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[Gofriends] [Reactome-announce] Reactome version 25 released

D'Eustachio, Peter Peter.D'Eustachio at nyumc.org
Tue Jul 1 10:26:12 PDT 2008


Version 25 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 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 additions to curated content include the pathway topics: An expanded and reorganized pathway module for biological oxidations along with the pathway topics: glutamate neurotransmitter release cycle, beta cell development, and integrin cell surface interactions. The pathway topics updated with new curated events include: apoptosis - regulatory reactions, metabolism of amino acids - ODC regulation, metabolism of vitamins, NGF signaling, and lipid metabolism - HDL synthesis. A new project annotating cellular transport events has been initiated.

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 expand the scope of pathway annotations in the Reactome model to more organisms can write to help at reactome.org. 

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 betwen 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 editorial at reactome.org.
For questions and comments please reply to this message or write to help at reactome.org.

 
-The Reactome team

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