Associate Editor Instructions

Instructions

• IMPORTANT: On the Volunteer Assignments and Opportunities Page, Track Progress in Real Time of assigning author to pages (pending) and completion of pages (complete) as well as the date you reviewed the page and any notes of importance such as "check permissions for a figure". Open spaces in the "Author" column in your area on this spreadsheet will alert the Editor-in-Chief to continue connecting potential authors with you. This is also the page to which potential new authors are directed to volunteer.
• Onboarding Process:

1. New authors will complete the Volunteer Form (if you're contacted directly, please inform the new volunteer to complete this form).
   1. This form is copied to the Technical Editor, who will then create and send CCGA account credentials (username and password) directly to the new author.
   2. This form will link to the Volunteer Assignments and Opportunities page for volunteers to find open disease entities; volunteers will then return to the form to indicate their disease page(s) they want to author. If no selection is made initially, a volunteer may be assigned to a general area of interest and work with the Associate Editor to select a page to author.
2. The Editor-in-Chief will email to introduce the appropriate Associate Editor and the new author (and mentor if applicable)
   1. This email will include standardized onboarding information such as referring them to the Author Instructions.
   2. This email will have attached a Word version of the page template if the author prefers to work with that instead of directly on the CCGA site. Note: text from the Word document can later be copy/pasted from Word into the tables and sections in the CCGA page, with references inserted using the "Cite" function and searching by PMID.
3. Once a page is assigned, ensure the author's name is IMMEDIATELY added both to the Volunteer Assignments and Opportunities page and to the top of the individual assigned page to clarity which pages are in progress.
4. Ensure the page has been created and has the most current template (found linked in here: Author Instructions), and if not, alert the Editor-in-Chief.
5. If the author is a trainee, ensure they are working with a mentor or perform the mentor function if you're able to do so.
6. Set up a reasonable due date for the author. For example, propose 4 weeks and if author agrees, send an Outlook invite for that due date that has a one week prior reminder prior to this deadline.

• After authors indicate their page is complete, Perform Editorial Review:

1. Review the content for accuracy and appropriate completeness.
2. Prioritize use of the tables, including helping the author convert the content or doing so yourself if applicable. If a table is not needed based on current knowledge, leave it in but add the words "not applicable" and remove any "examples" text.
3. Ensure the authors have inserted references in the standard format using the PubMed extension, and that no references have been repeated in the reference list.
4. Ensure any under construction notes or instructional text on the page has been removed.
5. Ensure appropriate and helpful images are included. Note: Amélie Giguère, Ph.D, FCCMG has offered to provide images for rare chromosomal translocations in hematological malignancies and most anomalies in WHO 2017.

• After Complete Editorial Review:

1. Approve the page using the FlaggedRevs system.
2. Add page to your personal Watchlist so that you can be alerted when new alterations are made and need additional review.
3. Add the editorial review completion date to the Volunteer Assignments and Opportunities page.
4. Send an Email with the heading "Complete Page" and the page name or link in the text. This will alert the Editor-in-Chief and the Technical Associate Editor to perform additional tasks such as adding linking categories to the page.

• Technical Issues:

1. To resolve technical issues you or your authors encounter, fully describe the issue in an Email. Please include the title of the page on which the error occurred, a screenshot of the error message, the web browser you were using (i.e. firefox, google chrome, internet explorer, etc) and any other pertinent information. This will be received by our IT support and the Technical Associate Editor who will coordinate resolution of the issue in a timely manner.

• For any applicable New Version of the WHO Classification of Tumours book:

1. Collaborate with the Technical Associate Editor to move content or create new pages as needed.
2. Solicit original page authors or help find new authors to update pages in a timely manner.
3. Perform editorial review of the updated content.

Technical Associate Editor-Specific Functions

• Onboarding Process:

1. Following receipt of the Volunteer Form, assess appropriateness of volunteer and flag any concerns to the Editor-in-Chief (see "Policy for Granting of CCGA Contributor Access" section below). Transfer the information from the form into the Google tracking spreadsheet.
2. Following receipt of the Editor-in-Chief email connecting the new author to the Associate Editor, assign credentials (username and password) to the new author (see "How to Create a New User Account" section below). IMPORTANT: Add the information to the User Access Log.

• After Editorial Review Completed Process:

1. Add Categories to the page to link searching functions on the homepage (see "How to Add Categories to a Page" section below).
2. For any disease overview page that shows WHO classification structure, add the WHO copyright permission information in the Notes section at the bottom (last entry).
   • Since wiki-specific syntax is required for the embedded external link to function, copy the following information using the wiki syntax in the "Edit source" tab, and add it in the appropriate place near the bottom of the target page using the "Edit source" tab (make sure there's a space after the previous entry): *The hierarchical tumour classification structure displayed on this page is reproduced from the WHO Classification of Tumours with permission from the copyright holder, ©International Agency for Research on Cancer.
3. Add the citation for the page in the Notes section at the bottom. For example: *Citation of this Page: Naeini Y, Quintero-Rivera F. “Myeloid Sarcoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated 03/4/2024, https://www.ccga.io/index.php/Myeloid_Sarcoma. See this in action at the bottom of Example.
   • In order to have the updated section autopopulate on each page, you must use wiki-specific syntax. Therefore, copy this example from the "Edit source" tab and place it in the correct location on the target page using the "Edit" tab or manually type or paste in the yellow highlighted text below.

• Page Conversion/Creation for New Versions of WHO Classification of Tumours Books:

1. Help move content or create new pages as needed to support updating content structured according to the most current version of each WHO Classification of Tumours book.

• Technical Issue Troubleshooting:

1. Be a direct liaison with IT Support to resolve technical issues noted by the other Associate Editors and authors in a timely manner.

• Streamlining and Automating Site:

1. Help develop ideas for process improvement and automation of the CCGA site.
2. Communicate the technical language for implementation of the improvements when possible.
3. Provide technical review as processes are being developed and implemented.

How to Create a New User Account

1. Sign into your personal CCGA account
2. Go to Create account.
3. Fill out form such as the example below and click "Create account"
4. As often the automatic email with a temporary password goes to junk mail, that option is not used. Instead, email the new user directly with their account credentials and let them know about the junk mail issue if they have to reset their password.
5. IMPORTANT: Add the information to the User Access Log.
   

How to Add Categories to a Page

1. At the bottom of each page, below the final Notes section, is a box with "Categories" in it. These represent links from the homepage's search options.
2. To create Categories on a page that doesn't yet have any, log into your account and select the "Edit" tab at the top of the screen.
3. Click on the hamburger icon on the upper right and select "Categories" from the drop down menu (see image below).
4. In the box, add in categories appropriate to the page using the exact language of the options available here: All Categories.
5. Save changes.
6. Of note, if the page already has categories, they can be edited (deleted or added) in the same place by selecting the "Categories" from the hamburger icon's drop down menu.

Policy for Granting of CCGA Contributor Access

The Compendium of Cancer Genome Aberrations (CCGA) is a crowdsourced resource, with content created and modified in real time by users given a username and password.  This policy defines the process for determining new user access for creating and editing content.

1. A member of the CCGA Knowledgebase workgroup or Genomic Resources Development Committee (GRDC) may provide access immediately if requested to do so by an individual.
2. The person who provides access will add the new contributor information into the user access log at User Access Log.
3. It is encouraged that ABMGG trainees, pathology residents or other post-graduate trainees collaborate with a mentor/sponsor who can help curate their work.
4. Individuals will be required to review and agree with the “Honor Code for CCGA Content Contributor” which is part of the initial Volunteer Form.
5. The CCGA leadership reserves the right to deny CCGA site authorship/editorial access to any applicant and to remove access as deemed appropriate.

Editorial Review Process

The editor will be responsible for regularly determining the appropriateness of author edits, discussing the proposed changes, and finally approving a final set of changes. The instructions below will provide a guide to performing this process on the site, as well as instructions for setting up and configuring the features built into the site to improve this process for the editor. The basic process for monitoring and approving changes will utilize two main functions on the site:

Revision Tracking

The revision tracking feature will prevent author edits from moving to the live version of pages until the associate editor has approved the changes.

Watchlist

The watchlist is a list of pages chosen by the editor which will help keep the editor notified of page changes, and will provide a single webpage where the editor can view all pending changes. For initial setup and configuration of the watch, see the appendix below.

Watchlist

Essential steps:

• Log in! You can not see your watchlist if you are not logged in.
• Create your watchlist. A new user will not have any pages on their watchlist initially. You will need to add the desired pages to your watchlist. See the appendix below.
• Make sure your watchlist filter isn’t removing pages! For instance, in this example any changes older than 1 day would not appear in the watch list.

Approving Revisions:

1. The review status of each page is indicated on the top right.  After an author makes any edits, the status will be “review pending changes”, indicating that an editor needs to approve/disapprove the edits.
   
   Note, as the FlaggedRevs system was recently implemented, all pages are currently listed as “no review versions”.
   
   
2. As editors, click on “review pending changes”, which will allow you to see the differences between the original and the suggested revised page.  Two modes to do so: visual mode and wikitext mode. The default view is Wikitext, but once you click on Visual, the site should remember your last setting.
   
   
   1. Visual mode
      
      Red text means removed and the Green text means added. This will be the preferred method for most editors. The functionality will be similar to popular document creation software.
   2. Wikitext mode Editors can have more control if the switch to “wikitext” to view the differences in wiki syntax (for advanced editors this may be the best way to review long pages and also to spot syntax errors)
      
3. To approve/disapprove edits, go to the “review the revision” box at the bottom of the page.  IMPORTANT NOTE: You can only accept or reject all the new revision (cannot accept some and reject some) – if need to add only some of the changes, the editor will need to reject the revision and then manually re-edit the page to add in the new wanted changes.  
   1. Editors can choose the quality of the revision So something may be approved even though it is marked with a low quality in (let’s say) readability.
   2. If an editor chooses to disapprove the review, a comment can be made for the reasoning.
      
      Until revisions are approved, they will not appear as the default view for a page.
      
4. Once editorial review is complete, please indicate the date in the corresponding “Date of Last Editor Review” column of the Volunteer Assignments and Opportunities page.

Conversion Notes:

• • Note: Most testing for this process has used Google Chrome as the browser. Other browsers may have issues in transferring data between sections.

For the HAEM4 to HAEM5 book conversion, several key automatic processes have been performed:

1. HAEM4 pages have been assigned to HAEM5 counterparts when possible
   1. It is possible for a HAEM5 page to be entirely new, to need content brought in from more than one HAEM4 page, or for a single HAEM4 page to be divided into several HAEM5 pages. It is also possible for an original HAEM4 page to no longer be relevant, and therefore to not be assigned to a HAEM5 page.
   2. The automated process has attempted to uplift older templates to the current template when possible. This changes the structure of several key tables in particular. Please take the relevant content from each section and incorporate it into the new section.

1. If a HAEM5 page has one of more HAEM4 pages, the contents of one of the pages will have been automatically transferred. The relevant pages HAEM4 pages can be found in the conversion nots box at the top of each page. The first indicated page will have had its contents transferred. Other relevant pages will be listed as well. If relevant pages were empty or if no relevant pages were identified, there will not be a conversion box.

There are several ways to view the revisions. Each revision represents a single "save" by an author/editor. There may be multiple revisions to review, and each revision may have multiple changes within it. A visual representation of the changes can be used to select and approve a subset of the changes. However, for any revision to be accepted, all previous revisions must also be accepted. To visualize the changes, click on the “Browse history interactively” bar on the top and compare different versions: