Why do we need Reactome?
Life at the molecular level is an intricate network of protein interactions and biochemical reactions. A pathway is a small part of this network – a series of connected events, typically characterised by the product or biological outcome. Researchers have defined many biological pathways. These pathways can be accessed via the scientific literature, textbooks, or electronic databases, but the information is of variable quality and is largely unavailable for computational re-use. Reactome provides access to a curated, quality-assured slice of this information, available as diagrams and descriptions on the Reactome website and as downloadable pathways in standard formats such as BioPAX and SBML.
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 using human reagents, or if these are not available, reagents from model organisms (as long as the author and reviewer agree that it is valid to infer that the equivalent event can take place in humans).
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 20 other species, including commonly-used model organisms. The EGFR signalling pathway is shown below in Figure 1.
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.
Figure 1 EGFR signalling pathway. EGFR is a tyrosine kinase receptor that plays a key role in the regulation of cell division and cell death.