QUANTUM - The Health Data Quality Label

Cite the code:

Introduction

The QUANTUM Data Quality Labelling Tool is a key component of the European Health Data Space (EHDS) initiative, designed to address the challenge of ensuring that health datasets are of high quality, accessible, and interoperable across EU member states. As healthcare data plays an increasingly vital role in research, policy, and innovation, this tool provides a standardized mechanism to evaluate and label the quality, utility, and maturity of datasets, supporting stakeholders such as healthcare institutions, research organizations, and policymakers.

Features

This tool empowers data holders by offering functionalities to:

• Feature 1: Catalogue and Dataset metadata creation
• Feature 2: Assess datasets quality based on a guided evaluation of the QUANTUM key dimensions (such as accuracy, accessibility, and compliance) using your own practices.
• Feature 3: Generate and visualise data quality certificates (labels) and download them in the HealthData@EU standardized RDF format.
• Feature 4: Facilitate compliance with EU-wide quality standards such as HealthDCAT-AP, DCAT, DQV.
• Feature 5: Provide a transparent and accessible method for assessing data holders maturity.

Ultimately, the QUANTUM tool aims to foster trust in health data across Europe by promoting reliable, reusable datasets that can be confidently shared within the European Health Data Space.

System Requirements

Minimum Hardware Requirements

• CPU: 1 core
• RAM: 1 GB
• Storage: 5 GB ### Recommended Hardware Requirements
• CPU: 2 to 4 cores
• RAM: 2 to 4 GB
• Storage: 10 to 20 GB ### Software Requirements
• Ubuntu 20.04.6 LTS or similar
• Python 3.11
• Docker 24.0.2 (if used)

Installation steps

bash git clone [repository_url] cd [repository_directory] pip install -r requirements.txt python manage.py migrate # if database is not generated previously python manage.py createsuperuser # for creating root user if desired (current root user is root for username and password)

Execution

bash python manage.py runserver 0.0.0.0:8000

• Access localhost:8000 through web browser
• Access localhost:8000/admin to visit the Admin dashboard (login is root for user and password by default)
• To register a user it is needed to 1) create the user, 2) create an organization, 3) relate a user with an organization (userorganization)

Dockerizing

• Download the repository. When unzipped, the folder will be named "quantumlabellingtool"
• For Dockerizing create a folder called "QUANTUM" where needed
• Inside QUANTUM create the folder "onlinequantumtool", which will contain the django web app.
• From "quantumlabellingtool" copy the following files and folders to the "QUANTUM/onlinequantumtool" folder:
  • code
  • quantum
  • static
  • staticfiles
  • templates
  • webapp
  • manage.py
• Copy the content of "quantumlabellingtool/docker" inside "QUANTUM" (keep in mind that it contains an .env file, which may be hidden)
• If the web app is meant to be executed under a sub path (e.g. myurl.com/tool-subpath/) it is required to change on "quantum/settings.py" the "SUBPATHNAME" to the desired subpath (e.g. /tool-subpath)
• In the "QUANTUM" folder execute by bash: bash docker build -t quantum_online_tool .
• When the image is built execute the docker-compose command inside the "QUANTUM" folder: bash docker-compose up
• Access the web app container through the following command: docker exec -it quantumtoolwebapp bash
• Fill the database with the initial information: python manage.py migrate

• Create a superuser to play with (root): python manage.py createsuperuser

• Exit from the container exit

• Access the database container: docker exec -it quantumtooldatabase bash

• Execute the following commands to add information to the database mysql -u root -p use quantum; source /docker-entrypoint-initdb.d/init.sql;

• See "Usage" sections

Technology Stack

Backend

• Python 3
• Django ### Frontend
• HTML
• CSS*
• JavaScript*

*It is used Bootstrap 5.3

Database

Development

• SQLite3 #### Production (Docker)
• MariaDB

Licence

This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/4.0/.

Credits

Version: 0.1

Authors: QUANTUM WP2: Claudio Proietti Mercuri (Sciensano), Ángel Sánchez-García (UPV), Nienke Schutte (Sciensano), Carlos Sáez (UPV); on behalf of QUANTUM.

Maintainers: Claudio Proietti Mercuri (Sciensano), Ángel Sánchez-García (UPV), Francisco Estupiñan Romero (IACS).

Acknowledgements: QUANTUM WP1, WP2, WP3 partners and all participants in the tool piloting for their feedback.

Funded by EU QUANTUM project.