Table 1: Useful public databases for TCM network pharmacology.


BOPHIDOnline predicted human interaction database: a web-based database of predicted interactions between human proteins, which contains 23889 predicted interactions currentlyPPIs retrieval[139]
STRINGA database of known and predicted protein interactionsPPIs retrieval[140]
BioGRIDBiological general repository for interaction datasets: providing protein-protein interaction data from model organisms and humans PPIs retrieval[24]
HPRDHuman protein reference database: depicting and integrating information related to domain architecture, posttranslational modifications, interaction networks, and disease association for each protein in the human proteomePPIs retrieval[13]
HAPPIHuman annotated and predicted protein interaction database: containing 142,956 nonredundant, medium to high-confidence level human protein interaction pairs among 10,592 human proteinsPPIs retrieval[17]
PDBProtein data bank: a key resource in areas of structural genomics for containing 3D biological macromolecular structureProtein information retrieval[14]
PDTDPDTD: a web-accessible protein database for drug target identification and focusing on those drug targets with known 3D structuresDrug target identification[141]
TTDTherapeutic target database: providing information about the known and exploring therapeutic protein and nucleic acid targets, the targeted disease, pathway information, and the corresponding drugsDrug target identification[15]
UniProtKBUniversal protein knowledge database: providing protein information in detail Protein analysis[142]
PharmGBKPharmacogenomics knowledge base: providing information of gene-drug associations and genotype-phenotype relationshipsComprehensive gene-drug-phenotype analysis[143]
DIPDatabase of interacting proteinsPPIs analysis[144]
C2MapsA network pharmacology database with comprehensive disease-gene-drug connectivity relationshipsComprehensive gene-drug-disease analysis[145]
MetaCoreAn integrated suite for functional analysis of microarray, metabolic, SAGE, proteomics, siRNA, microRNA, and screening dataComprehensive biological analysis[146, 147]
CPDBA database that integrates different types of functional interactions including protein-protein, genetic, metabolic, signaling, gene regulatory, and drug-target interactionsComprehensive gene-drug-disease analysis[16]
BioCartaAn interactive web-based resource giving four categories information: gene function, proteomic pathways, and research reagentsPPIs and pathway retrieval[148]
KEGGAs a collection of online databases, which deals with genomes, enzymatic pathways, and biological chemicals, especially giving pathway map in the forms of molecular networksPPIs and pathway retrieval[12]
SignaLinkA database containing eight major signaling pathways, which can be used for comparative and cross-talk analyses of signaling pathwaysPathway analysis[149]
ReactomeCurated knowledge base of biological pathways in humansPathway analysis[150]
NetPathA manually curated resource of signal transduction pathways in humansPathway analysis[151]

DOMIMDatabase of comprehensive, authoritative compendium of human genes and genetic phenotypesDisease-gene retrieval[18]
COSMICA database of catalogue of somatic mutations in cancerBiological information relating to human cancers retrieval[152]
HPOHuman phenotype ontology database: providing a standardized vocabulary of phenotype of human diseasePhenotype retrieval[153]

CSTITCHChemical-protein interactions database: providing known and predicted interactions of chemicals and proteinsChemical-protein interaction retrieval[154]
DrugBankA knowledge base for drugs, drug actions, and drug targetsComprehensive analysis for approved drugs[19]
ChEMBLA database of bioactive drug-like small molecules, which contains 2 D structures, calculated properties, and abstracted bioactivitiesIngredient and drug chemoinformatics information retrieval[20]
MMsINCA large-scale chemoinformatics databaseIngredient and drug chemoinformatics information retrieval[155]
CBA comprehensive chemical structures databaseIngredient and drug chemoinformatics information retrieval[156]
ChemProtA comprehensive disease-chemical biology databaseChemical-protein interaction analysis[157]
LookChemA comprehensive chemical structures databaseIngredient and drug chemoinformatics information retrieval[158]
ChemSpiderA chemical structure database providing structures, properties, and associated information of compoundIngredient and drug chemoinformatics information retrieval[159]

THITA comprehensive and fully curated database for linking herbal active ingredients to targetsHerbal ingredients' targets identification[160]
CHMIS-CA comprehensive herbal medicine information system for cancerComprehensive analysis for ingredient target of cancer[161]
TD@TTCM Database@Taiwan: providing chemical composition of Chinese medicinal herb including two- and three-dimensional structures of each TCM constituentTCM medical compound retrieval[162]
TCMGeneDITA database for associated traditional Chinese medicine, gene and disease information using text miningComprehensive analysis for ingredient-gene disease-effect of TCM[163]
TCM-IDTraditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredientsTCM formula and medical compound retrieval[164]
TCMIDTraditional Chinese medicine integrated database: a comprehensive database to provide information on drug-herb and its ingredient, prescription, target, and diseaseComprehensive analysis for TCM biological sciences[21]
TcmSPTraditional Chinese medicine systems pharmacology database and analysis platform: providing information on relationships between drugs, targets, and diseasesComprehensive analysis for TCM biological sciences[165]
SIRC-TCMTraditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredientsTCM formula and medical compound retrieval[166]

#B: biomolecular databases; D: disease/phenotype databases; C: chemical/drug-related databases; T: TCM related-databases.