| name | Drug-Repurposing-Hub |
| description | Query the Broad Institute Drug Repurposing Hub (~6,800 compounds). Look up drugs by name, gene target, MOA, disease area, Broad ID, or InChIKey. Returns clinical phase, mechanism of action, targets, disease area, indication, and chemical identifiers.
|
Drug Repurposing Hub Query Skill
Search the Broad Institute Drug Repurposing Hub by any entity.
Auto-detects input type by pattern:
| Input Pattern | Detected As | Match Logic |
|---|
BRD-A12345678 | Broad compound ID | prefix on broad_id |
ABCDEFGHIJKLMN-OPQRSTUVWX-Y | InChIKey | exact on InChIKey |
EGFR, BRAF, TOP1 | Gene / target | exact token in target (pipe-separated) |
| anything else | free text | substring on pert_iname, moa, indication, disease_area |
API
| Function | Input | Returns |
|---|
load_drugs(path) | drug TSV path | list[dict] |
load_samples(path) | sample TSV path | list[dict] |
load_merged() | — | list[dict] (drugs + chemical IDs from samples) |
search(entity) | single entity string | list[dict] |
search_batch(entities) | list of entity strings | dict[str, list[dict]] |
summarize(hits, entity) | hits + label | compact LLM-readable text |
to_json(hits) | list[dict] | list[dict] (JSON-serialisable) |
Usage
See if __name__ == "__main__" block in 29_Drug_Repurposing_Hub.py for
runnable examples covering: drug name, gene target, MOA keyword, disease
area, batch search, and JSON output.
from importlib.machinery import SourceFileLoader
hub = SourceFileLoader("hub", "29_Drug_Repurposing_Hub.py").load_module()
hits = hub.search("imatinib")
print(hub.summarize(hits, "imatinib"))
hits = hub.search("EGFR")
results = hub.search_batch(["metformin", "aspirin", "BRAF"])
Data
- Source: Broad Institute Drug Repurposing Hub (https://repo-hub.broadinstitute.org/repurposing)
- Drug file:
repo-drug-annotation-20200324.txt — tab-delimited, !-prefixed comment lines
- Columns:
pert_iname, clinical_phase, moa, target, disease_area, indication
- Sample file:
repo-sample-annotation-20240610.txt — tab-delimited, !-prefixed comment lines
- Columns include:
broad_id, pert_iname, InChIKey, pubchem_cid, smiles, vendor, purity, etc.
- Merge: on
pert_iname; first sample with non-empty InChIKey is kept per drug
- Path:
DATA_DIR variable in 29_Drug_Repurposing_Hub.py
- Citation: Corsello SM et al. Nature Medicine 23, 405–408 (2017). doi:10.1038/nm.4306
