This repository contains code and data for my article "Getting Insights from 3,000+ Clinical Trials in a Knowledge Graph".
- The Python scripts are for the chatbot.
Neo4j Desktop or AuraDB
GCP account
UMLS free tier
Enbale Vertex AI API in the GCP project, increase its quota (default 5)
501 VECTOR INDEX is not available in granular instances in preview 12: VECTOR INDEX is not available in granular instances in preview
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Set up the databases as described in the article.
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Install the necessary Python libraries (install.txt) and gcloud CLI
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Fill the necessary API key information in config.yaml
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Run
clinical_trials_to_kg.ipynb
and
get_meta_data_experiment.ipynb
to convert the clinical data to TSV
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Import the data into Neo4j
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Run
to_bigquery.ipynb
to export data to GCP and to create dashboard
- Sixing Huang - Concept and Coding
This project is licensed under the MIT License - see the LICENSE file for details