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Table 2 Overview of databases containing biomedical knowledge

From: New perspectives: systems medicine in cardiovascular disease

Name Description URL Reference
Molecular Information
 GenBank The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences [58]
 UniProt Provide a comprehensive and freely accessible resource of protein sequence and functional information. [59]
 Ensembl A genome browser for vertebrate genomes that supports cross-species research in genomics, evolution, sequence variation and transcriptional regulation. [107]
Signaling Pathways
 Reactome A free, open-source, curated and peer reviewed pathway database. [61]
 NDEx - the Network Data Exchange An online commons to upload, share, and publicly distribute networks. Networks receive globally unique accession IDs and can be stored for private use, shared in pre-publication collaboration, or released for public access. Includes Pathway Interaction Database (NCI) and the Cancer Cell Maps Initiative databases. [62]
 WikiPathways A database of biological pathways maintained by and for the scientific community using a wiki approach. [64]
Metabolic Pathways
 MetaCyc Database of non-redundant, experimentally elucidated metabolic pathways. It is curated from the scientific experimental literature and contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes [108]
 KEGG - Kyoto Encyclopedia of Genes and Genomes KEGG includes graphical diagrams and data of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways.   [63]
Protein-Protein Interactions
 IntAct – molecularinteractiondatabase Database system and analysis tools for molecular interaction data derived from literature curation or direct user submissions [67]
 BioGRID – biological general repository for interaction datasets Interaction repository with data compiled through comprehensive curation, containing protein and genetic interactions, chemical associations and posttranslational modifications [109]
 STRING – protein–proteininteractionnetworks Database of known and predicted protein–protein interactions, including direct (physical) and indirect (functional) associations [68]
Other Interaction Knowledge
 DrugBank Combines detailed drug data with comprehensive drug target and drug action information [110]
 PharmGKB - Pharmacogenetics Knowledge Base Contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies [111]
 DiseaseConnect Comprehensive knowledge base on mechanism-based disease connectivity [112]
 Connectivity Map A resource that uses transcriptional expression data to probe relationships between diseases, cell physiology, and therapeutics. [113]
 OMIM - Online MendelianInheritance in Man A comprehensive knowledge base of human genes and genetic disorders compiled to support human genetics research and education. [114]