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Table 1 Data resources widely used in drug repositioning research

From: A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Drug repositioning strategy

Data resource

Description (as of January 2020)

Genome

ArrayExpress Ê61]

A repository of high-throughput functional genomics experiments data

Cancer Cell Line Encyclopedia (CCLE) [62]

A combination of gene expression, chromosomal copy number, and massively parallel sequencing data from human cancer cell lines

Database for Annotation, Visualization and Integrated Discovery (DAVID) [63]

A comprehensive set of functional annotation tools

Drug versus Disease (DvD) [64]

A platform for comparing drug and disease gene expression profiles retrieved from publicly available microarray data resources

Expression Atlas [65]

A tool to explore gene expression data across species and different biological conditions

Gene Expression Omnibus (GEO) [66]

A repository of gene expression profiles

Gene Set Enrichment Analysis (GSEA) [67]

A tool for interpreting gene expression data

Gene Signature Database (GeneSigDB) [68]

A repository of gene signatures data reported in the literature

Gene Ontology (GO) [69]

A repository of functional genomics

International Cancer Genome Consortium [70]

A repository of genomic data for many cancer types

Kyoto Encyclopedia of Genes and Genomes (KEGG) [71]

A repository of genome sequencing and high-throughput functional genomics experiments molecular datasets

Library of Integrated Network-based Cellular Signatures (LINCS) [72]

A catalog of gene expression data and how human cells respond to different genetic and environmental conditions

Molecular Signature Database (MsigDB) [73]

A repository of annotated gene sets and expression profiles

The Cancer Genome Atlas (TCGA) [74]

A repository of genomic data for more than 30 cancer types

The Connectivity Map (CMap) [75]

A collection of genome-wide transcriptional expression data

The Universal Protein Resource (UniProt) [76]

A repository of protein sequence and functional information

Phenome

ClinicalTrials.gov [77]

A repository of publicly and privately funded clinical studies from around the world

Side Effect Resource (SIDER) [78]

A repository of adverse drug reactions related to drugs. Information includes drug side effects and side effects classifications

Chemical structure

ChEMBL [79]

A repository of drug structural information, such as 3D structures, and abstracted biological activities, extracted from the scientific literature

Chemicalize [80]

A repository of chemical structure information

ChemSpider [81]

A repository of chemical structure information

DrugBank [82]

A repository of drug-related information, such as chemical structure for drugs

Drug Central [83]

A repository of drug-related information such as chemical structure and biological activities

PubChem [84]

A repository of chemical substances and their biological activities

Protein Data Bank (PDB) [85]

A repository of 3D shape of proteins and nucleic acids information

SWEETLEAD [36]

A repository of 2D and 3D drug chemical structure information, including approved and illegal drugs

The NCGC Pharmaceutical Collection (NPC) [86]

A collection of chemical structure information related to approved and investigational drugs

Therapeutic Target Database (TTD) [87]

A repository of drug-related information such as 3D structure, therapeutic class, and clinical development status

Phenome/genome

repoDB [88]

A repository of approved and failed drug-disease associations

Online Mendelian Inheritance in Man (OMIM) [89]

A repository of human genes and genetic phenotype information

The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) [90]

A repository of drug-related information such as drug labels, drug-gene associations, and genotype-phenotype relationships

Phenome/chemical structure

Drugs@FDA Database [91]

A repository of FDA approved drugs and related information