Mondo MCP Server

@pipeworx/mondo

Resolves free-text condition/disease strings — clinical trial registry "conditions" fields, drug-label indication wording, anything a caller typed by hand — onto the Mondo Disease Ontology (MONDO), with a match-quality label the caller can trust and cross-ontology xrefs for the matched term.

Part of Pipeworx — an MCP gateway connecting AI agents to 1573+ live data sources.

Tools

• mondo_resolve_condition(conditions, expand?) — batch-resolves 1-25 free-text condition strings. For each, returns the original wording verbatim, the best MONDO id + label, and match_quality:

  • exact-label — identical (case/punctuation-insensitive) to the term's primary Mondo label.
  • exact-synonym — identical to one of the term's listed exact synonyms.
  • broader / narrower — the string exactly names a parent or child term reached via the Mondo hierarchy, not the top full-text hit itself. This includes a fixed-prefix strip of a LEADING stage/status qualifier a registry stacks onto the front of a disease name — "Stage IV Melanoma", "Metastatic Breast Cancer", "Recurrent X" — when the remainder after stripping is an exact label/synonym match, the response is broader (the input names a subtype/stage of the matched disease) with a note listing what was stripped.
  • fuzzy — the closest full-text match from EBI OLS4, not a confirmed exact term. Never presented as exact.
  • no-match — nothing plausible found. The response says what queries were tried (including relaxed variants — stripped parentheticals, un-inverted "Specific, General" MeSH form, progressively truncated trailing qualifiers like "Stage IV") and lists nearest candidates when the relaxation surfaced any. Never a bare empty result (docs/silent-zero-policy.md).

  Every non-no-match result also carries xrefs (OMIM, Orphanet, DOID, UMLS, MeSH) for the resolved id, pulled from the MyDisease.info record. Pass expand: true to also get descendant_mondo_ids — every subtype under the resolved term, capped at 500 — for building a subtype-inclusive registry filter (e.g. "any subtype of non-small cell lung carcinoma").

  The match_quality label is the product. A fuzzy or hierarchical match is never upgraded to "exact" — a caller doing a clinical-safety check or building a registry filter needs to know the difference.

No second tool: term detail, hierarchy walking (ancestors/children) and raw Mondo search already live in the ebi-ols pack — this pack only adds the resolution + match-quality layer on top, so it doesn't duplicate that surface.

Auth

Keyless. Both upstreams are public, unauthenticated APIs.

Data sources

• https://www.ebi.ac.uk/ols4/api/search (EBI Ontology Lookup Service, restricted to ontology=mondo) — full-text search over Mondo terms, with primary labels and exact/related synonyms. Same upstream the ebi-ols pack proxies; called directly here rather than chained through that pack.
• https://mydisease.info/v1/disease/{id} (MyDisease.info, BioThings) — per-term Mondo record: cross-ontology xrefs (mondo.xrefs.omim / .omimps, .orphanet, .doid, .umls, .mesh) and the full transitive mondo.ancestors / mondo.descendants id lists, used both for the broader/narrower hierarchy check and the expand flag. Same upstream the mydisease pack proxies; called directly here rather than chained through that pack.

Matching notes for the next person:

• Normalization is case-insensitive and treats any run of non-alphanumeric characters (hyphens, commas, punctuation) as a single space, so "Non-small Cell Lung Cancer" and "non small cell lung cancer" compare equal. It does not do stemming or synonym expansion beyond what OLS4 already returns as exact_synonyms — a string that isn't in that list will not register as exact even if a human would consider it a paraphrase.
• MeSH's inverted "Specific, General" comma form ("Carcinoma, Non-Small-Cell Lung") is the dominant condition shape in trial registries, so it's un-inverted ("Non-Small-Cell Lung Carcinoma") and checked for an exact match alongside the literal string before falling back to fuzzy — a fixed rewrite of a known convention counts as exact, not a guess.
• The leading-qualifier strip (STAGE_QUALIFIER_RE / STATUS_QUALIFIER_RE in src/index.ts) is a small, fixed, ordered list — a stage marker ("Stage IV", "Stage IIIA") or one of metastatic / recurrent / advanced / refractory / unresectable / relapsed / relapsing / progressive / localized / localised — checked BEFORE the trailing- word relaxation ladder, since it applies whether the literal string got zero hits ("Stage IV Melanoma") or some non-exact hits ("Metastatic Breast Cancer" already surfaces "breast cancer" as its top full-text hit, just not exactly). Deterministic prefix matching only, up to 3 passes, so a stacked "Advanced Metastatic Melanoma" strips both words.
• OLS4's exact=true search param did not reliably restrict results to exact matches when tested live (2026-09) — exactness is instead determined client-side by comparing normalized query text against each candidate's label and exact synonyms.
• The omim xref sometimes appears as omimps (OMIM phenotypic series) instead of omim in the MyDisease record; both are merged into the returned omim array.
• Every OLS4/MyDisease fetch is bounded via fetchWithTimeout; a MyDisease enrichment failure degrades to empty xrefs rather than failing the whole resolution (the OLS4 match still stands on its own).

Quick Start

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

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

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/mondo/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 1573+ 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/mondo_resolve_condition \
  -H 'Content-Type: application/json' \
  -d '{"conditions":["Carcinoma, Non-Small-Cell Lung","NSCLC Stage IV","type 2 diabetes mellitus","Carcinoid Tumors","Ehlers-Danlos syndrome"]}'

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

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

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

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-mondo

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

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 Mondo data" })

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

More

• Docs and guides
• pipeworx.io

License

MIT