Abstract

AbstractReactome ("http://www.reactome.org":http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms. Reactome instances are cross-referenced to corresponding ones in databases including EntrezGene, OMIM, Ensembl, UniProt, the UCSC Genome Browser, KEGG, ChEBI, and Gene Ontology.

Highlights

  • Expert and curator create outline of new pathway Expert provides the biological information Curator enters information into database Reviewer checks biological correctness

  • Its robust data model describes life processes ranging from metabolism to signal transduction and the cell cycle

  • Combined queries across UniProt, Ensembl, Wormbase and PRIDE BioMarts

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Summary

Introduction

Reactome - a knowledgebase of human biological pathways Nature Precedings : doi:10.1038/npre.2009.3200.1 : Posted 29 Apr 2009 www.reactome.org Bijay Jassal1, Esther E Schmidt1, Guanming Wu2,4, Imre Vastrik1, David Croft1, Bernard de Bono1, Gopal Gopinath2, Marc Gillespie2,4, Steven Jupe1, Gavin O’Kelly1, Lisa Matthews3, Phani V Garapati1, Michael Caudy2,4, Alexander Kanapin2,4, Bruce May2,4, Shahana Mahajan3, Ewan Birney1, Peter DEustachio3, Lincoln Stein2,4

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