SNOMED CT Database Creation and Import Tool (Swiss Edition)

This Java project creates a MySQL database and imports SNOMED CT data, including both the International Edition and the Swiss Extension (CH Edition), using the Full release format.

Features

• Creates a MySQL database
• Creates all required tables for SNOMED CT Full release:
  • full_concept
  • full_description
  • full_relationship
  • full_refset_Simple
  • full_refset_ExtendedMap
  • full_refset_Language
  • full_refset_ModuleDependency
• Imports SNOMED CT International Edition Full release files
• Imports Swiss Extension Full release files (German, French, Italian, English)
• Adds indexes to improve query performance

Requirements

• Java 8 or higher
• MySQL 8.x
• MySQL Connector/J (JDBC driver)
• SNOMED CT Full release files (download here: https://mlds.ihtsdotools.org/ (registration required):
  • International Edition
  • Swiss Extension

Configuration

1. Update paths and release identifiers

Open CreateDatabaseAndImportData.java and set the following variables to match your environment:

static String ReleaseFilePath = "PATH_TO_YOUR_INTERNATIONAL_EDITION";
static String ReleaseFilePathCH = "PATH_TO_YOUR_SWISS_EXTENSION";
static String ReleaseDate = "20250101"; // International Edition release date
static String ReleaseDateCH = "CH1000195_20241207"; // Swiss Extension release identifier

### 2. Database credentials

Set your local MySQL credentials and connection parameters:
```bash
String dbUser = "root";
String dbPassword = "";
String dbURL = "jdbc:mysql://localhost/";

Make sure allowLoadLocalInfile=true and allowMultiQueries=true are enabled in your connection string.

3. File structure expected

The tool expects SNOMED CT files to follow the official Full release folder structure, e.g.:

International Edition/
└── Full/
    └── Terminology/
        ├── sct2_Concept_Full_INT_20250101.txt
        ├── sct2_Description_Full-en_INT_20250101.txt
        └── sct2_Relationship_Full_INT_20250101.txt
    └── Refset/
        └── Language/
            └── der2_cRefset_LanguageFull-en_INT_20250101.txt

Swiss Extension/
└── Full/
    └── Terminology/
        ├── sct2_Concept_Full_CH1000195_20241207.txt
        ├── sct2_Description_Full-de-ch_CH1000195_20241207.txt
        ├── sct2_Description_Full-fr-ch_CH1000195_20241207.txt
        ├── sct2_Description_Full-it-ch_CH1000195_20241207.txt
        ├── sct2_Description_Full-en_CH1000195_20241207.txt
        └── sct2_Relationship_Full_CH1000195_20241207.txt
    └── Refset/
        └── Language/
            ├── der2_cRefset_LanguageFull-de-ch_CH1000195_20241207.txt
            ├── der2_cRefset_LanguageFull-fr-ch_CH1000195_20241207.txt
            ├── der2_cRefset_LanguageFull-it-ch_CH1000195_20241207.txt
            └── der2_cRefset_LanguageFull-en_CH1000195_20241207.txt

Note: Some optional imports (e.g., simple refsets, extended maps) are commented out in the code and can be enabled as needed.

How to Run (Eclipse IDE)

To run this project using Eclipse:

1. Import the project into Eclipse

   • Open Eclipse.
   • Go to File > Import... > General > Existing Projects into Workspace > Next.
   • Browse to the folder containing this project.
   • Click Finish.

2. Edit the configuration if needed

   • In the class CreateDatabaseAndImportData.java, update the following variables to match your system:

     static String ReleaseFilePath = "C:\\Path\\To\\InternationalEdition";
     static String ReleaseFilePathCH = "C:\\Path\\To\\SwissExtension";
     static String ReleaseDate = "20250101";
     static String ReleaseDateCH = "CH1000195_20241207";
     

3. Run the program

   • Right-click the class CreateDatabaseAndImportData.java.
   • Select Run As > Java Application.

4. Verify the result

   • The MySQL database SCT:CH_Dec24 should now be created.
   • Tables will be created and populated with SNOMED CT data.
   • The Eclipse console will show logs confirming successful steps.

Note: Ensure that:

• MySQL is running locally.
• The user has privileges to create/drop databases.
• LOAD DATA LOCAL INFILE is enabled in both MySQL server configuration and JDBC driver.

Acknowledgments

SNOMED International