomedical ontologies BioPortal carries — acronym, full name and type — so you can pick the right vocabulary acronym before searching or looking up a class. AUTHORITATIVE catalogue of what is available in BioPortal. Pass `filter` to narrow by acronym or name substring.
bioportal_search ~382 tokens
Search ~1,300 biomedical ontologies for a term and get back the matching classes with their preferred label, synonyms, definition, ontology and permanent class IRI. AUTHORITATIVE for mapping free text to a coded clinical concept (NCIT, SNOMEDCT, LOINC, RXNORM, MESH, HPO, ICD10CM) — these are the cur

Ebi Ols
EBI OLS4 MCP — Ontology Lookup Service.
Bioregistry
Bioregistry MCP.
EventTrader MCP
AI prediction market trading — real-time data, CLOB exchange, Prop Desk, 40+ tools
Delx Commerce — Pay-per-Result APIs for Agents
986 pay-per-result MCP/x402 APIs for web, data, Base, reliability and agent delivery.
Noodle Biomedical Literature Discovery MCP
Biomedical paper search and literature graph traversal.
Noodle Biomedical Literature Discovery MCP
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Hpo Api
HPO API MCP.
Flyvolo Knowledge
Sourced, task-level facts on how AI changes jobs, for agents answering 'what should I do?'

[![AptLynx](https://aptlynx.net/badge/io.github.pipeworx-io/bioportal.svg)](https://aptlynx.net/servers/io.github.pipeworx-io/bioportal)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents