| name | DrugRepoBank-query |
| description | Query the DrugRepoBank drug repurposing evidence database. Use whenever the user asks about repurposing candidates, drug–disease–target repurposing evidence, or wants to look up any entity (drug name, DrugBank ID, ChEMBL ID, PubChem CID, TTD target ID, UniProt ID, disease name) in DrugRepoBank.
|
DrugRepoBank Query Skill
Search four linked tables (Drug, Target, DrugTargetInteraction, Literature)
for repurposing evidence. Auto-detects entity type by prefix:
| Input Pattern | Detected As | Example |
|---|
DB00945 | DrugBank ID | exact on DrugBank_ID / DrugID |
T47101 | TTD Target ID | exact on TargetID |
FGFR1_HUMAN | UniProt ID | exact on UniprotID |
CHEMBL2103749 | ChEMBL ID | exact on ChEMBL ID in Drug table |
16129704 (digits) | PubChem CID | exact on PubChem_Compound_ID / PubChemID |
| anything else | free text | substring on drug Name, TargetName, Disease, NewDisease |
API
| Function | Input | Returns |
|---|
load_all() | — | dict with keys drug, dti, lit, target (lists of row-dicts) |
search(tables, entity) | tables dict + single entity string | dict with keys entity, entity_type, drug, target, dti, literature |
search_batch(tables, entities) | tables dict + list of entity strings | dict[str, search_result] |
summarize(result) | single search() result | compact one-line LLM-readable text |
to_json(result) | single search() result | JSON string (trimmed heavy fields) |
Usage
See if __name__ == "__main__" block in 42_DrugRepoBank.py for runnable
examples covering: drug name, DrugBank ID, TTD target ID, UniProt ID, ChEMBL
ID, disease free-text, batch search, and JSON output.
Data
Four CSV tables in DATA_DIR:
| File | Key Columns | Description |
|---|
Drug.csv | DrugBank_ID, Name, Drug Groups, PubChem_Compound_ID, ChEMBL ID, SMILES | Drug identifiers & structures |
DrugTargetInteraction.csv | UniprotID, PubchemID, TargetID, DrugID, Highest_status, MOA | Drug–target links with mechanism of action |
Literature.csv | DrugName, DrugID, Target, Disease, NewDisease, Evidence, Insilico, Invitro, Invivo, Clinicaltrial, PMID | Repurposing evidence & literature references |
Targets.csv | TargetID, UniprotID, TargetName, TargetGeneName, TargetType, Function | Target annotations & pathway memberships |
