The full upstream README, mirrored here for reference. Install config, tool schemas, adoption signals, and an original overview live on the Mondo listing page.
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 1683+ live data sources.
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.
Keyless. Both upstreams are public, unauthenticated APIs.
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.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:
exact_synonyms — a string that isn't in that list
will not register as exact even if a human would consider it a paraphrase.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.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.omim xref sometimes appears as omimps (OMIM phenotypic series)
instead of omim in the MyDisease record; both are merged into the
returned omim array.fetchWithTimeout; a MyDisease
enrichment failure degrades to empty xrefs rather than failing the whole
resolution (the OLS4 match still stands on its own).Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
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:
Both URLs reach the same gateway and the same 1683+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
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":"..."}.
This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:
Or run it directly to confirm it starts:
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.
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:
The gateway picks the right tool and fills the arguments automatically.
MIT