nachuss / snomedizer

An R Interface to the SNOMED CT API <https://github.com/IHTSDO/snowstorm>

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snomedizer: R Interface to the SNOMED CT Terminology Server REST API

snomedizer is an R package to manipulate the SNOMED clinical ontology using the SNOMED CT Terminology Server REST API.

Installation

You can install the development version from GitHub with:

install.packages("devtools")
devtools::install_github("ramses-antibiotics/snomedizer")

Example

snomedizer provides a direct interface to the SNOMED CT Terminology Server REST API.

By default, the package uses the public SNOMED International server available for reference purposes only (see terms & conditions).

For example, GET /branch/concepts is implemented in api_concepts():

library(snomedizer)
api_concepts(term = "pneumonia", activeFilter = TRUE)
#> Response [https://snowstorm.ihtsdotools.org/snowstorm/snomed-ct/MAIN/concepts?term=pneumonia&limit=50&offset=0&activeFilter=TRUE]
#>   Date: 2020-10-28 15:09
#>   Status: 200
#>   Content-Type: application/json
#>   Size: 18.4 kB
#> {
#>   "items" : [ {
#>     "conceptId" : "233604007",
#>     "active" : true,
#>     "definitionStatus" : "FULLY_DEFINED",
#>     "moduleId" : "900000000000207008",
#>     "effectiveTime" : "20150131",
#>     "fsn" : {
#>       "term" : "Pneumonia (disorder)",
#>       "lang" : "en"
#> ...

Simpler wrapper functions are available for common operations, which provide results as data frames:

concepts_find(term = "pneumonia", limit = 5) %>% 
  dplyr::select(conceptId, fsn.term, pt.term) 
#> Warning: 
#> This server request returned just 5 of a total 567 results.
#> Please increase the server `limit` to fetch all results.
#>   conceptId                         fsn.term            pt.term
#> 1 233604007             Pneumonia (disorder)          Pneumonia
#> 2 161525004 History of pneumonia (situation)     H/O: pneumonia
#> 3 416916004    Lipoid pneumonitis (disorder) Lipoid pneumonitis
#> 4 300999006       Basal pneumonia (disorder)    Basal pneumonia
#> 5 278516003       Lobar pneumonia (disorder)    Lobar pneumonia

Development and new features

Please share your experience as a user!

Do not hesitate to get in touch on GitHub to report bugs or request new features.

Terms & conditions

Server endpoint

By default, snomedizer queries the public SNOMED-CT terminology endpoint hosted by SNOMED International.

This server has no service level agreement and MUST NOT be used as part of production systems in healthcare settings, even if you hold a SNOMED CT licence.

Please refer to the Snowstorm documentation for instructions on how to build a dedicated endpoint for production.

SNOMED CT Terminology

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

SNOMED International maintains a public SNOMED-CT terminology server for strict ‘reference purposes’ under the SNOMED International SNOMED CT Browser License Agreement.

Use of SNOMED-CT terminology for data analysis or health care production systems is subject to other licences. Some users are eligible for free licences:

• UK-based users can obtain a licence free of charge on the NHS TRUD website.
• residents of other Member Countries and low-income countries are also eligible. More information can be found on the SNOMED International website.

Funders

     

Code of conduct

The snomedizer project is released with a Contributor Code of Conduct.

By contributing to this project, you agree to abide by its terms.