Reactome: A Curated Pathway Database

Version 43 Released

Topics with new or revised events include Immune system (TLR4 cascadeMyD88:Mal cascade on plasma membrane, and MyD88-independent cascade), Cell Cycle (Condensation of prometaphase chromosomesMitotic prophase: MASTL facilitates mitotic progression, and Resolution of sister chromatid cohesion), Extracellular matrix organization (Collagen degradationElastic fibre formation, and Assembly of collagen fibrils and other multimeric structures), Metabolism (Inositol Phosphate MetabolismArachidonic acid metabolismMitochondrial Iron-Sulfur Cluster Biogenesis, and Phosphate bond hydrolysis by NUDT proteins), Signal Transduction (Signaling by Activin and Signaling by IGF1R), and Gene expression. New pathway illustrations for this release include Cell Cycle and ApoptosisR Lill is our external author. A BurgessYG ChenKA FitzgeraldF GranucciM HolzenbergerR ItoS KalamajskiV MalhotraV MochidaL MuiznieksJ NapetschnigS RaleighF RauscherS Ricard-BlumTA RouaultM RushT SorsaWH TongT WundenbergI Zanoni, and N Zhang are our external reviewers. Reactome’s SBML export (available here) has been upgraded to Level2 Version4. Our SOAP and RESTful web services, have been moved to a new server. A new series of webinars, which will introduce the Reactome website and our suite of pathway and network visualization and analysis tools, will restart in January 2013. Registration details can be found on EventBrite. A new paper, describing the extension of the Reactome data model and enhancing the web tools to permit the annotation and visualization of protein variants, anti-cancer therapeutics, and other disease processes using Reactome, was published in Cancers.

Reactome Webinar Series

Posted on September 28th, 2012, by robinhaw, under Conference and Meeting, Reactome Meeting

Reactome is hosting a new series of webinars that will introduce the website and our suite of pathway and network visualization and analysis tools. The first two sessions will start in October, and will be repeated every month. Additional webinar topics will be added to the future schedule.

The first session on 8th October will describe Using Reactome Pathway Database. On 15th October, the second session will introduce the Reactome Functional Interaction Network Cytoscape plugin. If you are interesting in participating, please register at Eventbrite.

Feel free to pass this invitation along to colleagues who may benefit from learning about Reactome.

Registrants will receive detailed instructions about accessing the webinar via e-mail the Friday prior to the event. (Anyone registering between Friday and the close of registration will receive the message shortly after the registration is received, within normal business hours.)

Version 42 Released

Posted on September 21st, 2012, by robinhaw, under Conference and Meeting, Reactome Publication, Reactome Release Announcement

Topics with new or revised events include Immune system (STING mediated induction of type 1 IFN and DAP12 Interactions and signaling), Disease (Mucopolysaccharidoses and Signaling by PI3K/AKT in Cancer), Cell Cycle (Golgi Cisternae Pericentriolar Stack Reorganization), Metabolism (Regulation of Cholesterol Biosynthesis by SREBP), Metabolism of proteins (Metabolism of Angiotensinogen to Angiotensins), Membrane Trafficking (GLUT4 Translocation), and Gene expression. S AlvesJL AshworthA ColanziMF CoutinhoL JinJ JosephA KlipLL LanierG LiangF RauscherL ThorpeY WangH Yuzugullu, and J Zhao are our external reviewers. New pathway illustrations for this release include Signal transduction Signaling by Hippo, Signaling by SCF-KIT, and Mitochondrial Protein Import. Reactome is hosting two webinars, Using Reactome Pathway Database and Reactome Functional Interaction Network plugin in October. If you are interesting in participating, please register at Eventbrite. A new paper entitled Reactome – a curated knowledgebase of biological pathways: megakaryocytes and platelets has been published in the Journal of Thrombosis and Haemostasis.

Reactome will be attending COMBINE 2012

Posted on June 29th, 2012, by robinhaw, under Conference and Meeting

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats, initially in Systems Biology and related fields. The Annual COMBINE forum is a workshop-style event with oral presentations, posters and breakout sessions.  The meeting provides an opportunity for those involved in many related standardization and software efforts in systems biology to meet and discuss their efforts, with the aim of working more closely together to ensure smooth interoperability between systems.

COMBINE 2012 will take place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 to Sunday Aug. 19, 2012, immediately preceding the 13th International Conference on Systems Biology. The COMBINE conference location is a short walk from ICSB events and COMBINE 2012 is an official satellite meeting of ICSB, so you can follow the same travel and accommodation instructions for ICSB and use the same hotel discounts. Registration for COMBINE is $125 (Canadian) to cover costs associated with the meeting, including a workshop dinner and catering.

We hope to see you there!

Reactome will be visiting Korea and Japan

Posted on June 28th, 2012, by robinhaw, under Reactome Meeting

Reactome outreach coordinator, Robin Haw, will give a talk at the Current and Future in Pathway Research International Workshop at the Korea Institute of Science and Technology (KISTI), Daejeon, Korea on July 6. Robin will then travel onto Japan, to present a seminar entitled “Reactome – Linking pathways, networks and disease” at The Institute of Medical ScienceThe University of Tokyo on July 11 (Shirokanedai campus) and July 12 (Kashiwa campus).

Version 41 Released

Posted on June 26th, 2012, by robinhaw, under Reactome Feature, Reactome Release Announcement

New in Version 41 is the topic Cellular responses to stress, including Regulation of Hypoxia-inducible Factor by oxygen. Topics with new or revised events include Immune System (MHC Class II mediated antigen processing & presentation), Metabolism (Abacavir transport and metabolismGlycerophospholipid biosynthesisGlycosaminoglycan metabolismLinoleic acid and alpha-linolenic acid metabolismO2/CO2 exchange in erythrocytesPI MetabolismReversible hydration of carbon dioxide, and Activation of arylsufatases), Signal transduction (Signaling by TGF-beta Receptor Complex and Gastrin-CREB signalling pathway via PKC and MAPK), Extracellular matrix organization (Collagen biosynthesis and modifying enzymes) and Gene expression. New Disease pathways include Abnormal metabolism in phenylketonuriaLatent infection of H. sapiens with Mycobacterium tuberculosis, and Signaling by FGFR in disease.  R Stephan and S Tripathi are our external authors. EG Canty-LairdS EzzatT HuangJ NeefjesK RantanenF RauscherM Wakelam are our external reviewers. Based upon feedback from our users, Reactome has started to provide Pathway Illustrations. New ones for this release are: Signaling by EGFR, Hemostasis, Respiratory Electron Transport System, RAF/MAP kinase cascade, Signaling by NGF, PIP3 activates AKT signaling, Signaling by FGFR, Signaling by Insulin receptor, Signaling by BMP, Signaling by TGF beta, Signaling by Notch, Pre-NOTCH Expression and Processing, Signaling by NOTCH1, Signaling by NOTCH2, NOTCH3, and NOTCH4, Signaling by PDGF, Integrin cell surface interactions, Signaling by ERBB2 and ERBB4. For the systems biology community, we now offer SBGN export for all pathways.  Our SBGN is generated using libSBGN Milestone 2. Protein pages in Reactome now include link outs to GeneCards annotations. An updated Reactome tutorial has been published in Current Protocols in Bioinformatics.

Version 40 Released

Posted on March 22nd, 2012, by robinhaw, under Reactome Release Announcement

The pathway Extracellular matrix organization is new and includes Activation of Matrix Metalloproteinases. Topics with new or revised events include Immune System (Regulation of complement cascade, Trafficking and processing of endosomal TLRSignaling by B cell receptor, and DAI mediated induction of type I IFNs), Metabolism of proteins, (Mitochondrial Protein Import), Signal transduction (Signaling by HippoSignaling by Notch), Circadian clock, and Gene Expression (Regulatory RNA Pathways). Sean Egan is our external author. DT Bradley G ButlerF DelaunayHS EarpT EndoL FraczekCA LeiferAM MisiorES MocarskiCM OverallFJ RauscherWA RoseM SudolY TomariJW Upton, and J Wienands are our external reviewers. We have created short Reactome tutorial videos that demonstrate the use of our navigation and analysis tools. New ones for this release are Pathway BrowserPathway Analysis, and Expression Analysis. Others will be added to the Reactome YouTube Channel as they become available. Our SBML export (available here) has been enriched with a wide variety of additional annotations, including SBO terms.  We have switched from using the layout extension to embedded SBGN for conveying pathway layout.

Reactome will be participating in Google Summer of Code 2012

Posted on March 16th, 2012, by robinhaw, under Grants and Funding, Reactome Announcement

The Genome Informatics group, organizing the joint efforts of Galaxy, GBrowse, Generic Model Organism Database (GMOD), JBrowse, Reactome, Wormbase, and PortEco will be participating in the Google Summer of Code 2012. Here is the complete list of the 180 accepted organizations, chosen by Google to take part in this exciting program. This is a great opportunity for undergraduate students to contribute to the work of these bioinformatics projects, to participate in open source development and to do work related to their academic pursuits during the summer. Students wishing to apply for Google Summer of Code will have the next 10 days to learn more about the accepted projects before student applications open on Monday, March 26, 2012 at 19:00 UTC.  More information about the project ideas and the GSoC program is available on the GMOD website. If you have any questions or queries, please feel free to send a post to the Genome Informatics Google Groups.