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[Gofriends] [Reactome-announce] Reactome version 33 released
lmatthews.nyumc at gmail.com
Fri Jun 18 08:20:18 PDT 2010
Version 33 of the Reactome Knowledgebase has been released and is accessible
*New and Updated Topics*
Version 33 includes the new topic Chromosome maintenance, regrouping
existing annotations for Telomere maintenance with new annotations under
Nucleosome assembly (Deposition of New CENPA-containing Nucleosomes at the
Centromere). Topics in this release that contain new or revised and updated
events include: Axon Guidance (L1CAM interactions and Netrin-1 signaling),
Synaptic Transmission (Activation of Nicotinic Actetylcholine receptors),
Transmembrane transport of small molecules (SLC-mediated transmembrane
transport), Metabolism of proteins (N-Glycan biosynthesis), Diabetes
pathways (Binding of RNA by Insulin-like Growth Factor-2 mRNA Binding
Proteins and Unfolded Protein Response), Signaling in the immune system
(IL-1 signaling), and Signaling by GPCR (Olfactory Signaling Pathway).
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, RSCB
Protein Data Bank, Comparative Toxicogenomics Database, DockBlaster, BioGPS,
and dbSNP , KEGG, ChEBI and Gene Ontology (GO) .The web interface allows
users to view the curated annotations of human biological processes and the
Ensembl Compara orthology-based electronic inferences from these annotations
for 20 other species.
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, PSI MITAB, Protégé, and BioPAX Level 3 (Release 1.0) and
Level 2 format. Like everything in Reactome, these downloaded and exported
materials can be reused. Users can subscribe to Reactome announcement list
from the webpage *
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*.
*Recent Reactome publications*
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. (2010) R
spider: a network-based analysis of gene lists by combining signaling and
metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. Jun
2. [Epub ahead of print]. *PubMed<http://www.ncbi.nlm.nih.gov/pubmed/20519200>
Wu G, Feng X, Stein L. (2010) A human functional protein interaction network
and its application to cancer data analysis. Genome Biol. 11(5):R53.
*Other Reactome projects*
A preliminary list of projects now underway to extend Reactome pathway
curation spin-offs specific to non-human model organisms with contact
information is available from
Users interested in contributing to these endeavors or expanding them scope
of pathway annotations in the Reactome model to more organisms can write to
*help at reactome.org*.
*Reactome Outreach *
Reactome Outreach takes on a variety of forms, such as public talks,
lectures, visiting schools and colleges and supporting science events.
Education is a major focus of Reactome's community outreach and aims to
inform biologists, clinicians, and bioinformaticians about what Reactome can
do. Reactome training teaches new and current users how to use Reactome
resources to help meet the efforts of their organizations, groups, or
specific audiences. Training and outreach is managed by Robin Haw; please
contact him at *outreach at reactome.org* if you have an outreach request.
The development of Reactome is supported by a grant from the US National
Institutes of Health (P41 HG003751), EU grant LSHG-CT-2005-518254 "ENFIN",
and the EBI Industry Programme.
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