Table 2.

Online resources for network biology, network pharmacology, and gene enrichment analysis.

Sr. No.	Resources	Brief Summary	Application	Website/URL (Access Date: 7 October 2022)
1	BioCarta	Online maps of metabolic and signaling pathways	Database of gene interaction models	https://maayanlab.cloud/Harmonizome/dataset/Biocarta+Pathways
2	BioGRID	Biological General Repository for Interaction Datasets	Retrieval of protein–protein interaction network	http://thebiogrid.org/
3	C2Maps	Computational Connectivity Maps	Annotation of drug–protein pairs	http://bio.informatics.iupui.edu/
4	ChEMBL	Database of bioactive compounds	Retrieval of functional as well as binding information of active compounds	https://www.ebi.ac.uk/chembl/
5	ChemProt	Chemical–protein–disease annotation database	Analysis of interaction between chemical and protein	http://www.cbs.dtu.dk/services/ChemProt-2.0/
6	ChemSpider	Database of chemical structures	Retrieval of chemical structures	http://www.chemspider.com/
7	COGs	Clusters of Orthologous Gene	Classification of proteins on phylogenetic basis	https://www.ncbi.nlm.nih.gov/COG/
8	CPDB	Consensus Path DataBase	Molecular functional interaction database	http://cpdb.molgen.mpg.de/
9	Cytoscape	Database for network construction and visualization	Network analysis	https://cytoscape.org/
10	DAVID	Database for Annotation, Visualization & Integrated Discovery	Functional annotation	https://david.ncifcrf.gov/
11	DIP	Database of Interacting proteins	Analysis of protein–protein interaction network	http://dip.doe-mbi.ucla.edu
12	DisGeNET	Database of Interacting proteins	Pathway analysis	(https://www.disgenet.org/)
13	GeneCards	Database of human genes	For identification of disease-related genes	https://www.genecards.org/
14	Guess	Computer program for the analysis and visualization of networks	Network analysis	http://www.levmuchnik.net/Content/Networks/ComplexNetworksPackage.html
15	HAPPI	Human Annotated & Predicted Protein	Retrieval of protein–protein interaction network	http://bio.informatics.iupui.edu/HAPPI/
16	HPRD	Human Protein Reference Database	Retrieval of protein–protein interaction network	http://www.hprd.org/
17	InterPro	Integrative database of protein families	Collection of protein families	http://www.ebi.ac.uk/interpro/
18	KEGG	Kyoto Encyclopedia of Genes and Genomes	Pathway analysis	http://www.genome.jp/kegg/
19	MetaCoreTM	MetaCore (TM)	Pathway analysis	http://www.genego.com
20	Metascape	Computer program for the analysis and visualization of networks	Network and Pathway analysis	(https://metascape.org)
21	NetMiner	Computer program for the analysis and visualization of networks	Network analysis	http://graphexploration.cond.org/
22	NetPath	Network pathway analysis	Pathway analysis	http://www.netpath.org/
23	NetworkX	Computer program for the analysis and visualization of networks	Network analysis	http://www.analytictech.com/ucinet/
24	Network analyst	Computer program for the analysis and visualization of networks	Network analysis	(https://www.networkanalyst.ca/),
25	OPHID	Online predicted human interaction database	Retrieval of protein–protein interaction network	http://ophid.utoronto.ca
26	Pajek	Computer program for the analysis and visualization of network	Network analysis	http://pajek.imfm.si/doku.php
27	PDB	Protein Data bank	Retrieval of protein-related information	http://www.rcsb.org/pdb/
28	PharmGBK	Pharmacogenomics knowledge base	Analyze the genes’ response to drugs	http://www.pharmgkb.org/
29	Reactome	Database of pathways, reactions, and biological processes	Pathway analysis	http://www.reactome.org
30	SignaLink	Signaling pathway analysis resource	Pathway analysis	http://signalink.org/
31	STITCH	Search Tool for Interactions of Chemicals	Analysis of target–drug relationship and biological pathways	http://stitch.embl.de/
32	STRING	Search Tool for the Retrieval of Interacting Genes/Proteins	Retrieval of protein–protein interaction network	http://string-db.org/
33	SwissTargetPrediction	Estimate the macromolecular targets of a small molecule	Identification of compound-related genes	http://www.swisstargetprediction.ch/
34	Ucinet	Computer program for the analysis and visualization of networks	Network analysis	http://www.netminer.com/
35	UniProtKB	Universal protein knowledge database	Analysis of protein	http://www.uniprot.org/uniprot/