Table 1.

Resources of the most common biological networks that were used in the reviewed methods. We report the name, a short description, the website and which of the reviewed methods use them. The description indicates if the resource is a dataset (and therefore easy downloadable) or if it is a database accessible via web interface. The DrugBank database is included in two sections since it is used to collect the drug chemical structure and the information about DDIs.

	Database	Description & website		References
	Drug Repurposing Hub [22]	Curated database of FDA-approved drugs and clinical as well as pre-clinical chemical compounds		[23]
		https://clue.io/repurposing
	DrugBank [24]	Database of drug structure, drug-target information and DDIs		[25–28]
		https://www.drugbank.ca
	MUTAG [29]	Benchmark dataset reporting the molecular structure of 188 nitro compounds labeled as mutagenic & non-mutagenic on a bacterium		[30]
		http://graphlearning.io/
Chemical compounds	National Cancer Institute 1/109 (NCI1, NCI109) [31]	Benchmark datasets reporting the chemical structure of compounds showing activity against some cancer cell lines		[30]
		http://graphlearning.io/
	PubChem’s BioAssay database (PCBA) [32]	Benchmark dataset of small molecules reporting their high-throughput-measured biological activities		[33]
		http://moleculenet.ai/
	Predictive Toxicology Challenge (PTC) [34]	Benchmark dataset reporting the structure of 344 compounds classified as carcinogenic and non-carcinogenic on rats		[30]
		http://graphlearning.io/
	Quantum-Machine 9 (QM9) [35]	Dataset of small organic molecules with the structure & various properties		[36]
		http://quantum-machine.org/datasets
	Tox21 [37]	Benchmark dataset of compounds & their toxicity on some biological targets		[33]
		http://graphlearning.io/
	DrugBank [38], [39]	Database of drug structure, drug-target information and DDIs		[25], [40], [27], [41], [28]
		https://www.drugbank.ca
DDI Networks	Twosides [42]	Comprehensive database of DDIs with respect to millions of adverse reactions		[43–46]
		http://tatonettilab.org/offsides/
Gene regulatory networks	DREAM4 [47], [48]	Datasets of gene expression time series data & associated ground truth GRN structure from the DREAM4 100-gene in silico network inference challenge		[49]
		http://gnw.sourceforge.net/dreamchallenge.html
Metabolic networks	BioModels [50]	Database of mathematical models of biological & biomedical systems, such as the Systems Biology Markup Language models of metabolic pathways		[51]
		https://www.ebi.ac.uk/biomodels/
	Kyoto Encyclopedia of Genes and Genomes (KEGG) [53]	Biological pathways database for multiple model organisms		[52]
		https://www.genome.jp/kegg/
	Biological General Repository for Interaction	Curated database of PPIs for multiple model organisms		[54–56], [28]
	Datasets (BioGRID) [57]	https://thebiogrid.org
	Database of Interacting Proteins (DIP) [58]	Curated database of PPIs for multiple model organisms		[59], [60]
		http://dip.doe-mbi.ucla.edu
	High-quality INTeractomes (HINT) [61]	Curated database of PPIs for multiple model organisms		[62]
		http://hint.yulab.org/
PPI networks	Human Integrated PPI	Web tool to generate context-specific human PPI networks		[60]
	rEference (Hippie) [63]	http://cbdm-01.zdv.uni-mainz.de/∼mschaefer/hippie
	Human Protein Reference Database (HPRD) [66], [67]	Database of human PPIs from high-throughput experiments		[59], [64], [40], [28], [65]
		www.hprd.org
	Molecular INTeraction (MINT) [68]	Curated database of PPIs for multiple model organisms		[28]
		https://mint.bio.uniroma2.it/
	Protein Interaction Network Analysis (PINA) [69]	Curated database of PPIs for multiple model organisms		[28]
		https://omics.bjcancer.org/pina
	STRING [70]	Database of PPIs and tool for obtaining functional enriched PPI networks for multiple model organisms		[71], [55], [72], [41], [46]
		https://string-db.org
	Dobson & Doig (D&D) [73]	Benchmark dataset of 1178 protein structures		[30]
		https://graphlearning.io
Proteins	Protein Data Bank (PDB) [74]	Database of 3-dimensional structure of proteins for multiple model organisms		[75], [76], [26]
		https://www.rcsb.org/