reactome.org
Reactome Pathway Database
http://www.reactome.org/ReactomeGWT/entrypoint.html
Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. The current version (v57) of Reactome was released on June 27, 2016. Current Version: Reactome V57.
reactome.org
Computational inferred events | Reactome Pathway Database
http://www.reactome.org/pages/documentation/electronically-inferred-events
We use the set of manually curated human reactions to electronically infer reactions in twenty evolutionarily divergent eukaryotic species for which high-quality whole-genome sequence data are available, and hence a comprehensive and high-quality set of protein predictions exists. These species include the laboratory mouse and rat, the nematode C. elegans. Electronic inference proceeds in four steps. 1) Protein homology data were obtained from Ensembl Compara. For the purpose of inferring homologous even...
reactome.org
Content | Reactome Pathway Database
http://www.reactome.org/pages/content
The Reactome database embodies a reductionist data model, which asserts that all of biology can be represented as events located in subcellular compartments that convert input physical entities into output physical entities. Information is stored as a generic and qualitative parts list. Further information can also be found here about our contributors (authors, curators and reviewers) to the Reactome database and editorial content. Describes in a formal language, the structure of the Reactome database.
reactome.org
Referencing Reactome Publications | Reactome Pathway Database
http://www.reactome.org/pages/documentation/citing-reactome-publications
The following are examples that can be used to cite Reactome. To cite the Reactome project:. If you are citing your use of Reactome in your work please cite these two recent Reactome publications:. Fabregat et al. 2016 PMID: 26656494. Milacic et al. 2012 PMID:24213504. To cite a Reactome pathway:. Please use the appropriate DOI from the Table of Contents. You can read more about the way DOIs are assigned and used in Reactome here. Purdue U Online Writing Lab. Date of message or visit). When citing a Reac...
reactome.org
Reactome Outreach | Reactome Pathway Database
http://www.reactome.org/pages/community/outreach
Training and community outreach is managed by Robin Haw. If you have a particular outreach question or request, you can contact Robin thorough our HelpDesk. All our training and outreach materials are available under an Creative Commons Attribution 3.0 Unported License. We have just one simple request, please let us know if you use our presentations, posters or training resources. In addition to our established Mailing List.
reactome.org
Data Model | Reactome Pathway Database
http://www.reactome.org/pages/documentation/data-model
The goal of the Reactome knowledgebase is to represent human biological processes, but many of these processes have not been directly studied in humans. Rather, a human event has been inferred from experiments on material from a model organism. In such cases, the model organism reaction is annotated in Reactome, the inferred human reaction is annotated as a separate event, and the inferential link between the two reactions is explicitly noted. 8211; proteins and nucleic acids with known sequences. 8211; ...
reactome.org
Reactome Events | Reactome Pathway Database
http://www.reactome.org/pages/community/reactome-events
Here is a list of all the Reactome talks, poster presentations, training events and workshops. 251st American Chemical Society National Meeting & Exposition, San Diego, 13-16 March. Bioinformatics Resources for Protein Biology, Hinxton, UK, 2 February. WGC Advanced Course: Proteomics Bioinformatics, Hinxton, UK, 11 December. MiMS / NDPIA Bioinformatics Workshop – Umea, Hinxton, UK, 10-14 November. Networks & Pathways, Hinxton, UK, 5 November. EBI Open Day, Hinxton, UK, 29 October. Reactome Webinar, Toron...
reactome.org
Download Data | Reactome Pathway Database
http://www.reactome.org/pages/download-data
We have continuously supported the major open-data standards, including BioPAX. Export formats. The Reactome data and source code continues to be publicly accessible under the terms of a Creative Commons Attribution 3.0 Unported License. The Reactome website can be installed locally on Debian or Ubuntu Linux. This shell script. Will automate the Reactome local installation. More detailed instructions. GitHub Repository is accessible here. UniProt to pathways mapping file. ChEBI to pathways mapping file.
reactome.org
Documentation | Reactome Pathway Database
http://www.reactome.org/pages/documentation
A brief overview of our data model and orthology based electronic inference of non human events will provide a basis for describing the potential uses for the Reactome. The user documentation also describes some of the technical aspects of the Reactome website and data. Instructions are also available on how to link to and reference Reactome. Provides access to all the documentation relating to the Reactome APIs, Analysis and Visualization web services. Can be achieved by creating URLs containing the nam...
reactome.org
Reactome Training | Reactome Pathway Database
http://www.reactome.org/pages/community/training
One of our most valuable user documents is the Reactome User’s Guide. Please look through the guide and contact us. If our guide needs something new. These slides introduce new users to Reactome. This document provides additional information about the Reactome website and suite of data analysis tools, including exercises to allow you to check your understanding. Answers are provided and were correct when written, but please note that answers may change over time as more pathways are added to Reactome.
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