Bioportal MCP Server

@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, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

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

Both URLs reach the same gateway and the same 1863+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/bioportal_search \
  -H 'Content-Type: application/json' \
  -d '{"query":"melanoma","ontologies":"NCIT,DOID","limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/bioportal_search. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Run it from npm

@pipeworx/mcp-bioportal is a local stdio bridge to the Pipeworx gateway: your MCP client starts it with npx, and it forwards every call to the same https://gateway.pipeworx.io/bioportal/mcp endpoint shown above. It needs network access; there is no offline mode.

{
  "mcpServers": {
    "bioportal": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-bioportal"]
    }
  }
}

Without a key it calls anonymously, capped at 50 calls a day. A free account raises that to 200 a day: get a key at https://pipeworx.io/signup and add "env": { "PIPEWORX_API_KEY": "<your key>" } to the server entry. The key is sent as a Bearer token, the same way a hosted connection sends it, so calls are metered and billed exactly as they are there.

It lists only this pack's tools by default. Set PIPEWORX_META_TOOLS=1 to also list ask_pipeworx and the other gateway-wide tools.

Behind an HTTPS proxy: Node's built-in fetch does not read HTTPS_PROXY by default. Newer Node releases honour it when NODE_USE_ENV_PROXY=1 is set; check your Node version's documentation.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Bioportal data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT