@pipeworx/mondo

Connect: https://gateway.pipeworx.io/mondo/mcp · Install: one-click buttons

Tools: 1

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.

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).

Tools

• mondo_resolve_condition — Resolve free-text condition/disease strings — e.g. a clinical trial registry’s “conditions” field (“Carcinoma, Non-Small-Cell Lung”), or a drug label’s Indications and Usage wording — onto the Mondo D