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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 http://www.ncbi.nlm.nih.gov/genbank/ [58]
 UniProt Provide a comprehensive and freely accessible resource of protein sequence and functional information. http://www.uniprot.org/ [59]
 Ensembl A genome browser for vertebrate genomes that supports cross-species research in genomics, evolution, sequence variation and transcriptional regulation. http://www.ensembl.org/ [107]
Signaling Pathways
 Reactome A free, open-source, curated and peer reviewed pathway database. http://reactome.org/ [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. http://www.ndexbio.org [62]
 WikiPathways A database of biological pathways maintained by and for the scientific community using a wiki approach. http://www.wikipathways.org [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 http://metacyc.org [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 http://www.ebi.ac.uk/intact [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 http://thebiogrid.org [109]
 STRING – protein–proteininteractionnetworks Database of known and predicted protein–protein interactions, including direct (physical) and indirect (functional) associations http://string-db.org [68]
Other Interaction Knowledge
 DrugBank Combines detailed drug data with comprehensive drug target and drug action information http://www.drugbank.ca/ [110]
 PharmGKB - Pharmacogenetics Knowledge Base Contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies http://www.pharmgkb.org/ [111]
 DiseaseConnect Comprehensive knowledge base on mechanism-based disease connectivity http://disease-connect.org/ [112]
 Connectivity Map A resource that uses transcriptional expression data to probe relationships between diseases, cell physiology, and therapeutics. https://clue.io/ [113]
 OMIM - Online MendelianInheritance in Man A comprehensive knowledge base of human genes and genetic disorders compiled to support human genetics research and education. http://www.ncbi.nlm.nih.gov/omim/ [114]