omophub 1.8.1

Changed

• Canonical endpoint path — client$search$semantic() and client$search$semantic_all() now call GET /v1/search/semantic instead of GET /v1/concepts/semantic-search. The legacy path remains a permanent server-side alias (emits Deprecation: true + Link: …rel="successor-version" headers), so older installations of this SDK continue to work - no breaking change for callers.

omophub 1.8.0

New Features

• FHIR Value-as-Concept — the resolve_batch(as_tibble = TRUE) tibble now includes value_as_concept_id and value_as_concept_name columns, populated when the resolver decomposes a composite concept via the Maps to value relationship (HL7 FHIR-to-OMOP IG Value-as-Concept pattern — e.g. “Allergy to penicillin” yields a standard “Allergy to drug” plus a value “Penicillin G”).

• on_unmapped for FHIR resolution — resolve(), resolve_batch(), and resolve_codeable_concept() gained an on_unmapped argument ("error" default / "sentinel"). With "sentinel" the resolver returns a concept_id 0 record instead of a 404 when nothing resolves, so ETL pipelines always get a row (matches the Python SDK).

Behavior Changes

• Unmapped rows in the batch tibble — a coding that resolves to a source concept but has no standard Maps to target now reports status = "unmapped" (with standard_concept_id = 0) instead of "resolved", matching the OMOP / FHIR-to-OMOP IG convention that an unmapped concept is concept_id 0. Code that filters status == "resolved" will no longer treat these sentinels as successful mappings.

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