Output Format¶
Directory Structure¶
output/<patient_id>/
├── oncokb_output.tsv
├── pubmed_output.tsv
├── txgnn_output.tsv
├── clinicaltrials_output.tsv
├── top20_drugs.png
├── txgnn_graph.png
├── final_report.xlsx
└── final_report.pdf
Excel Report Sheets¶
The final_report.xlsx contains seven sheets:
| Sheet | Description |
|---|---|
Summary |
Cancer type, variant count, and top 20 ranked drugs |
Performance |
Runtime, API calls, and memory usage per module |
OncoKB |
Full OncoKB annotation output |
PubMed |
Gene-drug mention counts from PubMed |
TxGNN |
Graph-based drug candidates with category labels |
ClinicalTrials |
Raw clinical trial records |
Merged_Drugs |
Final merged and ranked drug table |
Merged Drug Table Columns¶
The Merged_Drugs sheet contains the final ranked output:
| Column | Description |
|---|---|
drug |
Drug name (uppercase) |
combined_score |
Percentile-normalized combined score |
tx_pct |
TxGNN percentile |
pm_pct |
PubMed percentile |
ok_pct |
OncoKB percentile |
support_count |
Number of evidence layers (0--3) |
clinical_flag |
Has matched clinical trials (0/1) |
source |
Evidence source labels (e.g., TxGNN\|PubMed) |
txgnn_score |
Raw TxGNN score |
mention_count |
Raw PubMed mention count |
oncokb_score |
Raw OncoKB score |
n_clinical_trials |
Number of matched trials |
top_nct_id |
NCT ID of highest-phase trial |
top_phase |
Highest trial phase |
PDF Report¶
The PDF report includes:
- Summary page -- Cancer type, variant count, top drugs
- Top 20 drugs bar plot -- Ranked by combined score
- TxGNN network graph -- Cancer type, mutated genes, and recommended drugs
- Clinical trials table -- Top 30 drugs with trial metadata
Visualizations¶
Top 20 Drugs (top20_drugs.png)¶
Horizontal bar chart of the 20 highest-scoring drugs by combined score.
TxGNN Network Graph (txgnn_graph.png)¶
Network visualization with:
- Red nodes: Cancer type
- Blue nodes: Mutated genes
- Green nodes: Recommended drugs
- Edges: Gene-drug associations from the knowledge graph