Table 2.

Data class, specific data, statistics and details of data sources used to generate DrugRepoBank

Data class	Specific data	Statistics	Details	Data source	Ref
Drug	Drug name, clinical status and drug identifiers	49 652 small-molecule drugs including 2877 approved drugs	DrugBank ID, drug name, Drug clinical status, drug identifiers including CAS Number, InChIKey, InChI, Formula and SMILES	DrugBank	(18)
	Drug chemical structures	29 733 structures	We use the PubChem Compound ID of drugs to search the drug chemical structures in MolView	PubChem	(19)
Drug–target interaction	Drug protein targets	880 945 drug–target interactions	Each drug–target pair records the mechanism of action (such as agonist, antagonist and so on) and activity (Kd, Ki or IC50).	DrugBank and TTD	(18, 20, 21)
Drug-disease association	Drug indications and clinical status	28 978 drug-indication associations, including 3620 ‘approved’	Drug disease indications are encoded by ICD-11. The clinical status includes Phase 1, Phase 1/2, Phase 2, Phase 3, Approved, Terminated, Investigated, Discontinued in Phase 1, Discontinued in Phase 2, Discontinued in Phase 3, Patented, Withdraw from market, Preclinical, Discontinued in Preregistration and Clinical trial	TTD	(20, 21)
Drug-side effects association	Drug-side effects association	109 698 Drug-side effect associations	Information on marketed medicines and their recorded adverse drug reactions	SIDER	(22)
Drug-pathway association	Drug-induced pathways	243 pathways and 3888 drug-pathway associations		KEGG	(23)
Target	Target name, sequence, target identifiers and other target information	4221 targets, including 620 successful targets	Target name, target gene name, target type, synonyms, biochemical class, EC Number and sequence	TTD	(20, 21)
	Target 3D structure	7082 structures of 2226 targets	We use PDB ID to search target 3D structures in https://molstar.org.	PDB	(29)
Target-disease association	Target indications and clinical status	11 268 target-indication associations, including 2679 ‘approved’	Target disease indications are encoded by ICD-11. The clinical status includes Phase 1, Phase 1/2, Phase 2, Phase 3, Approved, Terminated, Investigated, Discontinued in Phase 1, Discontinued in Phase 2, Discontinued in Phase 3, Patented, Withdraw from market, Preclinical, Discontinued in Preregistration and Clinical trial	TTD	(20, 21)
Target-pathway association	Target-involved KEGG pathways	387 pathways and 8528 target-pathway associations	We provide target-involved KEGG pathways for Homo sapiens	KEGG	(23)
	Target-involved WiKi pathways	516 pathways and 8149 target-pathway associations		WiKiPathways	(30)
	Target-involved PathWhiz pathways	98 pathways and 467 target-pathway associations		PathWhizPathway	(31)
	Target-involved Reactome pathways	577 pathways and 4332 target-pathway associations		REACTOME	(32)
	Target-involved NetPath pathways	25 pathways and 1106 target-pathway associations		NetPath	(33)
	Target-involved PANTHER pathways	124 pathways and 1786 target-pathway associations		PANTHER	(34)
Pathway	GO terms and annotations	6700 GO terms, including 446 CC, 1151 MF and 5103 BP terms, and a total of 250 734 protein-GO term associations	GO terms across categories of cellular components (CC), molecular functions (MF) and biological process (BP)	Enrichr	(35)
Disease signature	Diseases (Cancer) signature	25 types of cancer	Breast Cancer (BRCA), Bladder Cancer (BLCA), Cervical Cancer (CESC), Bile Duct Cancer (CHOL), Colon Cancer (COAD), Colon and Rectal Cancer (COADREAD), Esophageal Cancer (ESCA), Head and Neck Cancer (HNSC), Kidney Chromophobe (KICH), Kidney Clear Cell Carcinoma (KIRC), Kidney Papillary Cell Carcinoma (KIRP), Liver Cancer (LIHC), Lung Adenocarcinoma (LUAD), Lung Cancer (LUNG), Lung Squamous Cell Carcinoma (LUSC), Pancreatic Cancer (PADD), Pheochromocytoma & Paraganglioma (PCPG), Prostate Cancer (PRAD), Rectal Cancer (READ), Sarcoma (SARC), Melanoma (SKCM), Stomach Cancer (STAD), Thyroid Cancer (THCA), Thymoma (THYM) and Endometrioid Cancer (UCEC)	TCGA	(36)
Drug signature	Drug signature	473 647 replicate-consensus signatures	We downloaded the level 5 data of L1000 (GCTx format) from the Gene Expression Omnibus (accession number: GSE92742), which contains 473 647 replicate-consensus signatures (RCSs) generated by the official data pre-processing pipeline. The level 5 data of L1000 have been normalized, and the LINCS team suggests their direct use without extra processing. Each RCS represents the moderated z-score value of 12 328 genes for one profile	L1000	(37)
Literature	Drug repositioning-related literature	169 experimentally validated repositioned drugs from 134 valid literature	We extract important information such as old targets, new direct targets, new indirect targets, old diseases, new diseases, experiment evidence and supporting sentences from these articles	PubMed	(38)