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[Gofriends] [Reactome-announce] Reactome version 28 released

Lisa Matthews lmatthews.nyumc at gmail.com
Tue Mar 31 14:10:00 PDT 2009


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
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 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
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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