Dicom2OMOP

This project looks at creating a controlled vocabulary for the DICOM Pt 6 Data Dictionary with a focus on CS code strings in the OMOP vocabulary format and harmonizing common data elements (CDE).

Create a library that takes a dicom tag
- (eg Part 6 0010,0040 Patient Sex)
- (Link to Part 16 CID 7455 Sex)
- (Ingest FHIR JSON)
- (Create "maps to" from Source to Standard vocabulary for OMOP gender)
Identify current gaps in SNOMED and LOINC mapping from DICOM

Requirements

Developed and Tested for:

WSL Ubuntu 22.04.3 LTS (Jammy Jellyfish)
openjdk version "11.0.21" 2023-10-17
Python 3.10.12

Instructions

0. Ensure the system is up to date and install dependencies

sudo apt update && sudo apt upgrade
sudo apt install bzip2 default-jdk default-jre xsltproc libxml2-utils python3-pip python3.10-venv

Verify java installation

java -version

openjdk version "11.0.21" 2023-10-17

1. Download the current source and rendering pipeline from dicom.nema.org using curl (wget or another method will also work)

curl https://dicom.nema.org/medical/dicom/current/DocBookDICOM2023e_sourceandrenderingpipeline_20231120022735.tar.bz2 --output sourceandrenderingpipeline.tar.bz2

2. Extract to a directory, remove archive, and navigate to the directory

mkdir sourceandrenderingpipeline 

tar -xvf sourceandrenderingpipeline.tar.bz2 -C sourceandrenderingpipeline

rm sourceandrenderingpipeline.tar.bz2

cd sourceandrenderingpipeline

3. Update absolute paths using the provided bash script

./updateabsolutepaths.sh

4. Generate the databases for the parts (example for part 16)

./generateolinkdb.sh 16

5. Generate FHIR valuesets

5.1 Navigate to the valuesets subdirectory and download Java package dependencies

cd valuesets
curl https://repo1.maven.org/maven2/javax/json/javax.json-api/1.0/javax.json-api-1.0.jar --output javax.json-api-1.0.jar
curl https://repo1.maven.org/maven2/org/glassfish/javax.json/1.0.4/javax.json-1.0.4.jar --output javax.json-1.0.4.jar

5.2 Create a backup of the bash script used to extract valuesets, then modify the reference to the Java packages in the bash file and run it

cp extractvaluesets.sh{,.old}
sed -i 's|${HOME}/work/pixelmed/imgbook/lib/additional/|./|g' extractvaluesets.sh

./extractvaluesets.sh

5.3 Count the extracted json files to validate they match

find ./valuesets/fhir/json/ -type f -name "*.json" | wc -l

1341

6. Setup the Python virtual environment

note: this should be done in the root DICOM2OMOP directory. We use cd ../.. here to navigate there from DICOM2OMOP/sourceandrenderingpipeline/valuesets

This may take a few minutes as packages are installed.

cd ../..
python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

python DICOM_P16_harvest_fhir_json.py

haydenbspence / dicom2omop Goto Github PK

dicom2omop's Introduction

Dicom2OMOP

Requirements

Instructions

0. Ensure the system is up to date and install dependencies

1. Download the current source and rendering pipeline from dicom.nema.org using curl (wget or another method will also work)

2. Extract to a directory, remove archive, and navigate to the directory

3. Update absolute paths using the provided bash script

4. Generate the databases for the parts (example for part 16)

5. Generate FHIR valuesets

5.1 Navigate to the valuesets subdirectory and download Java package dependencies

5.2 Create a backup of the bash script used to extract valuesets, then modify the reference to the Java packages in the bash file and run it

5.3 Count the extracted json files to validate they match

6. Setup the Python virtual environment

References

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