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[Gofriends] [Reactome-announce] Version 30 of the Reactome Knowledgebase has been released

Steven Jupe sjupe at ebi.ac.uk
Wed Sep 30 04:38:00 PDT 2009


Version 30 of the Reactome Knowledgebase has been released and is 
accessible at http://www.reactome.org.
*
New and Updated Topics*

Version 30 includes the new topic_ _Cell-cell adhesion systems 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19331.1> 
with annotations of adherens junctions interactions and tight junction 
interactions. Pathway topics revised and updated to incorporate new 
events include the GPCR signaling pathway (Downstream events in GPCR 
signaling 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19184.1> 
and the Olfactory signaling pathway), Signaling in immune system 
(Costimulation by the CD28 family) 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_19344.1>, 
Transmembrane transport of small molecules (SLC-mediated transmembrane 
transport) 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19118.1>, 
Membrane Trafficking (Clathrin derived vesicle budding) 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19187.1>, 
Axon Guidance (Signaling by Robo receptor) 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19351.1> 
and Gene Expression (Nuclear receptor pathway). New metabolism topics 
include Sphingolipid metabolism 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19323.1> 
and Regulation of Lipid Metabolism by Peroxisome proliferator-activated 
receptor alpha (PPARalpha) 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_19241.1>. 
Diabetes pathways now cover Synthesis, Secretion, and Deacylation of 
Ghrelin 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_19189.1> 
and Regulation of Insulin Secretion by Free Fatty Acids 
<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19375.1>.

Pathway annotations from Reactome are now available through NCBI 
BioSystems 
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=biosystems&Cmd=DetailsSearch&Term=reactome%5Bsourcename%5D>.

*Reactome User Survey*
Reactome is committed to providing access to high-quality pathway 
information and useful data analysis tools. With this in mind, we are 
actively soliciting comments from the research community in order to 
assess community needs. We are interested to hear about your experience 
with Reactome, and would like to know about your background and research 
interests so that we can continue to improve the Reactome site and 
tools. Please help us by completing this short survey at: 
http://tinyurl.com/l48zzq

*About Reactome*
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.

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.

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.

-- 
Dr. Steven Jupe,
Reactome Group,
European Bioinformatics Institute,
Hinxton,
Cambridge.
CB10 1SA
UK

(01223) 492673

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