Reactome: A Curated Pathway Database

New SBML Level 3 Version 1 export is now available.

Posted on July 5th, 2017, by robinhaw, under Reactome Announcement, Reactome Feature

As part of our efforts to give our modeling user community better experience, we have updated the SBML export to Level 3 Version 1, which is organized in a modular manner.  Our initial export provides a richer annotation  syntax and we will explore supporting other SBML Level 3 Packages in the future. The SBML data export can be used by any tool that supports SBML L3V1.

The SBML Level 3 Version 1 export is available for download here: http://reactome.org/download/current/homo_sapiens.3.1.sbml.tgz.

We are also providing a programmatic interface to access these updated SBML files through our ContentService for all species at http://reactome.org/ContentService/#!/exporter/toSBMLUsingGET

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, Oregon Health and Science University, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

New Protein-protein Interaction files

Posted on June 28th, 2017, by robinhaw, under Reactome Announcement, Reactome Feature

The Reactome team has released new versions of our protein-protein interaction files derived from reactions and complexes. These files were updated following user feedback, with the goal of providing extra annotation features through support from the PSI-MITAB 2.7 data format. Interactions are computationally generated based on the data stored on complexes and reactions. The interactions provided by Reactome are not curated and are not experimental data. In addition, the complexes and reactions in species other than human are derived by orthology inference from the corresponding human complexes and reactions. Tab-delimited formatted files are also provided for human and all species.

The four new files are:

Documentation about these files is available from the Data Download page.

The former versions of the protein-protein interaction files are still available but will be removed from service as of Version 62 in September 2017. We encourage users that programmatically access these files to update the scripts.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, Oregon Health and Science University, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our helpdesk.

Updated Molecular Interaction Overlay feature now available.

Posted on February 15th, 2016, by robinhaw, under Reactome Announcement, Reactome Feature

EGFR_MIO

As part of our efforts to give our user community better experience, we have redesigned the Molecular Interaction Overlay to support quicker, easier, and more responsive access to protein-protein and protein-small molecule interaction data within the Reactome Pathway Browser.

New features and improvements include:

  • Diagram search feature includes the gene name and chemical name for interactors.
  • Interactors display name is now the gene name for proteins and the chemical name for the chemicals.
  • Tooltips are shown when hovering over the for interaction links.
  • Interactions include links to entities present in the diagram.
  • Loop-link is included when a protein/chemical interacts with itself.
  • Display option to show/hide interactors based upon a selected weighted score.
  • Crystal and chemical structures for the interactors are displayed at zoomed-in view.
  • Diagram image export for the zoomed-in view includes the protein structures in the final image.
  • Interactor file download is now available in both the Interactors toolbar and Settings panel.

New miRBase-Reactome pathway identifier mapping files are available

Posted on February 9th, 2015, by robinhaw, under Reactome Feature

The set of identifier mapping files, linking different source database identifiers to the Reactome pathway diagram, has been updated to include a miRBase-pathway identifier mapping file. These mapping files consist of a tab-separated table that indicates which external protein (UniProt), gene (Ensembl), microRNA (miRBase) or small molecule (ChEBI) identifiers were mapped to Reactome pathway annotations. Our goal with distributing two sets of files for each different identifier type is to provide these mapping files link the source database identifier to: i) the lowest level pathway diagram or subset of the pathway, and ii) all level pathway diagrams. These mapping files are available from our Download Data page.

New Reactome Pathway Analysis Portal Released

Posted on June 18th, 2014, by robinhaw, under Reactome Announcement, Reactome Feature

Pathway databases, like Reactome, are uniquely suited for interpreting the results of high-throughput functional genomics data sets such as microarray-based expression profiles, protein interaction sets, and chromatin IP. In response to user feedback and new feature requests, we have released a new Reactome Pathway Browser with an integrated suite of tools for pathway analysis. Using these improved features, you can map protein lists to Reactome pathways, perform pathway overrepresentation analysis for a set of genes, colourize pathway diagrams with gene expression data, and compare model organism and human pathways. To support third-party tool integration, the Reactome Pathway Analysis Portal is also available via RESTful web services. Further details about the new pathway analysis tool can be found in our User Guide.

Reactome FI Cytoscape plugin: 4.0.0 beta Released

Posted on January 8th, 2014, by Marc Gillepsie, under Reactome Feature

We have released a new version of the Reactome FI Cytoscape plugin: 4.0.0 beta. This version provides a suite of features to help users to explore Reactome pathways directly in Cytoscape. Using these features, you can load pathways in the Reactome database into Cytoscape, visualize Reactome pathways in either the native pathway diagram view or the FI network view, do pathway enrichment analysis for a set of genes, and check genes from your list in identified  pathways.

Read more about the Reactome FI Cytoscape Plugin here.

New Reactome Website and Data Analysis Portal

Posted on October 1st, 2013, by robinhaw, under Curation, Reactome Announcement, Reactome Feature, Reactome Release Announcement

Reactome has released a new web interface for its open-source curated database of pathways and reactions. The redesigned web site is a faster, more flexible tool to query, analyze and visualize pathway and network data. New features include:

  • Access to visualization and data analysis tools via a simpler home page.
  • New data model and visualization strategies to annotate and display disease counterparts of normal human processes, supporting descriptions of diseases due to infection and mutation at the molecular level.
  • Revised event hierarchy panel to provide interactivity and access to the entire listing of all the Reactome pathways.
  • Improved flexibility and performance of our pathway browser with a new pathway diagram visualization tool using HTML5 Canvas.
  • Extended data overlaying technologies to support molecular interaction data from the PSIQUIC registry, including BindingDB, DrugBank, and GeneMANIA.
  • New pathway diagram tools to search within the displayed pathway, overlay the pathway with functional interactors, and download the diagram as a snapshot or PNG file.
  • Enhanced “Details” panel providing alternative displays of graphical and textual information, such as 3D structural data and citations for proteins from PDB, for small molecules from ChEBI, for the stoichiometry of metabolic reactions from Rhea, and for expression data from Gene Expression Atlas.
  • Merged pathway identifier mapping, over-representation, and expression analysis tools into a tabbed data analysis portal with integrated visualization for improved pathway diagram colorization with user-supplied experimental data.
  • Updated Reactome Functional Interaction plugin supports Cytoscape v3.x., providing useful tools for the discovery of network patterns related to cancer and other types of disease.

Reactome is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and The European Bioinformatics Institute. Freely available to all users worldwide, the Reactome database offers human pathway data that span and integrate metabolism, signaling cascades, and cellular processes like apoptosis, extracted from the published literature in collaboration with experts from the scientific community and cross-referenced to a wide range of biological databases. Reactome data and software are distributed under the terms of the Creative Commons Attribution 3.0 Unported License.