Navigating Traditional Chinese Medicine Network Pharmacology and Computational Tools

Table 1

Useful public databases for TCM network pharmacology.

Type^#	Name	Description	Application	Webpage	Reference
B	OPHID	Online predicted human interaction database: a web-based database of predicted interactions between human proteins, which contains 23889 predicted interactions currently	PPIs retrieval	http://ophid.utoronto.ca	[139]
	STRING	A database of known and predicted protein interactions	PPIs retrieval	http://string-db.org/	[140]
	BioGRID	Biological general repository for interaction datasets: providing protein-protein interaction data from model organisms and humans	PPIs retrieval	http://thebiogrid.org/	[24]
	HPRD	Human protein reference database: depicting and integrating information related to domain architecture, posttranslational modifications, interaction networks, and disease association for each protein in the human proteome	PPIs retrieval	http://www.hprd.org/	[13]
	HAPPI	Human annotated and predicted protein interaction database: containing 142,956 nonredundant, medium to high-confidence level human protein interaction pairs among 10,592 human proteins	PPIs retrieval	http://bio.informatics.iupui.edu/HAPPI/	[17]
	PDB	Protein data bank: a key resource in areas of structural genomics for containing 3D biological macromolecular structure	Protein information retrieval	http://www.rcsb.org/pdb/	[14]
	PDTD	PDTD: a web-accessible protein database for drug target identification and focusing on those drug targets with known 3D structures	Drug target identification	http://www.dddc.ac.cn/pdtd/	[141]
	TTD	Therapeutic target database: providing information about the known and exploring therapeutic protein and nucleic acid targets, the targeted disease, pathway information, and the corresponding drugs	Drug target identification	http://bidd.nus.edu.sg/group/cjttd/	[15]
	UniProtKB	Universal protein knowledge database: providing protein information in detail	Protein analysis	http://www.uniprot.org/uniprot/	[142]
	PharmGBK	Pharmacogenomics knowledge base: providing information of gene-drug associations and genotype-phenotype relationships	Comprehensive gene-drug-phenotype analysis	http://www.pharmgkb.org/	[143]
	DIP	Database of interacting proteins	PPIs analysis	http://dip.doe-mbi.ucla.edu	[144]
	C2Maps	A network pharmacology database with comprehensive disease-gene-drug connectivity relationships	Comprehensive gene-drug-disease analysis	http://bio.informatics.iupui.edu/	[145]
	MetaCore	An integrated suite for functional analysis of microarray, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data	Comprehensive biological analysis	http://www.genego.com	[146, 147]
	CPDB	A database that integrates different types of functional interactions including protein-protein, genetic, metabolic, signaling, gene regulatory, and drug-target interactions	Comprehensive gene-drug-disease analysis	http://cpdb.molgen.mpg.de/	[16]
	BioCarta	An interactive web-based resource giving four categories information: gene function, proteomic pathways, and research reagents	PPIs and pathway retrieval	http://www.biocarta.com/	[148]
	KEGG	As a collection of online databases, which deals with genomes, enzymatic pathways, and biological chemicals, especially giving pathway map in the forms of molecular networks	PPIs and pathway retrieval	http://www.genome.jp/kegg/	[12]
	SignaLink	A database containing eight major signaling pathways, which can be used for comparative and cross-talk analyses of signaling pathways	Pathway analysis	http://signalink.org/	[149]
	Reactome	Curated knowledge base of biological pathways in humans	Pathway analysis	http://www.reactome.org	[150]
	NetPath	A manually curated resource of signal transduction pathways in humans	Pathway analysis	http://www.netpath.org/	[151]
D	OMIM	Database of comprehensive, authoritative compendium of human genes and genetic phenotypes	Disease-gene retrieval	http://www.omim.org/	[18]
	COSMIC	A database of catalogue of somatic mutations in cancer	Biological information relating to human cancers retrieval	http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/	[152]
	HPO	Human phenotype ontology database: providing a standardized vocabulary of phenotype of human disease	Phenotype retrieval	http://www.human-phenotype-ontology.org/	[153]
C	STITCH	Chemical-protein interactions database: providing known and predicted interactions of chemicals and proteins	Chemical-protein interaction retrieval	http://stitch.embl.de/	[154]
	DrugBank	A knowledge base for drugs, drug actions, and drug targets	Comprehensive analysis for approved drugs	http://www.drugbank.ca/	[19]
	ChEMBL	A database of bioactive drug-like small molecules, which contains 2 D structures, calculated properties, and abstracted bioactivities	Ingredient and drug chemoinformatics information retrieval	https://www.ebi.ac.uk/chembl/	[20]
	MMsINC	A large-scale chemoinformatics database	Ingredient and drug chemoinformatics information retrieval	http://mms.dsfarm.unipd.it/MMsINC/search/	[155]
	CB	A comprehensive chemical structures database	Ingredient and drug chemoinformatics information retrieval	http://www.chemicalbook.com/	[156]
	ChemProt	A comprehensive disease-chemical biology database	Chemical-protein interaction analysis	http://www.cbs.dtu.dk/services/ChemProt-2.0/	[157]
	LookChem	A comprehensive chemical structures database	Ingredient and drug chemoinformatics information retrieval	http://www.lookchem.com/	[158]
	ChemSpider	A chemical structure database providing structures, properties, and associated information of compound	Ingredient and drug chemoinformatics information retrieval	http://www.chemspider.com/	[159]
T	HIT	A comprehensive and fully curated database for linking herbal active ingredients to targets	Herbal ingredients' targets identification	http://lifecenter.sgst.cn/hit/	[160]
	CHMIS-C	A comprehensive herbal medicine information system for cancer	Comprehensive analysis for ingredient target of cancer	http://sw16.im.med.umich.edu/chmis-c/	[161]
	TD@T	TCM Database@Taiwan: providing chemical composition of Chinese medicinal herb including two- and three-dimensional structures of each TCM constituent	TCM medical compound retrieval	http://tcm.cmu.edu.tw/	[162]
	TCMGeneDIT	A database for associated traditional Chinese medicine, gene and disease information using text mining	Comprehensive analysis for ingredient-gene disease-effect of TCM	http://tcm.lifescience.ntu.edu.tw/	[163]
	TCM-ID	Traditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredients	TCM formula and medical compound retrieval	http://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid_ns.asp	[164]
	TCMID	Traditional Chinese medicine integrated database: a comprehensive database to provide information on drug-herb and its ingredient, prescription, target, and disease	Comprehensive analysis for TCM biological sciences	http://www.megabionet.org/tcmid/	[21]
	TcmSP	Traditional Chinese medicine systems pharmacology database and analysis platform: providing information on relationships between drugs, targets, and diseases	Comprehensive analysis for TCM biological sciences	http://tcmspnw.com	[165]
	SIRC-TCM	Traditional Chinese medicine information database: providing information on formulae, medicinal herbs, and herbal ingredients	TCM formula and medical compound retrieval	http://www.tcm120.com/1w2k/tcm_species.asp	[166]

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