Skip to contents

Get similar concepts from Columbia Open Health Data (COHD) API

Source: R/cohdSimilarConcepts.R
cohdSimilarConcepts.Rd

Queries the COHD API association/relativeFrequency endpoint to return concepts that co-occur with the given concept(s), ranked by relative frequency. Useful for finding clinically related conditions, drugs, or procedures based on EHR prevalence. When given multiple concept IDs, returns concepts that co-occur with the input set, ranked by how many input concepts they co-occur with and by mean relative frequency.

Usage

cohdSimilarConcepts(
  conceptId,
  datasetId = 1,
  topN = 50,
  timeoutSec = 30,
  baseUrl = "https://cohd-api.ci.transltr.io/api"
)

Arguments

conceptId

Integer or character vector. One or more OMOP concept IDs to find similar concepts for (e.g. conditions, drugs, or procedures).

datasetId

Integer. COHD dataset ID (1 = 5-year, 2 = lifetime; default 1).

topN

Integer. Maximum number of similar concepts to return (default 50). For a single concept, this limits rows by strength; for multiple concepts, this limits the aggregated result.

timeoutSec

Numeric. Request timeout in seconds (default 30).

baseUrl

Character. Base URL of the COHD API (default "https://cohd-api.ci.transltr.io/api").

Value

A data frame with one row per similar concept, or NULL if the API is unavailable or the request fails. When successful:

  • Single concept: data frame contains concept_id_1, concept_id_2, concept_count_1, concept_count_2, concept_count, relative_frequency, and other_concept_id; rows sorted by relative_frequency descending.

  • Multiple concepts: data frame contains other_concept_id, n_concepts (how many input concepts co-occur with this one), and mean_rf (mean relative frequency); rows sorted by n_concepts descending then mean_rf descending. If no results or an error occurs, returns NULL and a message is printed.

References

Ta, Casey N.; Dumontier, Michel; Hripcsak, George; P. Tatonetti, Nicholas; Weng, Chunhua (2018). Columbia Open Health Data, a database of EHR prevalence and co-occurrence of conditions, drugs, and procedures. figshare. Collection. doi:10.6084/m9.figshare.c.4151252.v1

Examples

if (FALSE) { # \dontrun{
# Single concept: top 25 similar to concept 201826 (Type 2 diabetes)
cohdSimilarConcepts(201826, datasetId = 1, topN = 25)

# Multiple concepts: concepts likely to co-occur with this set
cohdSimilarConcepts(c(201826, 316866, 255573), datasetId = 1, topN = 50)
} # }