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.

Terminology bundles are .ndjson.gz files with filenames matching *terminology-bundle.ndjson.gz wildcard.
Aidbox imports terminology bundles found in zen paths.
Import terminology bundle from local system
Put terminology bundle in /my/aidbox/project/my-terminology-bundle.ndjson.gz
Set AIDBOX_ZEN_PATHS=path:dir:/my/aidbox/project

Aidbox imports resources from ndjson.gz files *terminology-bundle.ndjson.gz.
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.
/terminology/$import
Terminology import operation allows you to load prepared terminology concept packages into you server.
1
POST /terminology/$import
2
​
3
url: <terminology-package-url>
Copied!
RxNorm
To import RxNorm concepts, execute the following request:
1
POST /
2
Content-Type: text/yaml
3
​
4
resourceType: Bundle
5
type: transaction
6
entry:
7
  - resource:
8
      resourceType: CodeSystem
9
      id: rxnorm
10
      url: http://www.nlm.nih.gov/research/umls/rxnorm
11
      date: '2019'
12
      description: RxNorm is just an RxNorm
13
      content: complete
14
      status: active
15
      version: '10072019'
16
    request:
17
      url: /CodeSystem/rxnorm
18
      method: PUT
19
​
20
  - resource:
21
      resourceType: ValueSet
22
      id: rxnorm
23
      status: active
24
      description: This value set includes all RxNorm codes.
25
      version: '10072019'
26
      compose:
27
        include:
28
          - system: http://www.nlm.nih.gov/research/umls/rxnorm
29
    request:
30
      url: /ValueSet/rxnorm
31
      method: PUT
32
​
33
  - resource:
34
      id: rxnorm
35
      inputFormat: application/fhir+ndjson
36
      contentEncoding: gzip
37
      mode: bulk
38
      inputs:
39
        - resourceType: Concept
40
          url: https://storage.googleapis.com/aidbox-public/fhir-terminology/rxnorm-10072019.ndjson.gz
41
    request:
42
      url: /$import
43
      method: POST
Copied!
How to search RxNorm concepts by RxCUI
Request
Response
1
GET /Concept/?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671
Copied!
1
resourceType: Bundle
2
type: searchset
3
entry:
4
- resource:
5
    code: '636671'
6
    system: http://www.nlm.nih.gov/research/umls/rxnorm
7
    display: varenicline 0.5 MG Oral Tablet
8
    valueset: [rxnorm]
9
    id: rxnorm-636671
10
    resourceType: Concept
11
    meta: {lastUpdated: '2019-12-18T21:18:10.885605Z', createdAt: '2019-12-18T21:18:10.885605Z', versionId: '199'}
12
  fullUrl: https://testrevinclude.edge.aidbox.app/Concept/rxnorm-636671
13
total: 1
14
link:
15
- {relation: first, url: '/Concept?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671&page=1'}
16
- {relation: self, url: '/Concept?system=http://www.nlm.nih.gov/research/umls/rxnorm&code=636671&page=1'}
17
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]
18
query-timeout: 60000
19
query-time: 1259
Copied!
SNOMEDCT
1
POST /
2
Content-Type: text/yaml
3
​
4
resourceType: Bundle
5
type: transaction
6
entry:
7
  - resource:
8
      resourceType: CodeSystem
9
      id: snomedct
10
      url: http://snomed.info/sct
11
      date: '2019-09-01'
12
      description: SNOMED CT is a standardized, multilingual vocabulary of clinical terminology
13
        that is used by physicians and other health care providers for the electronic exchange
14
        of clinical health information
15
      content: complete
16
      status: active
17
      version: snomed-version
18
    request:
19
      url: /CodeSystem/snomedct
20
      method: PUT
21
​
22
  - resource:
23
      resourceType: ValueSet
24
      id: snomedct
25
      description: This value set includes all RxNorm codes.
26
      version: snomed-version
27
      compose:
28
        include:
29
        - system: http://snomed.info/sct
30
      url: snomedct
31
      status: active
32
    request:
33
      url: /ValueSet/snomedct
34
      method: PUT
35
​
36
  - resource:
37
      id: snomedct
38
      inputFormat: application/fhir+ndjson
39
      contentEncoding: gzip
40
      mode: bulk
41
      inputs:
42
        - resourceType: Concept
43
          url: https://storage.googleapis.com/aidbox-public/fhir-terminology/snomedct-20190901.ndjson.gz
44
    request:
45
      url: /$import
46
      method: POST
Copied!

Terminology - Previous

Aidbox terminology module overview

Next - Terminology

Concept

Last modified 2mo ago

Copy link

Contents

Import using Aidbox project

/terminology/$import

RxNorm

SNOMEDCT