What does Reactome contain?

Reactome aims to represent all human biological processes as interconnected molecular events or ‘reactions’. Reactome broadly defines the term ‘reaction’ to include any molecular event in biology, such as binding, phosphorylation, catalysed biochemical events, spontaneous molecular events and transport. Every reaction stored in Reactome defines the precise form of the molecules that participate in the reaction and the cellular compartment in which the reaction takes place. Reactions can be considered as ‘steps’ in a pathway. Pathways are represented as diagrams containing a series of interconnected events, often organised into sub-pathways.

Quality control and attribution are key features of the data in Reactome. Pathways are authored by expert biologists and independently peer reviewed before inclusion. Reactions have literature citations that experimentally verify the described event in human reagents. When experiments are performed in model organisms, the event is inferred to occur in humans subject to reviewer approval.

Pathway and reaction information is provided in various graphical formats including textbook-style figures, ordered hierarchical trees and SBGN networks (Figure 1). Examples of pathways available in Reactome include immune system signalling, the cell cycle, apoptosis, and the host-parasite interactions of HIV.  These manually curated human pathways are used as templates to infer equivalent pathways in 15 other species, ranging from commonly-used model organisms such as mice to more distant species like yeast. 

Reactome uses primary external sources and extensively cross-references many other relevant sources of biological, chemical and literature information. Primary external references include: UniProt for proteins; ChEBI for small molecules; NCBI Taxonomy IDs for species; Gene Ontology (GO) terms for catalytic activity, cellular compartment and biological process.

In the latest version (v74), Reactome contains 52.6% of the 20,296 predicted human protein-coding genes. The manual curation effort to provide reliable information to users is an ongoing process and the coverage is expected to increase with new knowledge. Reactome data and software are open source, freely available to download and reuse from the Reactome website, under a Creative Commons Attribution 3.0 Unported licence.