Table 1: Useful public databases for TCM network pharmacology.

Type#NameDescriptionApplicationWebpageReference

BOPHIDOnline predicted human interaction database: a web-based database of predicted interactions between human proteins, which contains 23889 predicted interactions currentlyPPIs retrievalhttp://ophid.utoronto.ca[139]
STRINGA database of known and predicted protein interactionsPPIs retrievalhttp://string-db.org/[140]
BioGRIDBiological general repository for interaction datasets: providing protein-protein interaction data from model organisms and humans PPIs retrievalhttp://thebiogrid.org/[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 retrievalhttp://www.hprd.org/[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 retrievalhttp://bio.informatics.iupui.edu/HAPPI/[17]
PDBProtein data bank: a key resource in areas of structural genomics for containing 3D biological macromolecular structureProtein information retrievalhttp://www.rcsb.org/pdb/[14]
PDTDPDTD: a web-accessible protein database for drug target identification and focusing on those drug targets with known 3D structuresDrug target identificationhttp://www.dddc.ac.cn/pdtd/[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 identificationhttp://bidd.nus.edu.sg/group/cjttd/[15]
UniProtKBUniversal protein knowledge database: providing protein information in detail Protein analysishttp://www.uniprot.org/uniprot/[142]
PharmGBKPharmacogenomics knowledge base: providing information of gene-drug associations and genotype-phenotype relationshipsComprehensive gene-drug-phenotype analysishttp://www.pharmgkb.org/[143]
DIPDatabase of interacting proteinsPPIs analysishttp://dip.doe-mbi.ucla.edu[144]
C2MapsA network pharmacology database with comprehensive disease-gene-drug connectivity relationshipsComprehensive gene-drug-disease analysishttp://bio.informatics.iupui.edu/[145]
MetaCoreAn integrated suite for functional analysis of microarray, metabolic, SAGE, proteomics, siRNA, microRNA, and screening dataComprehensive biological analysishttp://www.genego.com[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 analysishttp://cpdb.molgen.mpg.de/[16]
BioCartaAn interactive web-based resource giving four categories information: gene function, proteomic pathways, and research reagentsPPIs and pathway retrievalhttp://www.biocarta.com/[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 retrievalhttp://www.genome.jp/kegg/[12]
SignaLinkA database containing eight major signaling pathways, which can be used for comparative and cross-talk analyses of signaling pathwaysPathway analysishttp://signalink.org/[149]
ReactomeCurated knowledge base of biological pathways in humansPathway analysishttp://www.reactome.org[150]
NetPathA manually curated resource of signal transduction pathways in humansPathway analysishttp://www.netpath.org/[151]

DOMIMDatabase of comprehensive, authoritative compendium of human genes and genetic phenotypesDisease-gene retrievalhttp://www.omim.org/[18]
COSMICA database of catalogue of somatic mutations in cancerBiological information relating to human cancers retrievalhttp://cancer.sanger.ac.uk/cancergenome/projects/cosmic/[152]
HPOHuman phenotype ontology database: providing a standardized vocabulary of phenotype of human diseasePhenotype retrievalhttp://www.human-phenotype-ontology.org/[153]

CSTITCHChemical-protein interactions database: providing known and predicted interactions of chemicals and proteinsChemical-protein interaction retrievalhttp://stitch.embl.de/[154]
DrugBankA knowledge base for drugs, drug actions, and drug targetsComprehensive analysis for approved drugshttp://www.drugbank.ca/[19]
ChEMBLA database of bioactive drug-like small molecules, which contains 2 D structures, calculated properties, and abstracted bioactivitiesIngredient and drug chemoinformatics information retrievalhttps://www.ebi.ac.uk/chembl/[20]
MMsINCA large-scale chemoinformatics databaseIngredient and drug chemoinformatics information retrievalhttp://mms.dsfarm.unipd.it/MMsINC/search/[155]
CBA comprehensive chemical structures databaseIngredient and drug chemoinformatics information retrievalhttp://www.chemicalbook.com/[156]
ChemProtA comprehensive disease-chemical biology databaseChemical-protein interaction analysishttp://www.cbs.dtu.dk/services/ChemProt-2.0/[157]
LookChemA comprehensive chemical structures databaseIngredient and drug chemoinformatics information retrievalhttp://www.lookchem.com/[158]
ChemSpiderA chemical structure database providing structures, properties, and associated information of compoundIngredient and drug chemoinformatics information retrievalhttp://www.chemspider.com/[159]

THITA comprehensive and fully curated database for linking herbal active ingredients to targetsHerbal ingredients' targets identificationhttp://lifecenter.sgst.cn/hit/[160]
CHMIS-CA comprehensive herbal medicine information system for cancerComprehensive analysis for ingredient target of cancerhttp://sw16.im.med.umich.edu/chmis-c/[161]
TD@TTCM Database@Taiwan: providing chemical composition of Chinese medicinal herb including two- and three-dimensional structures of each TCM constituentTCM medical compound retrievalhttp://tcm.cmu.edu.tw/[162]
TCMGeneDITA database for associated traditional Chinese medicine, gene and disease information using text miningComprehensive analysis for ingredient-gene disease-effect of TCMhttp://tcm.lifescience.ntu.edu.tw/[163]
TCM-IDTraditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredientsTCM formula and medical compound retrievalhttp://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid_ns.asp[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 http://www.megabionet.org/tcmid/[21]
TcmSPTraditional Chinese medicine systems pharmacology database and analysis platform: providing information on relationships between drugs, targets, and diseasesComprehensive analysis for TCM biological sciences http://tcmspnw.com[165]
SIRC-TCMTraditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredientsTCM formula and medical compound retrievalhttp://www.tcm120.com/1w2k/tcm_species.asp[166]

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