Reactome: a knowledge base of biologic pathways and processes

Abstract

Reactome http://www.reactome.org, an online curated resource for human pathway data, provides infrastructure for computation across the biologic reaction network. We use Reactome to infer equivalent reactions in multiple nonhuman species, and present data on the reliability of these inferred reactions for the distantly related eukaryote Saccharomyces cerevisiae. Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets.

Figure 1

Workflow for authoring and curation of new pathways. Red arrows indicate the part of the process involving interactions between curators and outside experts; black arrows indicate interactions between curators and software engineers. DB, database; RCDB, release candidate database.

Figure 2

The Reactome author tool provides authors with a graphical user interface to describe pathways and their component reactions in a structured manner.

Figure 3

The Reactome home page. The bold arrow in the reaction map at top points to the tricarboxylic acid (TCA) cycle.

Figure 4

A reaction page.

Figure 5

Reactions colored according to the most distant species from Homo sapiens in which the reaction could be inferred. Warmer colors indicate reactions found in distantly related species; cooler colors indicate reactions inferred only in closely related species.