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Author: alex-omophub

404.html

@@ -101,6 +101,77 @@ results <- client$search$basic(
 )
 ```
 
+## Semantic Search
+
+Search using natural language queries powered by neural embeddings:
+
+``` r
+# Natural language search - understands clinical intent
+results <- client$search$semantic("high blood sugar levels")
+for (r in results$data$results) {
+  cat(sprintf("%s (similarity: %.2f)\n", r$concept_name, r$similarity_score))
+}
+```
+
+Filter semantic search results:
+
+``` r
+results <- client$search$semantic(
+  "heart attack",
+  vocabulary_ids = "SNOMED",
+  domain_ids = "Condition",
+  threshold = 0.5
+)
+```
+
+Fetch all semantic search results with automatic pagination:
+
+``` r
+all_results <- client$search$semantic_all(
+  "chronic kidney disease",
+  page_size = 50,
+  max_pages = 5,
+  progress = TRUE
+)
+print(nrow(all_results))
+```
+
+## Similarity Search
+
+Find concepts similar to a reference concept:
+
+``` r
+# Find concepts similar to Type 2 diabetes mellitus
+similar <- client$search$similar(concept_id = 201826)
+for (s in similar$similar_concepts) {
+  cat(sprintf("%s (score: %.2f)\n", s$concept_name, s$similarity_score))
+}
+```
+
+Search by natural language query with different algorithms:
+
+``` r
+# Semantic similarity (neural embeddings)
+similar <- client$search$similar(
+  query = "high blood pressure",
+  algorithm = "semantic"
+)
+
+# Lexical similarity (string matching)
+similar <- client$search$similar(
+  query = "high blood pressure",
+  algorithm = "lexical"
+)
+
+# Hybrid (combined - default)
+similar <- client$search$similar(
+  query = "high blood pressure",
+  algorithm = "hybrid",
+  include_scores = TRUE,
+  include_explanations = TRUE
+)
+```
+
 ## Autocomplete
 
 Get suggestions for autocomplete:

LICENSE-text.html

@@ -13,12 +13,12 @@ Source:
 [`DESCRIPTION`](https://github.com/omopHub/omophub-R/blob/main/DESCRIPTION)
 
 Chen A (2026). *omophub: R Client for the 'OMOPHub' Medical Vocabulary
-API*. R package version 1.3.0, <https://github.com/omopHub/omophub-R>.
+API*. R package version 1.4.0, <https://github.com/omopHub/omophub-R>.
 
     @Manual{,
       title = {omophub: R Client for the 'OMOPHub' Medical Vocabulary API},
       author = {Alex Chen},
       year = {2026},
-      note = {R package version 1.3.0},
+      note = {R package version 1.4.0},
       url = {https://github.com/omopHub/omophub-R},
     }

LICENSE.html

@@ -112,6 +112,12 @@ results <- client$search$semantic(
 
 # Fetch all results with auto-pagination
 all_results <- client$search$semantic_all("chronic kidney disease", page_size = 50)
+
+# Find concepts similar to a reference concept
+similar <- client$search$similar(concept_id = 201826, algorithm = "hybrid")
+for (s in similar$similar_concepts) {
+  cat(sprintf("%s (score: %.2f)\n", s$concept_name, s$similarity_score))
+}
 ```
 
 ## Use Cases
@@ -201,7 +207,7 @@ concepts_df %>%
 | Resource       | Description                         | Key Methods                                                                                            |
 |----------------|-------------------------------------|--------------------------------------------------------------------------------------------------------|
 | `concepts`     | Concept lookup and batch operations | [`get()`](https://rdrr.io/r/base/get.html), `get_by_code()`, `batch()`, `suggest()`                    |
-| `search`       | Full-text and semantic search       | `basic()`, `advanced()`, `semantic()`, `semantic_all()`, `basic_all()`                                 |
+| `search`       | Full-text and semantic search       | `basic()`, `advanced()`, `semantic()`, `semantic_all()`, `similar()`, `basic_all()`                    |
 | `hierarchy`    | Navigate concept relationships      | `ancestors()`, `descendants()`                                                                         |
 | `mappings`     | Cross-vocabulary mappings           | [`get()`](https://rdrr.io/r/base/get.html), [`map()`](https://purrr.tidyverse.org/reference/map.html)  |
 | `vocabularies` | Vocabulary metadata                 | [`list()`](https://rdrr.io/r/base/list.html), [`get()`](https://rdrr.io/r/base/get.html), `stats()`    |