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[Gofriends] [Reactome-announce] Reactome version 29 released

Lisa Matthews lmatthews.nyumc at gmail.com
Wed Jun 24 14:23:03 PDT 2009


Version 29 of the Reactome Knowledgebase has been released at *
http://www.reactome.org*.

Reactome is a free, online, open-source, curated resource of core pathways
and reactions in human biology. Information is authored by expert biological
researchers, maintained by the Reactome editorial staff and cross-referenced
to the NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap
Genome Browsers, the KEGG and ChEBI small molecule databases, PubMed, and
the Gene Ontology (GO).

*New content.* As part of a project to annotate the general process of cell
motility and its involvement in key biological processes, Version 29
introduces a new topic, Axon guidance, with material now available for NCAM
signaling in neurite outgrowth. Pathway topics updated with new curated
events in this release include: Synaptic transmission (Glutamate Binding,
Activation of AMPA Receptors, and Synaptic Plasticity), DNA Repair
(regulation of FANCD2 and FANCI activity in the Fanconi Anemia pathway), and
pathways whose dysfunction plays a major role in the development of diabetes
(Regulation of insulin secretion and Unfolded protein response). With the
annotation of G-coupled protein receptors (GPCRs) for eicosanoids,
leukotrienes, nucleotide-like (purinergic) molecules, LPA and
lysosphingolipids, opsins, secretins, and GABA and related molecules (class
C/3 receptors), our annotation of interactions between GPCRs and their
ligands is essentially complete. The Telomere Maintenance pathway has been
revised in this release. Updated release statistics are available.

*Data access. *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. Data downloads
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 modified and reused
freely. Users can subscribe to Reactome announcement list from the webpage
at *http://mail.reactome.org/mailman/listinfo/reactome-announce*.

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/*.

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

*Work in progress.* Reactome is seeking expert help for the curation of new
modules – ones now underway are listed in our editorial calendar.. 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.

A list of projects underway to develop Reactome-like pathway databases for
non-human model organisms with contact information is available from *
http://www.reactome.org/other_reactomes.html*.

-The Reactome team
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