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Reactome – a knowledgebase of human biological pathways

Bijay Jassal¹, Esther E. Schmidt¹, Guanming Wu², Imre Vastrik¹, David Croft¹, Bernard de Bono¹, Gopal Gopinath², Marc Gillespie², Steven Jupe¹, Gavin O’Kelly¹, Lisa Matthews³, Phani V. Garapati¹, Michael Caudy², Alexander Kanapin², Bruce May², Shahana Mahajan³, Ewan Birney¹, Peter D’Eustachio³ & Lincoln Stein²

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1. European Bioinformatics Institute
2. Cold Spring Harbor Laboratory
3. NYU School of Medicine

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Document Type:

Poster

Date:

Received 29 April 2009 09:05 UTC; Posted 03 May 2009

Subjects:

Chemistry, Genetics & Genomics, Immunology, Molecular Cell Biology, Bioinformatics

Tags:

• data analysis
• database curation
• open source
• Data Mining
• open access
• Human
• pathways
• crosslinking
• peer-reviewed
• authored
• protein
• KEGG
• UniProtKB
• GO
• Ensembl
• EntrezGene

Abstract:

Reactome (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.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Jassal, Bijay, Schmidt, Esther, Wu, Guanming, Vastrik, Imre, Croft, David, de Bono, Bernard, Gopinath, Gopal, Gillespie, Marc, Jupe, Steven, O’Kelly, Gavin, Matthews, Lisa, Garapati, Phani, Caudy, Michael, Kanapin, Alexander, May, Bruce, Mahajan, Shahana, Birney, Ewan, D’Eustachio, Peter , and Stein, Lincoln. Reactome – a knowledgebase of human biological pathways. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3200.1> (2009)

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