Reactome

Version 40 Released

Robin Haw — Thu, 22 Mar 2012 15:19:19 +0000

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 TLR, Signaling by B cell receptor, and DAI mediated induction of type I IFNs), Metabolism of proteins, (Mitochondrial Protein Import), Signal transduction (Signaling by Hippo, Signaling by Notch), Circadian clock, and Gene Expression (Regulatory RNA Pathways). Sean Egan is our external author. DT Bradley , G Butler, F Delaunay, HS Earp, T Endo, L Fraczek, CA Leifer, AM Misior, ES Mocarski, CM Overall, FJ Rauscher, WA Rose, M Sudol, Y Tomari, JW 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 Browser, Pathway 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

Robin Haw — Fri, 16 Mar 2012 20:30:12 +0000

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.

Reactome RESTful API (beta) released.

Robin Haw — Tue, 14 Feb 2012 18:00:26 +0000

Reactome has a new RESTful interface, which has the ability to expose pathway data in Reactome as XML and JSON.

Google Summer of Code 2012 Announced

Robin Haw — Mon, 06 Feb 2012 13:59:43 +0000

Google Summer of Code 2012 was officially announced on February 4th, 2012. The Google Summer of Code is a mentoring scheme in which software developers from across the open source community pass on their knowledge to the next generation of coding enthusiasts. The Genome Informatics Group, organizing the joint efforts of Wormbase, Reactome, and GMOD will apply to participate in this year’s GSoC program. More information on project ideas and the program will be published at the GMOD website. If you have any questions, project suggestions, or interested in mentoring students, please feel free to send a post to the Genome Informatics Google group or contact robin.haw [at] oicr.on.ca. Student applicants will need to wait a little longer until the list of participating organizations is released in March.

Psimex: Network and Pathways Bioinformatics for Biologists: 16-18 May 2012 @ EBI

Robin Haw — Mon, 09 Jan 2012 12:19:47 +0000

Title: Network and Pathways Bioinformatics for Biologists
Date: 16 – 18 May 2012
Venue: EBI, Wellcome Trust Genome Campus, Hinxton

Course Overview

Is it right for me?
This practical course is specifically intended to give life scientists training on how to optimally explore and use protein-protein interaction bioinformatics resources. This course spans from the actual data repositories to resources and tools to explore and analysis the vast amounts of data available. We will also cover data resources related to pathways. Principles of biological network analysis will be introduced and case studies presented. Preference will be given to those actively involved in or commencing protein interaction and/or pathway-related projects.

What will I learn?

· Molecular interactions state of the art
· Making sense of interactions
· Interactions: regulation at the molecular, systems and genome level
· Network based tools for novelty finding
· Pathways informatics: databases and tools
· Ontologies and Standards in Interactions and Pathways

For further information or to register for this course please follow this link: http://www.ebi.ac.uk/training/onsite/120516_intpathpsimex.html

Proposed changes to Reactome Data Model

Robin Haw — Fri, 23 Dec 2011 05:13:17 +0000

We are planning to retire two classes from the Reactome data model, referenceGroupCount and referenceMoleculeClass. These classes were used to annotate structural features and relationships among small molecules, two functions now very well handled by ChEBI. If you have any concerns or comments please contact us at help@reactome.org.

UPDATE: Both these terms have been retired.

Version 39 Released

Robin Haw — Wed, 14 Dec 2011 15:34:40 +0000

As a first step toward systematically annotating human disease processes in Reactome, a new topic, Disease, has been created. It contains the existing HIV, Influenza, Botulinum neurotoxicity, Amyloids, and Diabetes pathways with the new Signaling by EGFR in Cancer. As described in the users’ guide, pathway diagrams have been revised to show the interplay between disease and normal processes and a new color scheme has been implemented to differentiate the two. Topics with new or revised events include Immune System (ISG15 antiviral mechanism, Prolactin receptor signalling, Defensins, and Interleukin-7 signalling), Metabolism (Sulfur amino acid metabolism, Sphingolipid metabolism, O-linked glycosylation of mucins, and Serine biosynthesis), Signal transduction (Signaling by ERBB2 and Signaling by ERBB4), and Gene expression.

Annotations of chicken (Gallus gallus) DNA replication and repair, toll receptor signaling, and metabolism available at gallus.reactome.org with limited browsing and data analysis tools are now also available, with full functionality, in the Reactome pathway browser (switch species to “Gallus gallus”).

KP Ray and R Stephan are our external authors. A Ferrer, V Goffin, H Greulich, RC Harris, AM McDermott, LM Neckers, J Puck, F Rauscher, S Savas, W Xu, F Zeng, and DE Zhang are our external reviewers.

Nature Paper features Reactome Pathway Curation and Analysis.

Robin Haw — Wed, 07 Dec 2011 20:51:47 +0000

Reactome data have been used to identify new gene functions in megakaryopoiesis and platelet formation, as described in this article published today in Nature. Hemostasis pathway diagrams and annotations can be viewed here.

Reactome servers are back online.

Robin Haw — Thu, 01 Dec 2011 14:30:14 +0000

Reactome is back online after suffering a hardware fault early Monday morning. Please report any anomalies to our helpdesk (help@reactome.org).

New Reactome paper

Robin Haw — Wed, 26 Oct 2011 15:00:43 +0000

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations was published in Database: The Journal of Biological Databases and Curation.