REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.
The rationale behind Reactome is to convey the rich information in the visual representations of biological pathways familiar from textbooks and articles in a detailed, computationally accessible format. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer theraputics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, innate and acquired immune function, transcriptional regulation, apoptosis and disease.
Reactome provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. Visualisation of Reactome data is facilitated by the Pathway Browser, a Systems Biology Graphical Notation (SBGN)-based interface, that supports zooming, scrolling and event highlighting. It exploits the PSIQUIC web services to overlay molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, ChEMBL, BioGRID and iRefIndex.
Pathway Analysis tools analyze user-supplied datasets permitting ID mapping, pathway assignment and over-representation or enrichment analysis. The curated human pathway data are used to infer orthologous events in 20 non-human species including mouse, rat, chicken, worm, fly, yeast, plant and bacteria. Species Comparison tool allows users to compare predicted pathways with those of human to find reactions and pathways common to a selected species and human. Additional pathway databases based upon the Reactome data model have been created by collaborating groups for the fruit fly, the chicken, and the plant Arabidopsis.
All data and software are freely available for download. Interaction, reaction and pathway data are provided as downloadable flat, MySQL, BioPAX, SBML and PSI-MITAB files and are also accessible through our Web Services APIs. Software and instructions for local installation of the Reactome database, website, and data entry tools (curator and author tools) are also available to support independent pathway curation.
Reactome is an all-inclusive resource of human pathways for basic research, genome analysis, pathway modeling, systems biology and education. If you would like to learn more about Reactome, please refer to the Reactome papers, published in Methods in Molecular Biology and Nucleic Acids Research. A tutorial paper, published in Proteomics, provides worked examples.