Table 1.
The investigated databases
| Category | Name | Description | Links | Ref. |
|---|---|---|---|---|
| Genome/Target | UCSC | A database with rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks | https://genome.ucsc.edu/ | 400 |
| GenBank | A database that contains publicly available nucleotide sequences for 400 000 formally described species | https://www.ncbi.nlm.nih.gov/genbank/ | 401 | |
| Connectivity Map | A database with genome-wide transcriptional expression data | https://portals.broadinstitute.org/cmap/ | 402 | |
| Ensembl | A database provides high-quality genome annotation across chordate species through a comprehensive set of methods | https://www.ensembl.org/index.html | 403 | |
| Gene Ontology | A database of functional genomics | http://geneontology.org/ | 404 | |
| Proteomics/Pathway | UniProt | A database with important collection of protein sequences and their annotation | https://www.uniprot.org/ | 405 |
| UniGene | A database with annotations for a majority of the human transcripts | https://www.ncbi.nlm.nih.gov/unigene/ | 406 | |
| UniRef | A database with cluster of protein sequence space based on sequence similarity | https://www.uniprot.org/uniref/query/ | 407 | |
| KEGG | A database with genome sequencing and high-throughput functional genomics experiments molecular datasets | https://www.kegg.jp/ | 408 | |
| STRING | A database with critical assessment and integration of protein-protein interactions | https://cn.string-db.org/ | 409 | |
| BiGRID | A database with archive of genetic and protein interactions | https://thebiogrid.org/ | 410 | |
| Proteomics/Pathway | HAPPI | A comprehensive database covering human PPI data | http://discovery.informatics.uab.edu/HAPPI | 411 |
| Reactome | A database with critical assessment and integration of protein-protein interactions | https://reactome.org/ | 412 | |
| The Human Protein Atlas | A database with critical assessment and integration of protein-protein interactions | http://www.proteinatlas.org/ | 413 | |
| Disease Database | The Cancer Genome Atlas | A database with genomic data for more than 30 cancer types | https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga | 414 |
| Cancer Cell Line Encyclopedia | A database pf large, annotated cell-line collections | https://portals.broadinstitute.org/ccle | 415 | |
| OMIM | A database with comprehensive compendium of information on human genes and genetic disorders | https://www.omim.org/ | 416 | |
| GEO | A database of gene expression profiles | https://www.ncbi.nlm.nih.gov/geo/ | 417 | |
| LINCS | A database of gene expression data and how human cells respond to different genetic and environmental conditions | https://lincsproject.org/ | 418 | |
| Phenome | RepoDB | A repository of approved and failed drug-disease associations | http://apps.chiragjpgroup.org/repoDB/ | 419 |
| Clinical Trials | A database of publicly and privately funded clinical studies | https://www.clinicaltrials.gov/ | 420 | |
| Drugs @FDA Database | A database of FDA approved drugs and related information | https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm | 421 | |
| DrugBank | A database of drug-related information | https://go.drugbank.com/ | 421 | |
| Drug database | STITCH | A database integrates data sources for 430 000 chemicals into a single, easy-to-use resource | http://stitch.embl.de/ | 422 |
| SFINX | A database with drug-drug interactions and related information | http://sfinx.ugent.be/ | 423 | |
| TTD | A database of drug-related information such as 3D structure, therapeutic class, and clinical development status | http://db.idrblab.net/ttd/ | 424 | |
| SIDER | A database of adverse drug reactions related to drugs. | http://sideeffects.embl.de | 425 | |
| Drug versus Disease | A database with comparison of drug and disease gene expression profiles from public microarray repositories | https://omictools.com/dvd-tool | 426 |