// Query the Gene-Drug Knowledge Database (GDKD) for variant-specific gene–drug associations in oncology. Use when the user asks about cancer genomic biomarkers, drug sensitivity/resistance by gene or variant, targetable mutations, or clinical evidence for cancer therapeutics.
Query the DrugComb drug combination database for cancer cell-line synergy and sensitivity data. Use whenever the user asks about drug combinations, synergy scores (ZIP/Bliss/Loewe/HSA), combination sensitivity (CSS), or wants to look up how two drugs interact in a specific cancer cell line.
Query canonical DrugCombDB combination records. Use when the user asks about drug pairs, synergy values, or cell-line-specific combination evidence.
Query or inspect the FDA Orange Book - FDA-Approved Drug Products Listing resource for drug-centric tasks with emphasis on drug knowledgebase Use whenever Codex needs the calling pattern, downloadable entrypoint, or example query flow from this skill example script.
Query the RepurposeDrugs single-agent drug repurposing database. Use whenever the user asks about drug-disease repurposing associations, clinical trial phases for repurposed drugs, or wants to look up any entity (drug name, disease name, NCT ID) in RepurposeDrugs.
Query canonical TarKG drug-target triplets. Use when the user asks about drug-target interactions, relation labels, disease/pathway context, or quick lookups for drugs/targets in TarKG.
Query the MecDDI mechanism-based drug-drug interaction database. Use whenever the user asks about drug-drug interactions, DDI mechanisms (PK/PD), enzyme or transporter-mediated interactions, or wants to look up interacting drug pairs by drug name or MecDDI drug ID. Trigger on keywords like DDI, drug interaction, MecDDI, mechanism-based interaction, pharmacokinetic interaction, pharmacodynamic interaction, or any query involving two drugs that may interact.
| name | GDKD-query |
| description | Query the Gene-Drug Knowledge Database (GDKD) for variant-specific gene–drug associations in oncology. Use when the user asks about cancer genomic biomarkers, drug sensitivity/resistance by gene or variant, targetable mutations, or clinical evidence for cancer therapeutics. |
Search canonical GDKD rows by drug or gene entity. Auto-detects input type by pattern:
| Input Pattern | Detected As | Match Logic |
|---|---|---|
ABL1, EGFR | Gene symbol | substring on gene |
imatinib, erlotinib | Drug name | substring on drug |
| anything else | Free text | substring on drug OR gene |
| Function | Input | Returns |
|---|---|---|
load_gdkd(path) | CSV path | list[dict] |
search(rows, entity) | single entity string | list[dict] |
search_batch(rows, entities) | list of entity strings | dict[str, list[dict]] |
summarize(hits, entity) | rows + label | compact text |
to_json(hits) | rows | list[dict] |
See if __name__ == "__main__" block in example.py for runnable
examples.
drug, gene, score, sourceresources_metadata/dti/GDKD/gdkd.csv (default DATA_PATH in example.py)