Reactome: A Curated Pathway Database

Documentation

A brief overview of our data model and orthology–based electronic inference of non–human events will provide a basis for describing the potential uses for the Reactome. The user documentation also describes some of the technical aspects of the Reactome website and data. Instructions are also available on how to link to and reference Reactome.

User Guide is an overview of the Reactome database of biological pathways and processes and its web site. This is not a comprehensive guide, but should provide you with enough information to browse the database and use its principal tools for data analysis.

Data Model in Reactome uses a frame-based knowledge representation. The data model consists of classes (frames) that describe the different concepts (e.g., reaction, molecule). These classes are hierarchically arranged into classes and parental superclasses.

Orthology Prediction includes information about how computationally inferred pathways and reactions are created for 20 non–human species, including Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, and Escherichia coli. These species represent more than 4,000 million years of evolution and span the main branches of life.

Object/Relational Mapping  explains the tables in the Reactome relational database.

Wiki is part of our online documentation and curation resources.

Linking to Reactome can be achieved by creating URLs containing the name of and an identifier from an “external” database.

Referencing Reactome will describe how to cite Reactome publications and website pages in your own papers.