SNOMED CT LOINC Collab Pipeline

Prerequisites

• JDK 24+
• Maven 3.9.9+
• Nexus Repository (optional)

Clone Project and Configure Maven Settings

1. Clone the snomed-ct-loinc-data repository

   git clone https://github.com/ikmdev/snomed-ct-loinc-data.git
   

2. Configure Maven settings.xml based on the provided sample.

3. Change local directory to snomed-ct-loinc-data

Run Origin Packaging

The following source data is required for this pipeline and can be obtained with a license from SNOMED:

• SnomedCT_LOINCExtension_PRODUCTION_LO1010000_20250321T120000Z.zip

More information can be found on: https://www.nlm.nih.gov/healthit/snomedct/index.html

1. Place the downloaded ZIPs in your ~/Downloads directory.

2. Ensure the properties defined in snomed-ct-loinc-data/pom.xml are set to the correct file names:

   • <source.zip>
   • <snomedct.version> (requires SNOMEDCT INT data artifact)

3. Run origin packaging and deployment.

   To deploy origin artifact to a shared Nexus repository, run the following command, specifying the repository ID and URL in -DaltDeploymentRepository

   mvn --projects snomed-ct-loinc-origin --also-make clean deploy -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false
   

   To install origin artifact to a local M2 repository, run the following command:

   mvn --projects snomed-ct-loinc-origin --also-make clean install -Ptinkarbuild,generateDataLocal -Dmaven.build.cache.enabled=false
   

Run Transformation Pipeline

The transformation pipeline can be built after origin data is available in Nexus or a local M2 repository.

1. Build the pipeline with the following command:

   mvn clean install -U -Ptinkarbuild -Dmaven.build.cache.enabled=false
   

2. Deploy transformed data artifacts to Nexus, run the following command:

   mvn --projects snomed-ct-loinc-export --also-make deploy -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false