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Type# | Name | Description | Application | Webpage | Reference |
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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] |
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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] |
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