Reactome

Reactome is an online bioinformatics database of biology described in molecular terms. The largest set of entries refers to human biology, but Reactome covers a number of other organisms as well. It is an on-line encyclopedia of core human pathways - DNA replication, transcription, translation, the cell cycle, metabolism, and signaling cascades - and can be browsed to retrieve up-to-date information about a topic of interest, e.g., the molecular details of the signaling cascade set off when the hormone insulin binds to its cell-surface receptor, or used as an analytical tool for the interpretation of large data sets like those generated by DNA microarray analysis. The information in Reactome is provided by expert biologists and gathered from the published research literature, is peer-reviewed before release on the Reactome website, and is periodically updated.

Database Organization
In Reactome, human biological processes are annotated by breaking them down into series of molecular events. Like classical chemistry reactions each Reactome event has input physical entities (substrates) which interact, possibly facilitated by enzymes or other molecular catalysts, to generate output physical entities (products).

Reactions include the classical chemical interconversions of intermediary metabolism, binding events, complex formation, transport events that direct molecules between cellular compartments, and events such as the activation of a protein by cleavage of one or more of its peptide bonds. Individual events can be grouped together into pathways.

Physical entities can be small molecules like glucose or ATP, or large molecules like DNA, RNA, and proteins, encoded directly or indirectly in the human genome. Physical entities are cross-referenced to relevant external databases, such as UniProt for proteins and ChEBI for small molecules. Localization of molecules to subcellular compartments is a key feature of the regulation of human biological processes, so molecules in the Reactome database are associated with specific locations. Thus in Reactome instances of the same chemical entity in different locations (e.g., extracellular glucose and cytosolic glucose) are treated as distinct chemical entities.

The Gene Ontology controlled vocabularies are used to describe the subcellular locations of molecules and reactions, molecular functions, and the larger biological processes that a specific reaction is part of.

Database Content
The Reactome data set currently includes information about a diverse set of domains of molecular and cellular biology:


 * Apoptosis
 * Cell cycle checkpoints
 * Cell cycle, mitotic
 * DNA repair
 * DNA replication
 * Electron transport chain
 * Gene expression (mRNA transcription and processing)
 * Hemostasis
 * HIV infection
 * Influenza infection
 * Insulin receptor mediated signaling
 * Integration of pathways of energy metabolism
 * Lipid metabolism
 * Metabolism of amino acids and related nitrogen-containing molecules
 * Metabolism of glucose and other sugars
 * mRNA processing
 * Notch signaling
 * Nucleotide metabolism
 * Oxidative decarboxylation of pyruvate and TCA cycle
 * Post-translational modification of proteins
 * Transcription (RNA synthesis)
 * Translation (protein synthesis)
 * Xenobiotic metabolism

A calendar of annotation projects currently underway is also available

Tools
The database can be browsed and searched as an on-line textbook. An on-line users' guide is available. Users can also download the current data set or individual pathways and reactions in a variety of formats including PDF, BioPAX, and SBML.