Import external (not-present) terminologies

Import using Aidbox project
Specify path or url to zen terminology bundle in AIDBOX_ZEN_PATHS environment variable.
Source is either url or path. url is used to download Aidbox project from a remote location; path is used to load Aidbox project from the filesystem.

Aidbox imports terminology bundles found in zen paths. Bundles are just .ndjson.gz files with filenames matching *terminology-bundle.ndjson.gz wildcard. By default, the import is done asynchronously. In some cases (e.g CI/CD pipeline) you might want to override such behavior. Setting BOX_FEATURES_TERMINOLOGY_IMPORT_SYNC environment variable will change the import mode to synchronous.
Import terminology bundle from local system using Aidbox project
Aidbox reads files from Aidbox projects on startup and imports files whose names end with terminology-bundle.ndjson.gz .
For example, path to terminology bundle GZIP fie is: /my/aidbox/project/my-terminology-bundle.ndjson.gz.
To load the terminology bundle into Aidbox set the AIDBOX_ZEN_PATHS environment variable:​
 AIDBOX_ZEN_PATHS=path:dir:/my/aidbox/project
Make sure that your Aidbox container has access to the specified path on your system.
Import terminology bundle from a remote location
Zip-archive your terminology bundle that is my-terminology-budnle.ndjson.gz file in my-terminology.zip file.
Upload your my-terminology.zip to a remote server e.g. https://example.com/terminologies/my-terminology.zip
Set AIDBOX_ZEN_PATHS=url:zip:https://example.com/terminologies/my-terminology.zip

Aidbox will import terminology from the specified path on start.
​
Import from flat file (CSV)
Import flat file (CSV)
/terminology/$import
Terminology import operation allows you to load prepared terminology concept packages into you server.
POST /terminology/$import
​
url: <terminology-package-url>
RxNorm
To import RxNorm concepts, execute the following request:
POST /
Content-Type: text/yaml
​
resourceType: Bundle
type: transaction
entry:
  - resource:
      resourceType: CodeSystem
      id: rxnorm
      url: http://www.nlm.nih.gov/research/umls/rxnorm
      date: '2019'
      description: RxNorm is just an RxNorm
      content: complete
      status: active
      version: '10072019'
    request:
      url: /CodeSystem/rxnorm
      method: PUT
​
  - resource:
      resourceType: ValueSet
      id: rxnorm
      status: active
      description: This value set includes all RxNorm codes.
      version: '10072019'
      compose:
        include:
          - system: http://www.nlm.nih.gov/research/umls/rxnorm
    request:
      url: /ValueSet/rxnorm
      method: PUT
​
  - resource:
      id: rxnorm
      inputFormat: application/fhir+ndjson
      contentEncoding: gzip
      mode: bulk
      inputs:
        - resourceType: Concept
          url: https://storage.googleapis.com/aidbox-public/fhir-terminology/rxnorm-10072019.ndjson.gz
    request:
      url: /$import
      method: POST
How to search RxNorm concepts by RxCUI
Request
Response
GET /Concept/?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671
resourceType: Bundle
type: searchset
entry:
- resource:
    code: '636671'
    system: http://www.nlm.nih.gov/research/umls/rxnorm
    display: varenicline 0.5 MG Oral Tablet
    valueset: [rxnorm]
    id: rxnorm-636671
    resourceType: Concept
    meta: {lastUpdated: '2019-12-18T21:18:10.885605Z', createdAt: '2019-12-18T21:18:10.885605Z', versionId: '199'}
  fullUrl: https://testrevinclude.edge.aidbox.app/Concept/rxnorm-636671
total: 1
link:
- {relation: first, url: '/Concept?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671&page=1'}
- {relation: self, url: '/Concept?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671&page=1'}
query-sql: ['SELECT "concept".* FROM "concept" WHERE (aidbox_text_search(knife_extract_text("concept".resource, $JSON$[["system"]]$JSON$)) ilike unaccent(?) AND aidbox_text_search(knife_extract_text("concept".resource, $JSON$[["code"]]$JSON$)) ilike unaccent(?)) LIMIT ? OFFSET ? ', '% http://www.nlm.nih.gov/research/umls/rxnorm%', '% 636671%', 100, 0]
query-timeout: 60000
query-time: 1259
SNOMEDCT
POST /
Content-Type: text/yaml
​
resourceType: Bundle
type: transaction
entry:
  - resource:
      resourceType: CodeSystem
      id: snomedct
      url: http://snomed.info/sct
      date: '2019-09-01'
      description: SNOMED CT is a standardized, multilingual vocabulary of clinical terminology
        that is used by physicians and other health care providers for the electronic exchange
        of clinical health information
      content: complete
      status: active
      version: snomed-version
    request:
      url: /CodeSystem/snomedct
      method: PUT
​
  - resource:
      resourceType: ValueSet
      id: snomedct
      description: This value set includes all RxNorm codes.
      version: snomed-version
      compose:
        include:
        - system: http://snomed.info/sct
      url: snomedct
      status: active
    request:
      url: /ValueSet/snomedct
      method: PUT
​
  - resource:
      id: snomedct
      inputFormat: application/fhir+ndjson
      contentEncoding: gzip
      mode: bulk
      inputs:
        - resourceType: Concept
          url: https://storage.googleapis.com/aidbox-public/fhir-terminology/snomedct-20190901.ndjson.gz
    request:
      url: /$import
      method: POST

Terminology - Previous

Aidbox terminology module overview

Import flat file (CSV)

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Outline

Import using Aidbox project

Import from flat file (CSV)

/terminology/$import

RxNorm

SNOMEDCT