Skip to main content

Table 2 Some of the most interesting databases for systems biology

From: Trends in modeling Biomedical Complex Systems

KEGG Kyoto Encyclopedia of Genes and Genomes
Incudes data on genes and proteins, endogenous and exogenous ligands, diagrams of interaction and reaction networks, and hierarchies and relationships of various biological objects
http://www.genome.ad.jp/kegg/
BRENDA The Comprehensive Enzyme Information System
Information on enzymes and their function
http://www.brenda-enzymes.org/
BioCyc Collection of Pathway/Genome Databases
Derived from literature (EcoCyc, MetaCyc) or computed (some 500 databases, maìnly for bacteria, but also incl. HumanCyc and MouseCyc, about 20 of which are partially corrected by volunteers)
http://biocyc.org/
CSNdb Cell Signaling Networks Database
Information on molecules, sequences, structures, functions, and reactions transferring cellular signals in human cells
http://geo.nihs.go.jp/csndb/
BioBase Many commercial databases offered on-line with reduced functionalities
Includes TRANSFAC (transcription factors and their binding sites and regulated genes) and TRANSPATH (molecules involved in signal transduction pathways and related reactions)
http://www.gene-regulation.com/pub/databases.html
BioModels A Database of Annotated Published Models
Includes mathematical models published in literature. Models are annotated and linked to esternal databases and to literature.
http://www.ebi.ac.uk/biomodels-main/
BioUML BioUML is framework for systems biology.
It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.
http://www.biouml.org/
CCDB The CCDB is a cell cycle database
Is an integrated data warehouse database for systems biology modelling and cell cycle analysis
http://www.itb.cnr.it/cellcycle
PID The Pathway Interaction Database
A curated database of biomolecular interactions and key cellular processes assembled into signaling pathways focused on human data. Human pathways from Reactome are also included. PID is a collaboration between the NCI and Nature Publishing Group.
http://pid.nci.nih.gov/PID/
Reactome A curated knowledgebase of biological pathways Information is authored by experts and curated by internal staff. It includes links to external data sources, like KEGG Compound, ChEBI, PubMed, and GO. http://www.reactome.org/