- Course overview
- Search within this course
- Why do we need a pathway database?
- When to use Reactome
- Who is Reactome for?
- Navigating Reactome
- Understanding the Pathway Browser
- Analysing data
- Programmatic access
- Contributing to Reactome
- Summary
- Try it yourself!
- Your feedback
- Get help and support on Reactome
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
What is Reactome?
Reactome is a free, manually curated knowledge base that provides a user-friendly platform to access and analyse information on molecular mechanisms of reactions and pathways. It provides highly detailed pathway diagrams of molecular processes and descriptions, available via the Reactome website and for download in standard formats such as BioPax and SBML.
Reactions
The basic unit of Reactome is a reaction, which is defined as any molecular event; including binding, phosphorylation, biochemical catalysis, molecular transport and spontaneous molecular events. These reactions can involve any biological molecule, but are typically between proteins and small molecules (chemical compounds).
Pathways
A pathway is defined as a series of connected reactions, with each individual reaction considered as a single step in the pathway. These are represented as pathways in detailed molecular diagrams. Examples of pathways include immune system signalling, the cell cycle and apoptosis. In Reactome, we create pathways using reactions as building blocks. Reactions are interconnected based on biological relevance resulting in the formation of pathways.
Curation
The key aspects of Reactome content are quality and attribution. Pathways are written by expert biologists and independently peer-reviewed before being included in the database. Reactions always cite scientific literature that experimentally verifies the described event. These manually curated human pathways are used as templates to computationally infer equivalent pathways in other species, including most commonly-used model organisms. More details of the curation process will be presented later in this course.
Reactome tools
In addition to being a reliable database of cellular pathways, Reactome also provides integrated tools for analysis of user data, for species comparison, distribution of reactions in various tissues and the extension of pathways with protein-protein interaction data. These are explained in the companion course Reactome: Tools for analysing biological pathways.