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omophub 1.7.0

New Features

  • Tibble output for batch FHIR resolution FhirResource$resolve_batch() (and the standalone fhir_resolve_batch()) gained an as_tibble parameter. When as_tibble = TRUE, the call returns a flat tibble::tibble with one row per input coding and columns for the source concept, standard concept, target CDM table, mapping type, and resolution status - ready to pipe into dplyr / tidyr. The batch summary (total / resolved / failed) is attached as attr(result, "summary"). Default behavior is unchanged: as_tibble = FALSE still returns the legacy list shape.

  • Standalone wrapper functions Thin, pipe-friendly wrappers around the R6 FhirResource methods:

    • fhir_resolve(client, ...)
    • fhir_resolve_batch(client, ...)
    • fhir_resolve_codeable_concept(client, ...)

    Both the R6 form (client$fhir$resolve(...)) and the standalone form work; pick whichever reads better in your pipeline.

  • FHIR client interop helper New exported function omophub_fhir_url(version) returning the OMOPHub FHIR Terminology Service base URL for a given FHIR version ("r4", "r4b", "r5", "r6"). Use it with httr2, fhircrackr, or any external FHIR client that wants to talk to OMOPHub's FHIR endpoint directly.

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.

Tests

  • Improved test coverage

omophub 1.5.0

New Features

  • 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.

omophub 1.4.0

New Features

  • 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.

omophub 1.3.0

New Features

  • 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().

Changes

  • 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

Bug Fixes

  • Fixed tests to use correct parameter names matching SDK implementation

omophub 1.1.0

New Features

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

Changes

  • User-Agent header updated to OMOPHub-SDK-R/{version}.

omophub 1.0.0

Initial CRAN Release

Features

  • Client: R6-based OMOPHubClient for accessing OMOPHub API
  • Concepts: Get, batch lookup, suggest, and explore medical concepts
  • Search: Basic and advanced search with filtering and pagination
  • Vocabularies: List and explore OMOP vocabularies
  • Domains: Browse concepts by clinical domain
  • Hierarchy: Navigate concept ancestors and descendants
  • Relationships: Query concept relationships
  • Mappings: Map concepts between vocabularies

Infrastructure

  • Automatic rate limiting with httr2::req_throttle()
  • Automatic retry with exponential backoff for transient errors
  • Pagination helpers (basic_all()) returning tibbles
  • Environment variable support for API key (OMOPHUB_API_KEY)
  • Vocabulary version pinning via vocab_version parameter

Documentation

  • Full roxygen2 documentation for all exported functions
  • Getting started vignette
  • pkgdown website support