// Query the DrugMechDB drug mechanism-of-action database. Use whenever the user asks about drug mechanisms, drug-to-disease paths, biological targets of a drug, or wants to look up any biomedical entity (drug name, protein, disease, DrugBank ID, MESH ID, UniProt ID, GO term, etc.) in DrugMechDB.
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 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 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.
| name | drugmechdb-query |
| description | Query the DrugMechDB drug mechanism-of-action database. Use whenever the user asks about drug mechanisms, drug-to-disease paths, biological targets of a drug, or wants to look up any biomedical entity (drug name, protein, disease, DrugBank ID, MESH ID, UniProt ID, GO term, etc.) in DrugMechDB. |
Search drug mechanism-of-action paths by entity name or ID. Each path is a directed graph: Drug → (intermediates) → Disease, with typed nodes and labeled edges.
indication_paths.jsonresources_metadata/drug_mechanism/DRUGMECHDB/indication_paths.json| Input pattern | Detected as | Example |
|---|---|---|
DB:DB00619 | DrugBank ID | exact on node/graph IDs |
MESH:D015464 | MESH ID | exact on node/graph IDs |
UniProt:P00519 | UniProt protein | exact on node IDs |
GO:0006915 | GO term | exact on node IDs |
CHEBI:*, HP:*, UBERON:*, CL:*, reactome:*, InterPro:*, PR:*, taxonomy:* | respective types | exact on node IDs |
| anything else | free text | substring match on drug/disease/node names |
| Function | Signature | Returns |
|---|---|---|
load(path) | path to JSON | list[dict] — full database |
build_index(db) | loaded db | (by_id, by_name, by_drug, by_disease) dicts for O(1) lookup |
search(db, entity, index=None) | single query string | list[dict] — matching paths |
search_batch(db, entities, index=None) | list of query strings | dict[str, list[dict]] |
summarize(paths, entity) | search results | compact multi-line text |
to_json(paths) | search results | list of flat dicts (id, drug, disease, nodes, links) |
BiologicalProcess, Cell, CellularComponent, ChemicalSubstance, Disease, Drug, GeneFamily, GrossAnatomicalStructure, MacromolecularComplex, MolecularActivity, OrganismTaxon, Pathway, PhenotypicFeature, Protein
import drugmechdb_query as dq
db = dq.load() # uses default DATA_PATH
idx = dq.build_index(db) # optional, recommended for repeated queries
# Single query — by name or ID
paths = dq.search(db, "imatinib", idx)
paths = dq.search(db, "UniProt:P00519", idx)
paths = dq.search(db, "MESH:D003920", idx)
print(dq.summarize(paths, "imatinib"))
# Batch query
results = dq.search_batch(db, ["metformin", "MESH:D003920", "asthma"], idx)
for entity, paths in results.items():
print(dq.summarize(paths, entity))
# JSON export
print(dq.to_json(paths))
graph: { _id, drug, disease, drugbank, drug_mesh, disease_mesh }
nodes: [{ id, label, name }, ...]
links: [{ source, target, key }, ...]
key examples: decreases activity of, causes, positively regulates, treats, increases expression of, etc. (66 relation types total).