The Reactome Knowledgebase is supported by both expert authors and reviewers. Both types of contributors are detailed below.
Authors are recruited based upon their participation and prominence in a particular field or domain of biology. Reactome authors are expected to be able to describe their particular domain of biology in depth, at the molecular level. Data entered into the Reactome knowledgebase is expected to be what the "overall field agrees upon". This often initially feels a little to conservative to authors, but a Reactome curators job is to enter data with solid experimental provenance in the species being annotated.
The Reactome Editorial Team meets regularly to review author recruitment. If you would like to contribute to Reactome please contact us at firstname.lastname@example.org.
Reactome authors are experts in a specific field or domain of biology. Authors are paired with an experienced Reactome curator who will handle all of the technical aspects of converting the author's biological description into Reactome readable data. Often the author's contribution is described as a module. The amount of work that an author must do to complete a module is comparable to writing a review paper. The steps vary, but generally include:
- An initial meeting to lay out the scope of the curation module
- The author sends the curator a list of comprehensive review papers that teh curator can use to get up to speed on that area of biology.
- The review papers are used to sketch out a rough description of the specific steps that are involved in the pathway.
- The molecules that participate in each step are identified
- An initial draft of the pathways is prepared by the curator.
- The author and curator meet and refine the initial draft, adding literature references for each step (reaction) in the pathway, images, and human readable summation text for each reaction and pathway.
- Once the author and the curator are satisfied the module is released for internal review
- After internal review (or sometimes during), the module is released for external review by another outside expert.
- Once the reviews are complete the module is scheduled for release.
- At the time of release the module receives a doi and is now accessible by the public.
Reactome Author's Tool
For now Authors are trained at their request. We offer online training sessions, as well as group training at various topic specific scientific jamborees sponsored by Reactome. For more information contact us.
Reviewing a module involves evaluating both a pathway report in text format and a corresponding online pathway diagram for completeness and accuracy. A sample pathway report is attached here. The website and pathway diagram provide more detailed dynamic descriptions of the composition and hierarchical organization of reactions and can be viewed here.
Your input will be used by the Reactome curator to revise the module, and you will be acknowledged as a reviewer on the pathway web page and in the Reactome table of contents. In addition, this pathway module will be associated with a DOI and may be cited as a publication.
In your review, we ask that you verify that the events described in the pathway report (pathways and reactions) are annotated clearly and that the molecular details of the reactions are accurate. The pathway report is a collation of all of the text descriptions of the events in this pathway.
Comments, questions or corrections can be added directly to the word document that we provide (tracking changes) or they can be sent as a separate document. Note that, due to limited resources, we may not have included all of the references that are relevant for a particular pathway or reaction, but we would be happy to add any that you might wish to see included.
We are aware that there are formatting problems for the non-ASCII characters of certain names and words and apologize for that.
The new Pathway Browser on our website gives a graphical and more detailed, dynamic description of the composition and hierarchical organization of reactions and the reaction components involved in this pathway. We would appreciate any comments or suggestions that you might have on this interface. You can access a sample pathway in the Pathway Browser here.
Selecting any event in the hierarchy (left panel) will bring you to its location in the pathway diagram, and the corresponding event(s) will be highlighted in blue in the diagram. A text and molecular description of the reaction or event can be viewed in the overview tab in the panel below the diagram. The description of the reaction may also be accessed by clicking on the reaction “node” in the diagram. A text description (and cross references) for individual reaction component molecules can be displayed by selecting the molecule of interest in the diagram.
For additional information on pathway diagram features and navigation, a very short guided tour is provided via a green box at the top center of the page.
Resources for reviewers
Citing pathways that you have contributed or reviewed
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. Generally you can add a DOI to the end of your citation following the appropriate style. Generally these citations follow this format:
Author, A. (year). Title of article. Journal Title, X, xxx–xxx. doi:xxxxxx
Please find examples here: