Table 2 Biomedical databases commonly used in DDI prediction tasks and their detailed information
Database | Entity | Introduction | Sample Size | Positive Rate | Update Frequency | Known Bias | URL |
|---|---|---|---|---|---|---|---|
Drug, Target, Interaction | DrugBank is a database containing drugs, drug targets and drug interactions, providing detailed pharmacological and clinical data. | 4563 FDA approved drugs, 6231 investigational drugs, 1,413,413 drug–drug interactions, 2475 drug-food interactions | TP_rate:0.96 FP_rate:0.32 | Monthly | — | ||
Structure, Chemical, Bioactivity | PubChem is a data platform containing chemical substances and their biological activities, covering the detailed information of various chemical molecules. | 121,458,159 Compounds, 334,561,470 Substances, 1,768,452 BioAssays, 250,942 Pathways | — | Weekly | — | ||
Gene, Pathway, Drug | KEGG provides data on biology, genomics and metabolic pathways, especially in drug discovery and disease research. | over 10 thousand complete genomes of cellular organisms, over 50 million genes | TP_rate:0.93 FP_rate:0.36 | 1–2 days | — | ||
Compound, Target, Bioactivity | ChEMBL is a data platform containing pharmaceutical compounds and their biological activities, focusing on the information in the process of drug discovery. | over 20.3 million bioactivity measurements and 2.4 million unique compounds | TP_rate:0.99 | Regularly | differences between various input data sources for an individual drug or clinical candidate drug | ||
Drug, Gene, Disease | PharmGKB provides related data about drugs and genes, which helps to study pharmacogenomics and individualized treatment. | 1994 genes involved in drug response, 240 genes high-quality genotype variation data, 1671 literature entries | — | Regularly | — | ||
SIDER242 | Drug, Side Effect | SIDER provides data on the relationship between drugs and their side effects, covering a large number of drugs and their side effects related to patients. | 1430 drugs, 5880 ADRs, 140,064 Drug-ADR pairs | FP_rate:0.012 | Irregularly | — | |
TWOSIDES56 | Drug, Side Effect, Interaction | TWOSIDES provides information about the correlation between drugs and side effects, and contains data of drug interaction, which is helpful to evaluate the safety of drugs. | 868,221 significant associations between 59,220 pairs of drugs and 1301 adverse events, | TP_rate:0.99 FP_rate:0.7 | Irregularly | — | |
Drug-Drug Interaction | DDInter recorded drug interactions, mechanisms, clinical risks and management suggestions to help avoid adverse drug reactions and interactions. | 2310 drugs, 302,516 drug-drug interaction records, 857 DFIs, 8359 DDSIs, 6033 therapeutic duplication records | — | Irregularly | — | ||
GDSC243 | Drug Sensitivity, Cancer Genomic Data | The GDSC database is a resource that provides drug sensitivity data and genomic information from cancer cell lines, aimed at discovering new therapeutic biomarkers for cancer treatment. | 73,169 cell line-drug interactions, 329–668 cell drug (mean = 525) | — | 4 months | — | |
Drug Combinations, Sensitivity, Synergy | DrugComb is a web-based portal website used for depositing and analyzing drug combination screening datasets, providing improved algorithms for drug synergy and sensitivity analysis. | 751,498 drug combinations, 717,684 single drug screenings | — | Irregularly | 93.2% of the data points lack replicates. | ||
Drug, Drug Combinations, cancer cell lines | DrugCombDB is a comprehensive database of cancer treatment drug combinations, which is crucial for both experimental and computational screening of synergistic drug combinations. | 448,555 drug combinations, 2887 unique drugs, 124 human cancer cell lines | — | Irregularly | Synergy scores fluctuate with dosage concentrations | ||
RepurposeDrugs248 | Drug | RepurposeDrugs is a web tool and database that offers drug-indication associations and predicted approval likelihoods for single drugs and combinations, with interactive visualizations. | 4314 compounds, 161 drug combinations, 28,148 drug-disease pairs | — | Irregularly | Initial database organization may have overlooked some approved drugs and disease indications |
