Bioportal

liveReference

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

4tools
0msauth
free tier50 calls/day

Tools

bioportal_ontologies

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

No parameters required.

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bioportal_class

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 cano

No parameters required.

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bioportal_mappings

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 ter

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/bioportal/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/bioportal/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"bioportal_search","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("bioportal_search", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("bioportal — ncbo's biomedical ontology repository (data");