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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]