omophub 1.6.0

New Features

FHIR-to-OMOP Concept Resolver (client$fhir): Translate FHIR coded values into OMOP standard concepts, CDM target tables, and optional Phoebe recommendations in a single API call.
- resolve(): Resolve a single FHIR Coding (system URI + code) or text-only input via semantic search fallback. Returns the standard concept, target CDM table, domain alignment check, and optional mapping quality signal.
- resolve_batch(): Batch-resolve up to 100 FHIR codings per request with inline per-item error reporting.
- resolve_codeable_concept(): Resolve a FHIR CodeableConcept with multiple codings. Automatically picks the best match per OHDSI vocabulary preference (SNOMED > RxNorm > LOINC > CVX > ICD-10). Falls back to the text field via semantic search when no coding resolves.

Bulk lexical search (bulk_basic()): Execute up to 50 keyword searches in a single API call. Supports shared default filters for vocabulary, domain, and other parameters. Each search is identified by a unique search_id for result matching. Maps to POST /v1/search/bulk.
Bulk semantic search (bulk_semantic()): Execute up to 25 natural-language searches using neural embeddings in a single call. Supports per-search similarity thresholds and shared defaults. Query length validated at 1-500 characters. Maps to POST /v1/search/semantic-bulk.

Semantic search (semantic(), semantic_all()): Natural language concept search using neural embeddings. Search for clinical intent like “high blood sugar levels” to find diabetes-related concepts. Supports filtering by vocabulary, domain, standard concept, concept class, and minimum similarity threshold. semantic_all() provides automatic pagination with progress bar.
Similarity search (similar()): Find concepts similar to a reference concept ID, concept name, or natural language query. Three algorithm options: 'semantic' (neural embeddings), 'lexical' (string matching), and 'hybrid' (combined). Configurable similarity threshold with optional detailed scores and explanations.

Hierarchy get() method: New method to retrieve complete concept hierarchy (ancestors and descendants) in a single call with support for “flat” or “graph” visualization formats.
Vocabulary domain_stats() method: New method to get statistics for a specific domain within a vocabulary.
Vocabulary concept_classes() method: New method to list all available concept classes.
Added vocab_release parameter to concepts, mappings, relationships, and hierarchy methods for explicit vocabulary version pinning.
Added include_hierarchy parameter to concepts$get() and concepts$get_by_code().

API parameter naming: Updated to match OMOPHub API v1.3.0 specifications:
- limit → page_size for pagination
- vocabulary, domain → vocabulary_ids, domain_ids for filtering
- max_results → page_size for result limits
- relationship_type → relationship_ids for relationship filtering
- target_vocabularies → target_vocabulary (singular) in mappings
- vocabulary_id → vocabulary_ids (plural) in hierarchy methods
API simplifications: Several methods now have fewer parameters to match the simplified backend API:
- mappings$get(): Removed direction, include_indirect, standard_only, include_mapping_quality, include_synonyms, include_context, pagination
- domains$list(): Simplified to single include_stats parameter
- vocabularies$get(): Now takes only vocabulary_id
- vocabularies$domains(): Now takes no parameters
Batch limits: concepts$batch() maximum reduced from 1000 to 100 concepts per request.
Default changes:
- concepts$batch() standard_only default changed from FALSE to TRUE
- relationships$get() default page_size changed from 50 to 100

Added include_synonyms and include_relationships parameters to get_by_code() for retrieving concept synonyms and relationships in a single request.