39 lines
1.5 KiB
Markdown
39 lines
1.5 KiB
Markdown
# study2neo4j
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This repo is for integrating data from ClinicalTrials.gov into Neo4j.
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## Quickstart
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Create a configuration file, storing your details for the database-connection.
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E.g. in your home-directory with the name `study.conf`.
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```ini
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[neo4j]
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uri = bolt://localhost:7687
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username = neo4j
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password = myfancypassword
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```
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Start the program by providing the location of your configuration-file and the location of the json files.
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```sh
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python3 src/run.py --conf ~/study.conf --files ~/Desktop/datasource
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```
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## Requirements
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- make sure, `python3` is installed
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- install the required libraries with `pip install -r requirements.txt`
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- download all json files from [ClinicalTrials.gov]( https://clinicaltrials.gov/ ) and place all json files you want to load in one folder
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- have a running Neo4j DB (Neo4j version 5)
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- create the configuration-file as described in the [Quickstart section](#quickstart)
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## Acknowledgements
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`ct2neo4j.py` is adapted from the MeDaX pipeline (see [1], [2]) graphCreation, with permission from the authors.
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[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
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[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.
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