Mondo through GeneFoundry

Router invocation: mondo_get_server_capabilities()

Return the mondo-link discovery surface: identity/build/Mondo release, the tool list WITH call signatures, response modes, recommended workflows, the cross-reference predicate ranking, the error taxonomy, and limits. detail='full' adds the full policy notes. Call this first in a cold session, or read mondo://tools / mondo://capabilities. Signature: get_server_capabilities(detail=).

Router invocation: mondo_get_diagnostics()

Report the local Mondo index status: whether the data is built, the loaded Mondo release version, term/obsolete/xref/closure counts, schema version, and when it was built, plus a runtime block (request/error counts and latency percentiles p50/p95/p99). Use this to confirm freshness or diagnose an upstream_unavailable error. Signature: get_diagnostics().

Router invocation: mondo_resolve_disease()

Resolve a disease label, synonym, MONDO id, or external cross-reference CURIE (OMIM/Orphanet/DOID/...) to the canonical Mondo term {mondo_id, name, match_type}. A near-miss or acronym-like label falls back to a conservative fuzzy match (match_type='fuzzy'); an ambiguous label returns ambiguous_query with candidates; an obsolete id returns not_found with its successor. Signature: resolve_disease(query, response_mode=).

Router invocation: mondo_search_diseases()

Full-text search over Mondo disease names, synonyms, and definitions (FTS, relevance-ranked). Returns {mondo_id, name, score} -- compact adds a short definition_snippet; standard/full add the complete definition -- plus a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step (offset advanced) and a widen step. Obsolete terms are excluded unless include_obsolete=true. Signature: search_diseases(query, limit=, offset=, include_obsolete=, response_mode=).

Router invocation: mondo_get_disease()

Return a Mondo disease term: definition, synonyms, grouped cross-references, direct parents and children, top-level groupings, subsets, and obsolescence (replaced_by/consider). The term accepts a MONDO id, a label/synonym, or an external xref CURIE (resolved first). Pass fields=['xrefs.OMIM', ...] for a sparse projection. Signature: get_disease(term, response_mode=, fields=).

Router invocation: mondo_get_disease_ancestors()

Return all transitive is_a ancestors (broader diseases) of a Mondo term via the precomputed closure, with a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step (offset) so you can walk a >limit closure without re-sending rows. Use get_disease_parents for only the immediate parents. Signature: get_disease_ancestors(term, limit=, offset=, response_mode=).

Router invocation: mondo_get_disease_descendants()

Return all transitive is_a descendants (more specific diseases) of a Mondo term via the precomputed closure, with a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step (offset) so you can walk a >limit closure without re-sending rows. Use get_disease_children for only the immediate children. Signature: get_disease_descendants(term, limit=, offset=, response_mode=).

Router invocation: mondo_get_disease_parents()

Return the direct is_a parents (immediate broader diseases) of a Mondo term. Use get_disease_ancestors for the full transitive set. Signature: get_disease_parents(term, response_mode=).

Router invocation: mondo_get_disease_children()

Return the direct is_a children (immediate more-specific diseases) of a Mondo term. Use get_disease_descendants for the full transitive set. Signature: get_disease_children(term, response_mode=).

Router invocation: mondo_resolve_xref()

Resolve an external cross-reference CURIE (OMIM/Orphanet/DOID/NCIT/UMLS/MeSH/MedGen/SNOMED/GARD) back to the Mondo term(s) that map to it, ranked by mapping predicate (exactMatch > equivalentTo > closeMatch > ...). Returns matches[] plus a pagination block {total, returned, limit, offset, truncated, next_offset}; when truncated, next_commands carries a forward-page step (offset). Signature: resolve_xref(xref_id, limit=, offset=, response_mode=).

Router invocation: mondo_map_cross_ontology()

List a Mondo term's cross-references to other ontologies, grouped by target prefix. get_disease surfaces every source; this tool's `prefixes` filter is the first-class set (OMIM/ORPHA/DOID/NCIT/UMLS/MESH/MEDGEN/SCTID/GARD), each with its mapping predicate and origin (obo_xref|sssom). An unrecognised prefix is rejected with invalid_input. Signature: map_cross_ontology(term, prefixes=, response_mode=).

Router invocation: mondo_resolve_disease_batch()

Resolve many labels/ids/xrefs in one call (partial success: each item returns its resolution {mondo_id, name, match_type} or its own ok=false/error_code/message; the call never fails wholesale). Every row carries its `index` (0-based, 1:1 with the input) so results key back uniformly regardless of ok. Max 50 items; compact per item. Signature: resolve_disease_batch(queries, response_mode=).

Router invocation: mondo_get_disease_batch()

Fetch many disease records in one call (partial success per item: each row is the record or its own ok=false/error_code/message). Each term accepts a MONDO id, label, or xref CURIE; pass fields=[...] for a sparse projection. Every row carries its `index` (0-based, 1:1 with the input). Max 50 items; compact per item. Signature: get_disease_batch(terms, response_mode=, fields=).