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

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

Resolve a phenotype label, synonym, HP id (HP:0000118), or external cross-reference CURIE (UMLS:C0000737, SNOMEDCT_US:263681008, ...) to the canonical HPO term {hpo_id, name, match_type}. An ambiguous label returns ambiguous_query with candidates (each {hpo_id, name}); an obsolete HP id resolves with success:true, obsolete:true, and its successor in replaced_by. This is the recommended first step — resolve any query to a canonical HP id before calling get_term. Signature: resolve_term(query, response_mode=).

Full-text search over HPO phenotype term names, synonyms, and definitions (FTS, relevance-ranked). Returns {hpo_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_terms(query, limit=, offset=, include_obsolete=, response_mode=).

Return an HPO phenotype term record: definition, synonyms (exact/related/broad/narrow), alt_ids, subsets, comments, cross-references, direct parents and children, and obsolescence (replaced_by). The term accepts an HP id, a label/synonym, or an external xref CURIE (resolved first). Pass fields=['synonyms', 'definition'] for a sparse projection. Note on synonyms shape: compact (default) returns synonyms as plain strings; standard/full return {text, scope} objects. Signature: get_term(hpo_id, response_mode=, fields=).

Return all transitive is_a ancestors (broader phenotype terms) of an HPO 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_term_parents for only the immediate parents. Signature: get_term_ancestors(hpo_id, limit=, offset=, response_mode=).

Return all transitive is_a descendants (more specific phenotype terms) of an HPO 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_term_children for only the immediate children. Signature: get_term_descendants(hpo_id, limit=, offset=, response_mode=).

Return the direct is_a parents (immediate broader phenotype terms) of an HPO term. Use get_term_ancestors for the full transitive set. Signature: get_term_parents(hpo_id, response_mode=).

Return the direct is_a children (immediate more-specific phenotype terms) of an HPO term. Use get_term_descendants for the full transitive set. Signature: get_term_children(hpo_id, response_mode=).

Resolve an external cross-reference CURIE (UMLS/SNOMEDCT_US/NCIT/MEDDRA/ICD-10/ICD-9/MONDO/DOID/ORPHA) back to the HPO term(s) that cross-reference it. 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=).

List an HPO term's cross-references to other ontologies/vocabularies, grouped by target prefix (UMLS/SNOMEDCT_US/NCIT/MEDDRA/ICD-10/ICD-9/MONDO/DOID/ORPHA/EFO/MSH/MESH). Optionally restrict to a subset of prefixes. Signature: map_cross_ontology(hpo_id, prefixes=, response_mode=, fields=).

Return the HPO phenotype terms annotated to a gene (symbol or NCBI id). Signature: get_phenotypes_for_gene(gene, limit=, offset=, response_mode=).

Return the genes annotated to an HPO phenotype term, optionally expanded to include descendants. Signature: get_genes_for_phenotype(hpo_id, include_descendants=, limit=, offset=, response_mode=).

Return the HPO phenotype terms annotated to a disease CURIE (e.g. OMIM:106210, ORPHA:550). Signature: get_phenotypes_for_disease(disease_id, limit=, offset=, response_mode=).

Return diseases annotated to an HPO phenotype term, optionally expanded to include descendants. Signature: get_diseases_for_phenotype(hpo_id, include_descendants=, limit=, offset=, response_mode=).

Return genes associated with a disease CURIE (e.g. OMIM:106210, ORPHA:550). Signature: get_genes_for_disease(disease_id, limit=, offset=, response_mode=).

Return diseases associated with a gene (symbol or NCBI id). Signature: get_diseases_for_gene(gene, limit=, offset=, response_mode=).