Orphadata through GeneFoundry

Router invocation: orphanet_get_server_capabilities()

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

Router invocation: orphanet_get_diagnostics()

Report the local Orphanet index status: whether the data is built, the loaded Orphanet release version, disorder counts, schema version, and when it was built, plus a runtime block (request/error counts, latency percentiles p50/p95/p99, a response_mode distribution that surfaces over-fetch, and a version-hash cache hit/miss ratio). Use this to confirm freshness or diagnose a data_unavailable error. Signature: get_diagnostics().

Router invocation: orphanet_resolve_disease()

Resolve a disease label, synonym, or ORPHAcode (ORPHA:166024 or 166024) to the canonical Orphanet term {orpha_code, name, match_type}. An ambiguous label returns ambiguous_query with candidates. Signature: resolve_disease(query, response_mode=).

Router invocation: orphanet_search_diseases()

Full-text search over Orphanet disease names, synonyms, and definitions (FTS, relevance-ranked). Returns {orpha_code, name, score} plus a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step. Obsolete terms are excluded unless include_obsolete=true. Signature: search_diseases(query, limit=, offset=, include_obsolete=, response_mode=).

Router invocation: orphanet_get_disease()

Return an Orphanet disease record: definition, synonyms, grouped cross-references, classification parents/children, age of onset, inheritance, and disorder type. The term accepts an ORPHAcode, a label/synonym, or an external xref CURIE (resolved first). xrefs are grouped by source; any nested count is leaf rows, not groups. Pass fields=['xrefs.OMIM', ...] for a sparse projection, or include=['genes','phenotypes','prevalence','disability'] to compose a full entity in ONE call. Signature: get_disease(term, response_mode=, fields=, include=).

Router invocation: orphanet_get_disease_genes()

Return gene-disease associations for an Orphanet disorder: gene symbol, HGNC id, association type, and cross-references (OMIM, Ensembl, etc.). count is the number of leaf gene rows, not grouped associations. Signature: get_disease_genes(term, response_mode=).

Router invocation: orphanet_get_disease_phenotypes()

Return HPO phenotype annotations for an Orphanet disorder: HPO id, term name, and frequency category. Optionally filter by frequency label. Frequency values: Obligate (100%), Very frequent (99-80%), Frequent (79-30%), Occasional (29-5%) (and others). Signature: get_disease_phenotypes(term, frequency=, response_mode=).

Router invocation: orphanet_get_disease_prevalence()

Return prevalence data for an Orphanet disorder: prevalence class, geographic area, and source reference. Signature: get_disease_prevalence(term, response_mode=).

Router invocation: orphanet_get_disease_natural_history()

Return natural history data for an Orphanet disorder: age of onset categories and inheritance patterns. Signature: get_disease_natural_history(term, response_mode=).

Router invocation: orphanet_get_disease_disability()

Return functional consequence (disability) data for an Orphanet disorder: ability categories affected and severity grades. Data coverage is partial: many disorders carry no Orphadata functional-consequence annotation, so a valid result can be empty -- coverage:'none' with count:0 marks this explicitly (it is NOT an error); coverage:'present' means rows exist. Signature: get_disease_disability(term, response_mode=).

Router invocation: orphanet_find_diseases_by_gene()

Find all Orphanet disorders associated with an HGNC gene symbol. Returns {orpha_code, name} per disorder with pagination. Signature: find_diseases_by_gene(gene_symbol, limit=, offset=, response_mode=).

Router invocation: orphanet_find_diseases_by_phenotype()

Find all Orphanet disorders annotated with an HPO term id. Returns {orpha_code, name} per disorder with pagination. Signature: find_diseases_by_phenotype(hpo_id, limit=, offset=, response_mode=).

Router invocation: orphanet_get_disease_classification()

Return the immediate Orphanet classification parents and children for a disorder. Use get_disease_ancestors / get_disease_descendants for the transitive closure. Signature: get_disease_classification(term, response_mode=).

Router invocation: orphanet_get_disease_ancestors()

Return all transitive ancestors (broader diseases) of an Orphanet disorder via the precomputed closure, with a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step. Use get_disease_classification for only the immediate parents. Signature: get_disease_ancestors(term, limit=, offset=, response_mode=).

Router invocation: orphanet_get_disease_descendants()

Return all transitive descendants (more specific diseases) of an Orphanet disorder via the precomputed closure, with a pagination block {total, returned, limit, offset, truncated, next_offset}. When truncated, next_commands carries a forward-page step. Use get_disease_classification for only the immediate children. Signature: get_disease_descendants(term, limit=, offset=, response_mode=).

Router invocation: orphanet_resolve_xref()

Resolve an external cross-reference CURIE (OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA) back to the Orphanet disorder(s) that map to it. Returns matches[] plus a pagination block {total, returned, limit, offset, truncated, next_offset}; when truncated, next_commands carries a forward-page step. Miss semantics (list-shaped, unlike resolve_disease): a malformed CURIE is rejected with invalid_input, while a well-formed but unmapped CURIE returns an empty page (total: 0), not not_found. Signature: resolve_xref(xref_id, limit=, offset=, response_mode=).

Router invocation: orphanet_map_cross_ontology()

List an Orphanet disorder's cross-references to other ontologies, grouped by source (OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA), each with its mapping relation. Returns them under `mappings` (get_disease returns the same data under `xrefs`). Use prefixes=['OMIM'] to restrict to a subset of sources. count is the number of leaf mapping rows (individual targets), not the number of source groups. Signature: map_cross_ontology(term, prefixes=, response_mode=).

Router invocation: orphanet_resolve_disease_batch()

Resolve many labels/ORPHAcodes/xrefs in one call (partial success: each item returns its resolution {orpha_code, name, match_type} or its own ok=false/error_code/message; the call never fails wholesale). Max 50 items; compact per item. Signature: resolve_disease_batch(queries, response_mode=).

Router invocation: orphanet_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 an ORPHAcode, label, or xref CURIE; pass fields=[...] for a sparse projection. Max 50 items; compact per item. Signature: get_disease_batch(terms, response_mode=, fields=).