inst/doc/vignettes/vignette.md

In yvoawk/getUMLS: Query the UMLS metathesaurus

How to use {getUMLS} ?

Yvon K. AWUKLU 2021-08-07

library(getUMLS)

For use this package, you will need an UMLS license. If you do not have a UMLS account, you may apply for a license on the UMLS Terminology Services (UTS) website.

1. Authentication : UMLS TICKET-GRANT TICKET

First, you need to authentify yourself in order to have access to UMLS REST API. This function help you to do that. It receives in argument the apikey received by UMLS.

getUMLS::umls_pass()

 Access granted.

2. Retrieves information about a known CUI

This function provides you a way to retrieve information (name, semantic types, number of atoms, etc) for a known CUI from latest UMLS version. It receives as argument a CUI.

getUMLS::fromCUI(CUI = "C0018689")

## # A tibble: 1 x 6
##   name                     type    id      semanticType  atomCount relationCount
##   <chr>                    <chr>   <chr>   <chr>             <int>         <int>
## 1 Health Care (MeSH Categ… Concept C00186… Classificati…         1             2

3. Atoms et Information

The first function provides you a way to retrieve atoms and information about atoms for a known CUI. It receives as argument a CUI, a UMLS sources vocabularies (optional), a language (optional) and the page size (optional). You can consult the allowed vocabularies on: vocabulary.

The second function provides you a way to retrieve information about atoms for a known AUI. It receives as argument a AUI.

getUMLS::atomsfromCUI(CUI = "C0018689")

getUMLS::CUIfromAtoms(AUI = "A8345234")

##                          name termType rootSource      id
## 1 Health Care (MeSH Category)       HT        MSH U000008

4. CUI Definition

This function provides you a way to retrieve the source-asserted definitions for a known CUI. It receives as argument a CUI.

getUMLS::defromCUI(CUI = "C0155502")

##    classType sourceOriginated rootSource
## 1 Definition             TRUE        MSH
## 2 Definition             TRUE     MSHPOR
## 3 Definition             TRUE     MSHCZE
##                                                                                                                                                                                                                                                   value
## 1  Idiopathic recurrent VERTIGO associated with POSITIONAL NYSTAGMUS. It is associated with a vestibular loss without other neurological or auditory signs. Unlike in LABYRINTHITIS and VESTIBULAR NEURONITIS, inflammation in the ear is not observed.
## 2 VERTIGEM idiopática recorrente associada com NISTAGMO FISIOLÓGICO. Está associada com uma perda vestibular sem outros sinais neurológicos ou auditivos. Diferentemente da LABIRINTITE e da NEURONITE VESTIBULAR, não se observa inflamação na ouvido.
## 3                                                        Idiopatické rekurentní vertigo spojené s polohovým nystagmem. Je způsobené poruchou vestibulárního aparátu. Na rozdíl od labyrintitidy a vestibulární neuronitidy se neprojevuje zánětem ucha.

5. CUI Relation

This function provides you a way to retrieve the NLM-asserted relationships for a known CUI. It receives as argument a CUI and the pageSize (optional).

getUMLS::relfromCUI(CUI = "C0155502")

##         id                                                relatedIdName
## 1 C0042571                                                      Vertigo
## 2 C0155501                                          Vertigo, Peripheral
## 3 C0494557                                    Benign paroxysmal vertigo
## 4 C0522351                                           Positional Vertigo
## 5 C0022890                                        Labyrinthine disorder
## 6 C0153113                              Acute Peripheral Vestibulopathy
## 7 C0302851                                              Cupulolithiasis
## 8 C2239166 (Labyrinthine disorders NOS) or (vertigo, benign positional)
##   rootSource        ui
## 1        MTH R02886477
## 2        MTH R13332710
## 3        MTH R02946952
## 4        MTH R44194411
## 5        MTH R29933744
## 6        MTH R03377694
## 7        MTH R03266972
## 8        MTH R91960384

6. ID from String

This function provides you a way to retrieve a source-asserted identifiers (codes) associate with a search term (string) in UMLS specific source vocabulary. You can consult the allowed vocabularies on: vocabulary.

getUMLS::IdfromString(String = "bone fracture", vocabulary = "MSH")

## [1] "D050723"

7. CUI from String

This function provides you a way to retrieve a UMLS Concept Unique Identifier (CUI) associate with a search term (string).

getUMLS::CUIfromString(String = "bone fracture")

## [1] "C0016658"

8. CUI from another source-asserted identifier

This function provides you a way to retrieve a UMLS Concept Unique Identifier (CUI) associate with a specific source-asserted identifier (code). It receives as argument a Id (source-asserted identifier) and a vocabulary abbreviation (source vocabulary). You can consult the allowed vocabularies on: vocabulary.

getUMLS::CUIfromId(Id = "J45", vocabulary = "ICD10")

## [1] "C0004096"

9. Hierarchical information

This function provides you a way to retrieve a hierarchical information about a known source-asserted identifier. You can :

• Retrieve the immediate parents of a known source asserted identifier.
• Retrieve all immediate children of a known source asserted identifier.
• Retrieve all ancestors or descendants of a known source asserted identifier.

getUMLS::hierarchyfromSource(vocabulary = "ICD10", Id = "J45", type = "children")

## result                                            
## 1 Asthma, unspecified          
## 2 Predominantly allergic asthma
## 3 Nonallergic asthma           
## 4 Mixed asthma

Reference

« UMLS REST API Home Page ». https://documentation.uts.nlm.nih.gov/rest/home.html

yvoawk/getUMLS documentation built on Aug. 2, 2022, 5:08 p.m.