# 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`.

```ini
[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.

```sh
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]( https://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](#quickstart)


## 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.