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Reactome Knowledgebase version 28 PDF Print E-mail
Written by Sebastian Bassi   
Thursday, 02 April 2009 02:05

Version 28 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org.

Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team (Lincoln Stein's group at OICR/CSHL, Ewan Birney's group at the European Bioinformatics Institute, and Peter D'Eustachio's group at NYU). Reactome covers human biological processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO).

The web interface allows users to view the curated annotations of human biological processes and orthology-based electronic inferences from these annotations for 22 other species.

New topics in Version 28 include signaling by PDGF and striated muscle contraction as well as chaperonin-mediated protein folding and post-chaperonin tubulin folding (grouped with translation and post-translational protein modification into a new "Metabolism of protein" super-pathway). Pathways updated with new curated events include GPCR signaling (olfactory signaling, amine and hormone ligand-binding receptor events and additional peptide ligand-binding receptor events) synaptic transmission (Electrical transmission across Gap Junctions), hemostasis and signaling in the immune system (Tie2 signaling events and Basigin interactions). New metabolism topics include peroxisomal metabolism of lipids and glyoxylate and integration of energy metabolism (glucose regulation of insulin secretion).

A preliminary list of Reactome spin-offs specific to non-human model organisms with contact information is available from http://www.reactome.org/other_reactomes.html. Users interested in contributing to these endeavors or expanding the scope of pathway annotations in the Reactome model to more organisms can write to This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

The pathway visualization tool (beta version) is available on the website from the Tools menu. A new look Search tool with features of popular search engines has been implemented. Please try these tools and let us know your comments

Pathway annotations from Reactome are now incorporated into the Pathway Interaction Database (PID), a collaborative project between the US National Cancer Institute and Nature Publishing Group. Access to 703 Reactome curated pathways and a primer for using Reactome data are available from PID's website at http://pid.nci.nih.gov/

Updated release statistics and the Editorial Calendar are available. Data download including database dumps and protein-protein interaction datasets are available from the download page on the website. Reactome data can be exported in SMBL, Protégé, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused. Users can subscribe to Reactome announcement list from the webpage at http://mail.reactome.org/mailman/listinfo/reactome-announce.

Reactome is seeking expert help for the curation of new modules. The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes, and to integrate these with other processes already in Reactome. We are seeking new author-collaborators. If you're interested, or would like more information about our data acquisition process, please contact us at This e-mail address is being protected from spambots. You need JavaScript enabled to view it . For questions and comments please reply to this message or write to This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

-The Reactome team