|
| Database name | Short description | Web address |
|
| BioGRID [53] | A database of proteins, genes, and posttranslational modifications curated from the scientific literature | http://thebiogrid.org/ |
|
| BRENDA [54] | A database of molecular and biochemical information on enzymes | http://www.brenda-enzymes.org/ |
|
| ChEBI [55] | A database and ontology of molecular entities | http://www.ebi.ac.uk/chebi/ |
|
| ChemSpider [56] | A database of chemicals. It contains more than 34 million unique molecules from over 450 data sources | http://www.chemspider.com/ |
|
| DIP [57] | A manually curated database of experimentally elucidated interactions between proteins | http://dip.doe-mbi.ucla.edu/dip/ |
|
| EcoCyc [58] | A database of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways in Escherichia coli K-12, curated from the literature | http://ecocyc.org/ |
|
| GenBank [59] | A comprehensive database of publicly available nucleotide sequences | http://www.ncbi.nlm.nih.gov/genbank/ |
|
| Gene Ontology [60] | A database of annotations of genes and gene products for aiming to provide a common language to make data machine readable | http://geneontology.org/ |
|
| IntAct [61] | A database of molecular interaction derived from literature curation or direct user submissions | http://www.ebi.ac.uk/intact/ |
|
| InterPro [62] | A database for classification and analysis of protein sequences. It includes resources from PROSITE, HAMAP, Pfam, PRINTS, PRoDom, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, CATH-Gene3D, and PANTHER | http://www.ebi.ac.uk/interpro/ |
|
| KEGG [63] | An integrated database resource consisting of seventeen databases which are categorized into systems, genomic, chemical, and health information | http://www.genome.jp/kegg/ |
|
| KNApSAcK [64, 65] | An integrated database constituting a database of manually curated metabolite-plant species, metabolic pathways, biological activities, and so forth for metabolomics studies | http://kanaya.naist.jp/KNApSAcK_Family/ |
|
| MetaboLights [66] | A data repository for metabolomics experiments and obtained information | http://www.ebi.ac.uk/metabolights/ |
|
| MetaCyc [67] | A metabolic database containing metabolic pathways, enzymes, metabolites, and reactions from many organisms | http://metacyc.org/ |
|
| OMIM [68] | A database of diseases with human genes and genetic conditions | http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim |
|
| ProteomeScout [69] | A database of proteins and post-translational modifications | https://proteomescout.wustl.edu/ |
|
| PubChem [70] | A database of chemical molecules and their activities | http://pubchem.ncbi.nlm.nih.gov/ |
|
| Reactome [71, 72] | A database of human biological processes authored by expert biologists | http://www.reactome.org/ |
|
| RegulonDB [73] | A database of regulatory network and operon organization in Escherichia coli K-12 | http://regulondb.ccg.unam.mx/ |
|
| STRING [74] | A database of protein interactions (direct or indirect) derived from manual curation or text mining | http://string-db.org/ |
|
| TAIR [75] | A comprehensive database of information and materials of Arabidopsis thaliana | https://www.arabidopsis.org/ |
|
| TRANSFAC [76] | A manually curated database of eukaryotic transcription factors, their experimentally elucidated binding sites and DNA binding profiles. It needs a license for the up-to-date version | http://genexplain.com/transfac-db |
|
| TRANSPATH [77] | A database of mammalian signal transduction and metabolic pathways | http://genexplain.com/transpath-db |
|
| UniProtKB [78] | A database of functional information on proteins. It consists of UniProtKB/Swiss-Prot (manually annotated, reviewed) and UniProtKB/TrEMBL (automatically annotated, not reviewed) | http://www.uniprot.org/ |
|
