Find SNOMED CT concepts

A wrapper function for api_concepts searching for a term or a list of concepts

concept_find(
  term = NULL,
  conceptIds = NULL,
  ecl = NULL,
  activeFilter = TRUE,
  encoding = "UTF-8",
  silent = FALSE,
  limit = snomedizer_options_get("limit"),
  ...
)

Arguments

term

a string containing search terms

conceptIds

a character vector of one or more SNOMED CT codes to search

ecl

a character expression constraint query (with full inference). Consult the Expression Constraint Language guide for more detail.

activeFilter

whether to restrict results to active concepts. Default is `TRUE`. Consult the SNOMED glossary for more detail.

encoding

HTTP charset parameter to use (default is "UTF-8")

silent

whether to hide progress bar. Default is FALSE

limit

a positive integer for the maximum number of results to return. See snomedizer_options. The maximum limit on public endpoints is 10,000.

...

other optional arguments listed in api_operations, such as endpoint, branch or limit

Value

a data frame

Disclaimer

In order to use SNOMED CT, a licence is required which depends both on the country you are based in, and the purpose of your work. See details on snomedizer.

See also

Other wrapper: concept_ancestors(), concept_descriptions(), release_version()

Examples

# Free text search
str(concept_find("asthma"))
#> Warning: 
#> This server request returned just 50 of a total 246 results.
#> Please increase the server `limit` to fetch all results.
#> 'data.frame':	50 obs. of  16 variables:
#>  $ conceptId       : chr  "195967001" "160377001" "56968009" "406162001" ...
#>  $ active          : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
#>  $ definitionStatus: chr  "PRIMITIVE" "FULLY_DEFINED" "FULLY_DEFINED" "PRIMITIVE" ...
#>  $ moduleId        : chr  "900000000000207008" "900000000000207008" "900000000000207008" "900000000000207008" ...
#>  $ effectiveTime   : chr  "20040731" "20040731" "20020731" "20040131" ...
#>  $ id              : chr  "195967001" "160377001" "56968009" "406162001" ...
#>  $ idAndFsnTerm    : chr  "195967001 | Asthma (disorder) |" "160377001 | Family history: Asthma (situation) |" "56968009 | Asthma caused by wood dust (disorder) |" "406162001 | Asthma management (regime/therapy) |" ...
#>  $ fsn.term        : chr  "Asthma (disorder)" "Family history: Asthma (situation)" "Asthma caused by wood dust (disorder)" "Asthma management (regime/therapy)" ...
#>  $ fsn.lang        : chr  "en" "en" "en" "en" ...
#>  $ pt.term         : chr  "Asthma" "Family history of asthma" "Asthma caused by wood dust" "Asthma management" ...
#>  $ pt.lang         : chr  "en" "en" "en" "en" ...
#>  $ total           : int  246 246 246 246 246 246 246 246 246 246 ...
#>  $ limit           : int  50 50 50 50 50 50 50 50 50 50 ...
#>  $ offset          : int  0 0 0 0 0 0 0 0 0 0 ...
#>  $ searchAfter     : chr  "WzQxODM5NTAwNF0=" "WzQxODM5NTAwNF0=" "WzQxODM5NTAwNF0=" "WzQxODM5NTAwNF0=" ...
#>  $ searchAfterArray: int  418395004 418395004 418395004 418395004 418395004 418395004 418395004 418395004 418395004 418395004 ...

# Retrieve multiple concepts
concept_find(conceptIds =  c("233604007", "68566005"))
#>   conceptId active definitionStatus           moduleId effectiveTime        id
#> 1  68566005   TRUE    FULLY_DEFINED 900000000000207008      20020131  68566005
#> 2 233604007   TRUE    FULLY_DEFINED 900000000000207008      20150131 233604007
#>                                               idAndFsnTerm
#> 1 68566005 | Urinary tract infectious disease (disorder) |
#> 2                       233604007 | Pneumonia (disorder) |
#>                                      fsn.term fsn.lang
#> 1 Urinary tract infectious disease (disorder)       en
#> 2                        Pneumonia (disorder)       en
#>                            pt.term pt.lang total limit offset
#> 1 Urinary tract infectious disease      en     2    50      0
#> 2                        Pneumonia      en     2    50      0
#>            searchAfter searchAfterArray
#> 1 WyIyMzM2MDQwMDciXQ==        233604007
#> 2 WyIyMzM2MDQwMDciXQ==        233604007

# Use the SNOMED CT Expression Constraint Language
concept_find(
  ecl = paste(
    "<! 68566005 | Urinary tract infectious disease (disorder) |",
    "AND",
    "< 87628006 | Bacterial infectious disease (disorder) |"
    )
  )
#>   conceptId active definitionStatus           moduleId effectiveTime        id
#> 1 312124009   TRUE    FULLY_DEFINED 900000000000207008      20030131 312124009
#>                                           idAndFsnTerm
#> 1 312124009 | Bacterial urinary infection (disorder) |
#>                                 fsn.term fsn.lang                     pt.term
#> 1 Bacterial urinary infection (disorder)       en Bacterial urinary infection
#>   pt.lang total limit offset      searchAfter searchAfterArray
#> 1      en     1    50      0 WzMxMjEyNDAwOV0=        312124009