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