Users

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Welcome to the Reactome Wiki User documentation space. Documents in this area are here to help the user get started, learn more about Reactome, and take advantage of Reactome more advanced features. If you are just getting started with Reactome. We suggest that review the Reactome user's guide. The guide contains all of the information to get you started with Reactome.

User's Guide

One of our most valuable user documents is the Reactome User's Guide. Please look through the guide and let us know if we can help. The guide starts with an explanation of the concepts that the Reactome data model is based upon. After that the guide takes the reader through examples of the information and the tools that are available in the Reactome data set. It now included videos, which we hope to update on a regular basis. Please let us know if the guide needs something new!

Naming Conventions

Reactome annotation takes advantage of a number of standardized conventions that biologists and bioinformatacists have developed. These names appear throughout the Reactomedataset. Reactome is in the process of standardizing names for pathway events (reactions) and the molecules and groups of molecules that participate in these events. For more information please refer to this publication and read the information provided below.

List of Abbreviations

The abbreviations used for small molecules in Reactome are available here.

Systematic Peptide Names

A description of the process used to create systematic peptide names in Reactome can be found here.

Reaction Naming by Function

Reactions can be grouped into classes, based on the nature of the event taking place, e.g. binding, phosphorylation. For events with a protein catalyst we have constructed a 'verb from GO term' table that we will use to identify a verb that will be used in the name of the reaction. This table is available here.

Video Tutorials

The Reactome Team has produced a series of user video tutorials designed to help users get the most out of Reactome's resources. Please note that features described may change over time as improvements are made.

The series is available here

PSI-MITAB Interactions

Our PSI-MITAB Interactions Document details Reactome's implementation of the HUPO Proteomics Standards Initiative (PSI)using the MITAB tab delimited data exchange format.

Reactome FI Cytoscape Plugin

Reactome Cytoscape Plugin is designed to find pathways and network patterns related to cancer and other types of diseases. This plugin accesses the Reactome pathways stored in the database, help you to do pathway enrichment analysis for a set of genes, visualize hit pathways using manually laid-out pathway diagrams directly in Cytoscape, and investigate functional relationships among genes in hit pathways. The plugin can also access the Reactome Functional Interaction (FI) network, a highly reliable, manually curated pathway-based protein functional interaction network covering over 50% of human proteins Reactome Functional Interaction (FI) Cytoscape Plugin was designed to find network patterns related to cancer and other types of diseases. For an example how we use Reactome FIs for cancer data analysis, please see our publication. For details on how to use this Cytoscape plugin, please see Reactome FI Cytoscape Plugin.

Citing Reactome

  • Please find guidance and examples for how to cite Reactome here.
  • A list of scientific works that cite Reactome publications can be found here.
  • A list of scientific works that cite Reactome publications organized by biological and functional topic can be found here.
  • The list of Reactome publications produced by Reactome Team members can be found here.

Digital Object Identifiers (DOIs)

For each discrete module that an expert/author provides Reactome a Digital Object Identifier (DOI) is generated. The DOI can be used to cite this work in Reactome. You can read more about how we use and maintain DOIs in Reactome here.