R/x_vocabulary_relationships.R
vocab_lookup_relationships.RdLookup a Source Vocabulary's Relationships
vocab_lookup_relationships( vocabulary_id, conn, conn_fun = "connectAthena()", vocab_schema = "omop_vocabulary", cache_only = FALSE, skip_cache = FALSE, override_cache = FALSE, render_sql = FALSE, render_only = FALSE, verbose = FALSE, sleepTime = 1 )
| vocabulary_id | Vector of 1 or more `vocabulary_id` from the OMOP Vocabulary |
|---|---|
| conn | Connection object. If provided, diverts queries to the connection instead of the local Athena instance without caching features. |
| cache_only | Loads from the cache and does not query the database. A NULL object is returned if a resultset was not cached. |
| skip_cache | Skip the caching altogether and directly query the database. |
| override_cache | If TRUE, the cache will not be loaded and will be overwritten by a new query. For override_cache to take effect, skip_cache should be FALSE. |
| render_sql | If TRUE, the SQL will be printed back in the console prior to execution. Default: FALSE |
| verbose | If TRUE, prints loading and querying operations messages to the console. Default: FALSE |
| sleepTime | Argument for `Sys.sleep()` in between queries to allow for halting function execution, especially in cases where other chariot functions are executing multiple queries in succession and require cancellation. |
Lookup all of a Source Vocabulary's non-null relationships in the Concept Relationship Table.
library(chariot) library(tidyverse) # Lookup relationships on the Vocabulary-Concept Class Id axis vocab_lookup_relationships(vocabulary_id = "HemOnc")#> [2021-05-26 16:08:01] Connected to 'athena' #> [2021-05-26 16:08:01] Postgres connection to 'athena' closed#> # A tibble: 96 x 5 #> vocabulary_id_1 concept_class_id_1 relationship_id vocabulary_id_2 #> <chr> <chr> <chr> <chr> #> 1 HemOnc Brand Name Brand name of HemOnc #> 2 HemOnc Brand Name NA NA #> 3 HemOnc Component Antineoplastic of HemOnc #> 4 HemOnc Component Biosimilar of HemOnc #> 5 HemOnc Component Concept replaces HemOnc #> 6 HemOnc Component Has FDA indication HemOnc #> 7 HemOnc Component Has accepted use HemOnc #> 8 HemOnc Component Has biosimilar HemOnc #> 9 HemOnc Component Has brand name HemOnc #> 10 HemOnc Component Has route HemOnc #> # … with 86 more rows, and 1 more variable: concept_class_id_2 <chr># Relationships between HemOnc concepts only can also be looked up vocab_lookup_intrarelation(vocabulary_id = "HemOnc")#> [2021-05-26 16:08:01] Connected to 'athena' #> [2021-05-26 16:08:01] Postgres connection to 'athena' closed#> # A tibble: 68 x 5 #> vocabulary_id_1 concept_class_id_1 relationship_id vocabulary_id_2 #> <chr> <chr> <chr> <chr> #> 1 HemOnc Brand Name Brand name of HemOnc #> 2 HemOnc Component Antineoplastic of HemOnc #> 3 HemOnc Component Biosimilar of HemOnc #> 4 HemOnc Component Has FDA indication HemOnc #> 5 HemOnc Component Has accepted use HemOnc #> 6 HemOnc Component Has biosimilar HemOnc #> 7 HemOnc Component Has brand name HemOnc #> 8 HemOnc Component Has route HemOnc #> 9 HemOnc Component Immunosuppressor of HemOnc #> 10 HemOnc Component Is a HemOnc #> # … with 58 more rows, and 1 more variable: concept_class_id_2 <chr># Relationships between HemOnc and non-Hemonc Concepts vocab_lookup_interrelation(vocabulary_id = "HemOnc")#> [2021-05-26 16:08:01] Connected to 'athena' #> [2021-05-26 16:08:01] Postgres connection to 'athena' closed#> # A tibble: 20 x 5 #> vocabulary_id_1 concept_class_id_1 relationship_id vocabulary_id_2 #> <chr> <chr> <chr> <chr> #> 1 HemOnc Component Maps to RxNorm #> 2 HemOnc Component Maps to RxNorm #> 3 HemOnc Component Maps to RxNorm #> 4 HemOnc Component Maps to RxNorm Extension #> 5 HemOnc Component Class Subsumes RxNorm #> 6 HemOnc Component Class Subsumes RxNorm #> 7 HemOnc Component Class Subsumes RxNorm #> 8 HemOnc Component Class Subsumes RxNorm Extension #> 9 HemOnc Component Class Subsumes RxNorm Extension #> 10 HemOnc Condition Maps to ICDO3 #> 11 HemOnc Condition Maps to SNOMED #> 12 HemOnc Regimen Has antineopl Rx RxNorm #> 13 HemOnc Regimen Has antineopl Rx RxNorm #> 14 HemOnc Regimen Has antineopl Rx RxNorm #> 15 HemOnc Regimen Has antineopl Rx RxNorm Extension #> 16 HemOnc Regimen Has antineopl Rx RxNorm Extension #> 17 HemOnc Regimen Has immunosuppr Rx RxNorm #> 18 HemOnc Regimen Has local therap Rx RxNorm #> 19 HemOnc Regimen Has local therap Rx RxNorm Extension #> 20 HemOnc Regimen Has support med Rx RxNorm #> # … with 1 more variable: concept_class_id_2 <chr>