@pipeworx/bioportal

Term search, class lookup and cross-ontology mappings over the ~1,300 biomedical ontologies NCBO's BioPortal carries — NCIT, SNOMEDCT, LOINC, RXNORM, MESH, HPO, ICD10CM, GO and the rest.

Part of Pipeworx — an MCP gateway connecting AI agents to 1863+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.

Tools

• bioportal_search(query, ontologies?, exact_match?, require_definitions?, limit?) — free text to coded concept, with preferred label, synonyms, definition, CUI and the permanent class IRI.
• bioportal_ontologies(filter?, limit?) — the catalogue of ontologies, so you can find the acronym before you search.
• bioportal_class(ontology, class_id) — the full record for one class.
• bioportal_mappings(ontology, class_id, to_ontology?, limit?) — the equivalent concept in other ontologies, with the mapping method.

Auth

BioPortal requires an apikey on every request. Resolution order in this pack:

1. caller-supplied _apiKey (free key, https://bioportal.bioontology.org/accounts/new),
2. otherwise the demo key NCBO publishes in its own REST documentation, which is shared across all of its users and rate-limited accordingly.

Every response carries key_source so a caller can see which one answered.

When a platform key is provisioned (PLATFORM_BIOPORTAL_KEY), the change is one line: add "platformKeyEnv": "PLATFORM_BIOPORTAL_KEY" to this pack's entry in workers/gateway/src/pack-manifest.json and re-run node scripts/sync-pack-manifest.mjs. The gateway then injects it as _apiKey and the demo fallback stops being reached. It is deliberately NOT declared today: keyBlockedTools() in the gateway marks every tool of a pack that declares an UNSET platformKeyEnv as key-blocked, which would sink a pack that currently works for everyone.

Data sources

• https://data.bioontology.org/search — q, ontologies, exact_match, require_definitions, pagesize.
• https://data.bioontology.org/ontologies — the catalogue.
• <https://data.bioontology.org/ontologies/{acronym}/classes/{URL-encoded IRI}> and its /mappings child.

Things that will otherwise cost you an afternoon:

• display_links=false is the difference between 4.4 MB and 312 KB on /ontologies. Use it there.
• But do NOT set it on /search: a search hit's ontology acronym is only derivable from links.ontology. Its @id is a purl (http://purl.bioontology.org/ontology/MESH/D008545) whose path segment is not reliably the acronym.
• The class IRI must be URL-encoded as a single path segment — # and / included — e.g. /ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224.
• A mapping record lists BOTH ends in classes, including the class you asked about. Pick the one whose ontology is not the source, or every mapping looks like a self-mapping.
• Not every concept maps to the big terminologies. NCIT "Melanoma" (C3224) has 114 mappings and none of them are to SNOMEDCT — the targets are CADSR-VS, RH-MESH, MESH, MEDDRA, LOINC and a long tail. An empty to_ontology filter result is a real answer, not a failure.

Scope, so nobody builds this twice

The ols pack covers EBI's Ontology Lookup Service — a different repository with a different, OBO-leaning set of ontologies. BioPortal is the one carrying the US clinical terminologies. cbioportal is cancer genomics and is unrelated despite the name.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

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

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/bioportal/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, `discove

... View full README on GitHub