Lookup a Concept Id

Lookup a Concept Id

get_concept(
  concept_id,
  vocab_schema = "omop_vocabulary",
  conn,
  conn_fun = "connectAthena()",
  cache_only = FALSE,
  skip_cache = FALSE,
  override_cache = FALSE,
  render_sql = FALSE,
  verbose = FALSE,
  sleepTime = 1
)

Value

Concept Class object if the `concept_id` argument is found in the Concept table. If it is not found, nothing is returned.

Examples

library(tidyverse)
library(chariot)

lookup_atc_class_ingredients(atc_concept_obj = 21601787)
#> 
#> ── Retrieve Concept Object ─────────────────────────────────────────────────────
#> 
#> ── Is Concept Id Valid Integer? ────────────────────────────────────────────────
#> ✓ Concept Id is a valid integer
#> 
#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> ✓ Concept Id `21601787` found in Concept Table
#> 
#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> 
#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> 
#> ── QA Concept Object ───────────────────────────────────────────────────────────
#> ✓ Concept belongs to ATC Vocabulary
#> ✓ Concept is an OMOP vocabulary class
#> 
#> ── Render & Query ──────────────────────────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> # A tibble: 1 x 10
#>   concept_id concept_name domain_id vocabulary_id concept_class_id
#>        <int> <chr>        <chr>     <chr>         <chr>           
#> 1    1308216 lisinopril   Drug      RxNorm        Ingredient      
#> # … with 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>

lisinopril_class <- get_concept(concept_id = 21601787)
#> 
#> ── Is Concept Id Valid Integer? ────────────────────────────────────────────────
#> ✓ Concept Id is a valid integer
#> 
#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> ✓ Concept Id `21601787` found in Concept Table
#> 
#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
#> 
#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────
#> [2021-05-26 16:00:52]	Connected to 'athena'
#> [2021-05-26 16:00:52]	Postgres connection to 'athena' closed
lisinopril_class
#> An object of class "concept"
#> Slot "concept_id":
#> [1] 21601787
#> 
#> Slot "concept_name":
#> [1] "lisinopril; oral"
#> 
#> Slot "concept_synonym_names":
#> [1] "lisinopril"
#> 
#> Slot "maps_to_concept_names":
#> [1] "lisinopril"
#> 
#> Slot "domain_id":
#> [1] "Drug"
#> 
#> Slot "vocabulary_id":
#> [1] "ATC"
#> 
#> Slot "concept_class_id":
#> [1] "ATC 5th"
#> 
#> Slot "standard_concept":
#> [1] "C"
#> 
#> Slot "concept_code":
#> [1] "C09AA03"
#> 
#> Slot "valid_start_date":
#> [1] "1970-01-01"
#> 
#> Slot "valid_end_date":
#> [1] "2099-12-31"
#> 
#> Slot "invalid_reason":
#> [1] NA
#> 

lookup_atc_class_ingredients(atc_concept_obj = lisinopril_class)
#> 
#> ── QA Concept Object ───────────────────────────────────────────────────────────
#> ✓ Concept belongs to ATC Vocabulary
#> ✓ Concept is an OMOP vocabulary class
#> 
#> ── Render & Query ──────────────────────────────────────────────────────────────
#> [2021-05-26 16:00:53]	Connected to 'athena'
#> [2021-05-26 16:00:53]	Postgres connection to 'athena' closed
#> # A tibble: 1 x 10
#>   concept_id concept_name domain_id vocabulary_id concept_class_id
#>        <int> <chr>        <chr>     <chr>         <chr>           
#> 1    1308216 lisinopril   Drug      RxNorm        Ingredient      
#> # … with 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>