chariot

Query, analyze, and explore a Postgres instance of the OMOP Vocabularies for a multitude of use cases, including standardizing data to the OMOP Vocabularies, automatically annotating data pulled from the OMOP CDM with the concept attributes, and calculating cumulative drug dosage from data found in the Drug Exposures table.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("meerapatelmd/chariot")

Related Packages

• setupAthena: sets up a Postgres instance of the Athena vocabularies downloaded from athena.ohdsi.org.
• amphora: plots concept ancestries to assist in knowledge management projects such as data standardization.
• metaorite: the UMLS Metathesaurus equivalent of this package

Concept Objects

This package was inititally written with the objective of exploring the vocabularies for concept mapping. To avoid the challenge of using solely the Concept Id in the R environment when exploring a certain concept, an S4 Concept class is introduced, where Concept objects store all the concept attributes found in the Concept Table as slots. This is a basic example which shows you how to solve a common problem:

library(chariot)
aspirin <- get_concept(concept_id = 1112807,
                       vocab_schema = "omop_vocabulary",
                       conn = conn)
#> [2021-01-10 14:30:09]    [2021-01-10 14:30:09]   [2021-01-10 14:30:09]   [2021-01-10 14:30:10]   [2021-01-10 14:30:10]   [2021-01-10 14:30:10]   
class(aspirin)
#> [1] "concept"
#> attr(,"package")
#> [1] "chariot"

aspirin
#> An object of class "concept"
#> Slot "concept_id":
#> [1] 1112807
#> 
#> Slot "concept_name":
#> [1] "aspirin"
#> 
#> Slot "concept_synonym_names":
#> [1] ""
#> 
#> Slot "maps_to_concept_names":
#> [1] "aspirin"
#> 
#> Slot "domain_id":
#> [1] "Drug"
#> 
#> Slot "vocabulary_id":
#> [1] "RxNorm"
#> 
#> Slot "concept_class_id":
#> [1] "Ingredient"
#> 
#> Slot "standard_concept":
#> [1] "S"
#> 
#> Slot "concept_code":
#> [1] "1191"
#> 
#> Slot "valid_start_date":
#> [1] "1970-01-01"
#> 
#> Slot "valid_end_date":
#> [1] "2099-12-31"
#> 
#> Slot "invalid_reason":
#> [1] NA

Concept class objects keep the user informed of all the attributes of a concept during a session using the chariot package. For example, I can look up the RxNorm Ingredients belonging to the ATC 5th Concept Class lisinopril using the Concept Id 21601787 alone.

resultset <-
lookup_atc_class_ingredients(conn = conn, 
                             vocab_schema = "omop_vocabulary",
                             atc_concept_obj = 21601787)

resultset
#> # A tibble: 1 x 10
#>   concept_id concept_name domain_id vocabulary_id concept_class_id
#>        <dbl> <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>

However, upon viewing the output, the only knowledge known based on the arguments is the 21601787 concept id. When using the Concept class, this information is not lost.

lisinopril_class_concept <- get_concept(conn = conn,
                                        concept_id = 21601787, 
                                        vocab_schema = "omop_vocabulary")
resultset <-
lookup_atc_class_ingredients(conn = conn, 
                             vocab_schema = "omop_vocabulary",
                             atc_concept_obj = lisinopril_class_concept)

resultset
#> # A tibble: 1 x 10
#>   concept_id concept_name domain_id vocabulary_id concept_class_id
#>        <dbl> <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>

The resultset can be referenced back to the lisinopril_class_concept object that has retained all the concept attributes:

lisinopril_class_concept
#> 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

Code of Conduct

Please note that the chariot project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.