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Snowstorm Lite FHIR Terminology Server

License: Other

Java 99.96% HTML 0.04%

fhir-server fhir-terminology snomed snomed-api snomed-ct snomed-ecl

snowstorm-lite's Introduction

Snowstorm Lite FHIR Terminology Server (Beta)

A fast FHIR Terminology Server for SNOMED CT with a small memory footprint.

Use Case
Features
Limitations
Technical Details
Quick Start
Try the API with Postman
Roadmap

Use Case

Scaling architecture
Supporting user data input with SNOMED CT driven search where responsiveness is critical
Using SNOMED CT offline:
- Locations with poor connectivity and limited machine memory
- Trusted research environments that are not able to make external API requests
Not suitable as a national terminology server

Features

Host a single SNOMED CT Edition with incredible speed
SNOMED query support using a subset of ECL
Perfect for search
- Most relevant results first
- Supports terminology binding
- Multiple language support with configurable character folding
FHIR Terminology Operations
- CodeSystem lookup
  - Including parents, children, designations, normal form
- ValueSet expand using SNOMED CT Implicit Value Sets
  - SNOMED CT isa and ecl filters are supported
- ConceptMap translate using SNOMED CT Implicit Maps

Limitations

Only supports the FHIR API
Only ValueSets support create/update/delete
Only supports one snapshot of the SNOMED CT International Edition at this time
- Support for other SNOMED CT editions and include multiple language search is planned

Technical Details

Only supports one SNOMED CT CodeSystem at a time
Minimal memory footprint is perfect for autoscaling
- After creating the index the app can run with just 500mb memory
Self-contained application using Apache Lucene™
Uses Spring Boot and HAPI FHIR Frameworks
Requires JDK 17

Quick Start

Choose an admin password and replace yourAdminPassword values in the following commands.

Option 1: Using a SNOMED Syndication Service

If you have access to the SNOMED International MLDS service then Snowstorm Lite can download a release automatically from there.

Run Snowstorm Lite in your local Docker:

docker pull snomedinternational/snowstorm-lite:latest
docker run -i -t -p 8080:8080 snomedinternational/snowstorm-lite \
  --admin.password=yourAdminPassword \
  --syndicate --version-uri=http://snomed.info/sct/900000000000207008

Set version-uri to the URI of the SNOMED Edition to be loaded. See SNOMED Edition URI Examples.

The console will ask for the syndication service username and password before downloading the relevant packages and building the index. By default the SNOMED International MLDS feed is used, this uses the same credentials as MLDS. The feel URL can be changed using the syndication.url configuration option.

Then Snowstorm Lite will be ready for use! The FHIR interface is here: http://localhost:8085/fhir.

Option 2: Using a SNOMED Archive File

If you have access to a SNOMED CT Edition release archive this can be imported.

Run Snowstorm Lite in your local Docker:

docker pull snomedinternational/snowstorm-lite:latest
docker run -p 8080:8080 snomedinternational/snowstorm-lite \
  --admin.password=yourAdminPassword

Upload a SNOMED CT package:

curl -u admin:yourAdminPassword \
  --form file=@SnomedCT_InternationalRF2_PRODUCTION_20240101T120000Z.zip \
  --form version-uri="http://snomed.info/sct/900000000000207008/version/20240101" \
  http://localhost:8080/fhir-admin/load-package

Importing a SNOMED CT release takes about 5 minutes.

When the import is complete Snowstorm Lite will be ready for use! The FHIR interface is here: http://localhost:8085/fhir.

It is possible to import extension or derivative packages.

It is also possible to deploy as a Java application, without Docker.

Postman

This Postman collection allows you to try the various API functions of the Snowstorm Lite server. It's similar to a Swagger UI.
You will need a local Snowstorm Lite instance running.

Roadmap

Nothing currently planned.

Full ECL support is not planned. Snowstorm Lite supports the most often used ECL features without the full complexity and memory demands of the complete ECL specification.

snowstorm-lite's People

Contributors

Stargazers

Watchers

Forkers

jonzammit

snowstorm-lite's Issues

Snowstorm 1.3.0-beta preferred term bug when specific language but no specific dialect requested

When expanding a ValueSet using a specific language but no specific dialect the term selected to be the "display" term is the correct language but is selected at random. The term should be preferred in some dialect.

$expand operation with ECL, "member of" syntax, reference set types

Inconsistent results when using $expand operation in combination with ECL, ^ "member of" syntax, and different reference set types.

Example 1) - query to expand 723264001 |Lateralizable body structure reference set|, a simple reference set type. This produces the expected results. 20,000+ members in expansion:

{{url}}ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=ecl/%5E723264001

URI-decoded ecl query: ^723264001

Example 2) - query to expand 446608001 |SNOMED CT to ICD-O simple map|, a simple map type refset. Response indicates 0 concepts in expansion:

{{url}}ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=ecl/%5E446608001

URI-decoded ecl query: ^446608001

ECL Bug, ancestors of concept set

There is a bug in the ECL engine. When requesting the ancestors of a concept set all concepts are returned rather than only the ancestors.

For example, the results of this ECL should not include 195967001 |Asthma|:

> ( >> 195967001 |Asthma| )

The current release is returning Asthma.

$expand sorting is different (worse) than the full snowstorm version

Example:

curl --silent 'https://snowstorm.ihtsdotools.org/fhir/ValueSet/$expand?url=http://snomed.info/sct?fhir_vs&filter=Breast+Cancer&count=5' | jq

responds with:

{
  "resourceType": "ValueSet",
  "id": "5fc7dd97-888a-4385-aa05-8c2fabce0fe1",
  "url": "http://snomed.info/sct?fhir_vs",
  "status": "active",
  "copyright": "This value set includes content from SNOMED CT, which is copyright © 2002+ International Health Terminology Standards Development Organisation (SNOMED International), and distributed by agreement between SNOMED International and HL7. Implementer use of SNOMED CT is not covered by this agreement.",
  "expansion": {
    "id": "7cc5cd7b-f6ca-4602-9e76-76d2499dd01b",
    "timestamp": "2024-01-15T14:43:46+00:00",
    "total": 45,
    "offset": 0,
    "parameter": [
      {
        "name": "version",
        "valueUri": "http://snomed.info/sct|http://snomed.info/sct/900000000000207008/version/20240101"
      },
      {
        "name": "displayLanguage",
        "valueString": "en"
      }
    ],
    "contains": [
      {
        "system": "http://snomed.info/sct",
        "code": "254837009",
        "display": "Malignant tumor of breast"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "372064008",
        "display": "Malignant neoplasm of female breast"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "724451007",
        "display": "Fear of breast cancer"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "134405005",
        "display": "Suspected breast cancer"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "268547008",
        "display": "Screening for malignant neoplasm of breast"
      }
    ]
  }
}

Whereas local snowstorm-lite server is returning

curl -u admin:yourAdminPassword --silent 'http://localhost:8085/fhir/ValueSet/$expand?url=http://snomed.info/sct?fhir_vs&filter=Breast+Cancer&count=5' | jq

{
  "resourceType": "ValueSet",
  "url": "http://snomed.info/sct?fhir_vs",
  "name": "SNOMED CT Implicit ValueSet of all concepts.",
  "status": "active",
  "copyright": "This value set includes content from SNOMED CT, which is copyright © 2002+ International Health Terminology Standards Development Organisation (SNOMED International), and distributed by agreement between SNOMED International and HL7. Implementer use of SNOMED CT is not covered by this agreement.",
  "expansion": {
    "identifier": "1e115cd2-d887-4b14-b399-4362974939b0",
    "timestamp": "2024-01-15T14:47:43+00:00",
    "total": 50,
    "parameter": [
      {
        "name": "version",
        "valueUri": "http://snomed.info/sct|http://snomed.info/sct/900000000000207008/version/20230131"
      }
    ],
    "contains": [
      {
        "system": "http://snomed.info/sct",
        "code": "717129004",
        "display": "Claus Model"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "724451007",
        "display": "Fear of breast cancer"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "134405005",
        "display": "Suspected breast cancer"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "254843006",
        "display": "Familial cancer of breast"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "254837009",
        "display": "Malignant tumor of breast"
      }
    ]
  }
}

Where "Fear of breast cancer" is higher on the list than "Malignant tumor of breast" ... not the response we were expecting (and the full version was correctly returning).

Maybe we have to configure / reindex something to make it work the same as the full version?

Docker image version: snomedinternational/snowstorm:9.2.0