Data Sources
Databases and sources used in this project
Source Overview
| Data Type | Source | Usage |
|---|---|---|
| AI Predictions | TxGNN | Drug-disease association predictions |
| EU Drug Data | EMA | Approved medicines information |
| Drug Identifiers | DrugBank | Drug mapping and metadata |
| Clinical Trials | ClinicalTrials.gov | Evidence validation |
| Literature | PubMed | Research evidence |
TxGNN Model
Introduction
TxGNN is a drug repurposing prediction model developed by Professor Marinka Zitnik’s team at Harvard Medical School.
Publication
- Title: A foundation model for clinician-centered drug repurposing
- Journal: Nature Medicine (2023)
- DOI: 10.1038/s41591-023-02233-x
Model Statistics
| Item | Count |
|---|---|
| Total Nodes | 17,080 |
| Drug Nodes | 4,465 |
| Disease Nodes | 2,870 |
| Known Drug-Disease Relations | 14,573 |
Data Access
- Harvard Dataverse: TxGNN Dataset
- GitHub: TxGNN Code
EMA Medicines Database
Introduction
The European Medicines Agency provides data on centrally authorized medicines.
Data Accessed
| Dataset | Description |
|---|---|
| Medicines Output | All authorized human medicines |
| Article 57 Database | Pharmaceutical product submissions |
Access
- EMA Website: Download Medicine Data
DrugBank
Introduction
DrugBank is a comprehensive drug database with detailed drug information.
Usage in EuTxGNN
- Drug name standardization
- DrugBank ID mapping
- Drug metadata (targets, pathways)
Access
- Website: DrugBank
- License: Academic use requires registration
ClinicalTrials.gov
Introduction
Registry of clinical studies conducted around the world.
Usage in EuTxGNN
- Validating drug-disease associations
- Evidence level determination
- Clinical trial status tracking
Access
- Website: ClinicalTrials.gov
- API: CTGOV API
PubMed
Introduction
Biomedical literature database from NCBI.
Usage in EuTxGNN
- Literature evidence for predictions
- Mechanistic support
- Case reports and studies
Access
- Website: PubMed
- API: NCBI E-utilities
Citation
When using EuTxGNN data, please cite:
@article{huang2023txgnn,
title={A foundation model for clinician-centered drug repurposing},
author={Huang, Kexin and others},
journal={Nature Medicine},
year={2023},
doi={10.1038/s41591-023-02233-x}
}
License Information
| Source | License |
|---|---|
| TxGNN | See original repository |
| EMA Data | Open data |
| DrugBank | Academic license |
| EuTxGNN Generated Data | CC BY 4.0 |