BRAinS-Graph/src/study2neo4j/README.md

study2neo4j

This repo is for integrating data from ClinicalTrials.gov into Neo4j.

Quickstart

Create a configuration file, storing your details for the database-connection. E.g. in your home-directory with the name study.conf.

[neo4j]
uri = bolt://localhost:7687
username = neo4j
password = myfancypassword

Start the program by providing the location of your configuration-file and the location of the json files.

python3 src/run.py --conf ~/study.conf --files ~/Desktop/datasource

Requirements

• make sure, python3 is installed
• install the required libraries with pip install -r requirements.txt
• download all json files from ClinicalTrials.gov and place all json files you want to load in one folder
• have a running Neo4j DB (Neo4j version 5)
• create the configuration-file as described in the Quickstart section

Acknowledgements

ct2neo4j.py is adapted from the MeDaX pipeline (see [1], [2]) graphCreation, with permission from the authors.

[1] Gebhardt, T., Mazein, I., Michaelis, L., Henkel, R., Lobentanzer, S., Waltemath, D., & Wodke, J. (2025). MeDaX pipeline (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.15229077

[2] Mazein, I., Gebhardt, T., Zinkewitz, F., Michaelis, L., Braun, S., Waltemath, D., Henkel, R., & Wodke, J. A. (2024). MeDaX: A Knowledge Graph on FHIR. In Digital Health and Informatics Innovations for Sustainable Health Care Systems (pp. 367-371). IOS Press.