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Load ICD-10 terminology into Aidbox

In this post, you will learn how to load ICD-10 terminology into aidbox.
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With a new version of Aidbox we provide you with a set of terminology packages like ICD-10 and LOINC and a special bulk operation to import these code sets.
You can read more about how terminology service is designed in a our CTO blog post - Two-phase terminology.
Aidbox team prepared terminology packages with popular code systems. These packages are essentially ndjson files with a set of concept resources and they are available by public url in our cloud.
Here are a few packages you can start with:
Rx-Norm, SNOMED-CT and basic FHIR CodeSystems/ValueSets packages are in progress. If you need something specific, ping us in a Aidbox Community Chat.
In this tutorial, we will load ICD-10 deceases codes into Aidbox and see how we can look up codes using Concept resource Search API.
To import these terminology packs, you can use terminology/$import operation. Let's load ICD-10 (Classification of Deceases): just copy-paste the following snippet into REST console in Aidbox UI:
request.yalm
POST /terminology/$import
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url: 'https://storage.googleapis.com/aidbox-public/icd10/icd10cm.ndjson.gz'
You will get a response with numbers of resources loaded:
response.yaml
status: 200
result: {CodeSystem: 1, ValueSet: 1, Concept: 44487}
As you can see, a package consists of one CodeSystem, one ValueSet and about 40K concepts with decease codes.
Let's go to REST console and see what we have:
GET /CodeSystem
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# response 200
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resourceType: Bundle
type: searchset
entry:
- resource:
url: ICD-10
id: icd-10
name: ICD-10-CM
status: active
content: complete
version: '2019'
date: '2019'
resourceType: CodeSystem
description: International Classification of Diseases
GET /ValueSet
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# response 200
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resourceType: Bundle
type: searchset
entry:
- resource:
url: icd-10
id: icd-10
name: ICD-10
status: active
compose:
include:
- {system: ICD-10}
version: 0.0.1
date: '2019-01-01'
resourceType: ValueSet
description: This value set includes all ICD-10 codes.
Now we can search diagnoses with, for example, _ilike parameter:
GET /Concept?system=ICD-10&_ilike=flue
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# response 200
resourceType: Bundle
type: searchset
entry:
- resource:
code: A08
system: ICD-10
display: Viral and other specified intestinal infections
property:
icd10:
excludes1: ['influenza with involvement of gastrointestinal tract (J09.X3, 10.2, J11.2)']
valueset: [icd-10]
id: ICD-10-A08
resourceType: Concept
- resource:
code: A41.3
system: ICD-10
display: Sepsis due to Hemophilus influenzae
valueset: [icd-10]
id: ICD-10-A41-3
resourceType: Concept
...
Or inspect concepts in Aidbox Console UI:
Health Samurai Team is working on declarative search indexing in the future release. For now, let's create a trigram index to make _ilike search faster. Go to SQL Console and execute the following statement:
CREATE INDEX concept_trgm_idx on concept
USING gin (
(id || ' ' || resource::text) gin_trgm_ops
);
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VACUUM ANALYZE concept;
Try _ilike search again - is it faster?

Clean up

To clean up all terminology, you can truncate all related tables from db console:
truncate concept;
truncate codesystem;
truncate valueset;