Difference between revisions of "Associate Editor Instructions"

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==Instructions==
 
==Instructions==
  
*IMPORTANT: '''<u>On the [[Volunteer Assignments and Opportunities]] Page, Track Progress in Real Time</u>''' 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 "non-WHO entity page" or check permissions for a figure. ''Open spaces in your area on this spreadsheet will alert the Editor-in-Chief to continue connecting potential authors with you.''
+
*IMPORTANT: '''<u>On the [[Volunteer Assignments and Opportunities]] Page, Track Progress in Real Time</u>''' 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.''
 
*<u>'''Onboarding Process'''</u>:
 
*<u>'''Onboarding Process'''</u>:
  
#New authors will complete the [https://mms.cancergenomics.org/members/form.php?orgcode=CGC&fid=3830649 <u>Volunteer Form</u>] (if you're contacted directly please inform the new volunteer to complete this form).
+
#New authors will complete the [https://mms.cancergenomics.org/members/form.php?orgcode=CGC&fid=3830649 <u>Volunteer Form</u>] (if you're contacted directly, please inform the new volunteer to complete this form).
#The Editor-in-Chief will send a link to the <u>[[Volunteer Assignments and Opportunities]]</u> page for volunteers to select which content to complete (informing which Associate Editor will be involved).
+
##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.
#The Editor-in-Chief will introduce by email the Associate Editor and the new author (and mentor if applicable), including standardized onboarding information such as referring them to the [[Author Instructions|<u>Author Instructions</u>]]. This email will be copied to the Technical Associate Editor, triggering them to assign CCGA account credentials (username and password) to the new author.
+
##This form will link to the <u>[[Volunteer Assignments and Opportunities]]</u> 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.
#Once a page is assigned, ensure the author's name is added both to the <u>[[Volunteer Assignments and Opportunities]]</u> page and to the top of the individual assigned page to clarity which pages are in progress.
+
#The Editor-in-Chief will email to introduce the appropriate Associate Editor and the new author (and mentor if applicable)
 +
##This email will include standardized onboarding information such as referring them to the [[Author Instructions|<u>Author Instructions</u>]].
 +
##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.
 +
#Once a page is assigned, ensure the author's name is IMMEDIATELY added both to the <u>[[Volunteer Assignments and Opportunities]]</u> page and to the top of the individual assigned page to clarity which pages are in progress.
 +
#Ensure the page has been created and has the most current template (found linked in here: [[Author Instructions|<u>Author Instructions</u>]]), and if not, alert the Editor-in-Chief.
 
#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.
 
#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.
#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.
+
#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 a page is complete, '''<u>Perform Editorial Review</u>'''<u>:</u>
+
*After authors indicate their page is complete, '''<u>Perform Editorial Review</u>'''<u>:</u>
  
 
#Review the content for accuracy and appropriate completeness.
 
#Review the content for accuracy and appropriate completeness.
#Prioritize use of the tables, including helping the author to convert the content or doing so yourself if applicable.  If a table is not needed based on current knowledge, remove it so that the page doesn’t look unfinished, but if in the future information is added that could be put in one of the tables, convert it.
+
#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.
#Ensure the authors have inserted references in the standard format using the PubMed extension.
+
#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.
#Ensure the under construction note at the top of the page has been removed.
+
#Ensure any under construction notes and instructional text (in blue color) on the page has been removed.
 
#Ensure appropriate and helpful images are included.  Note: [Mailto:Agiguere.hmr@ssss.gouv.qc.ca <u>Amélie Giguère, Ph.D, FCCMG</u>] has offered to provide images for rare chromosomal translocations in hematological malignancies and most anomalies in WHO 2017.
 
#Ensure appropriate and helpful images are included.  Note: [Mailto:Agiguere.hmr@ssss.gouv.qc.ca <u>Amélie Giguère, Ph.D, FCCMG</u>] has offered to provide images for rare chromosomal translocations in hematological malignancies and most anomalies in WHO 2017.
  
*Once you '''<u>Complete Editorial Review</u>''':
+
*After '''<u>Complete Editorial Review (further technical details in "Technical Editorial Review Process" below)</u>''':
  
 
#Approve the page using the FlaggedRevs system.
 
#Approve the page using the FlaggedRevs system.
#Add page to your personal watchlist so that you can be alerted when new alterations are made and need additional review.
+
#Ensure the page has been added to your personal Watchlist so that you can be alerted when new alterations are made and need additional review.
 
#Add the editorial review completion date to the [[Volunteer Assignments and Opportunities|<u>Volunteer Assignments and Opportunities</u>]] page.
 
#Add the editorial review completion date to the [[Volunteer Assignments and Opportunities|<u>Volunteer Assignments and Opportunities</u>]] page.
#Send an [Mailto:CCGA@cancergenomics.org <u>Email</u>] 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.
+
#Send an [Mailto:CCGA@cancergenomics.org <u>Email</u>] 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.
  
 
*'''<u>Technical Issues</u>''':
 
*'''<u>Technical Issues</u>''':
  
#To resolve technical issues you or your authors encounter, fully describe the issue in an [Mailto:CCGA@cancergenomics.org <u>Email</u>] (including what internet browser used, what page involved, and images of error messages if helpful), which will be received by our IT support and the Technical Associate Editor who will coordinate resolution of the issue in a timely manner.
+
#To resolve technical issues you or your authors encounter, fully describe the issue in an [Mailto:CCGA@cancergenomics.org <u>Email</u>]. 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.
  
==Technical Associate Editor-Specific Functions==
+
*For any '''<u>New Version of a WHO Classification of Tumours book</u>''':
  
*'''<u>Onboarding Process</u>''':
+
#Content from any pertinent prior page will be automatically pulled into the new book page, with any conversion notes highlighted in boxes with purple headers.
 +
#Solicit original page authors or help find new authors to update pages in a timely manner.
 +
#Perform editorial review of the updated content.
  
#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.
+
==Policy for Granting of CCGA Contributor Access==
#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|<u>User Access Log</u>]].
+
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.
  
*
+
#Any member of the CCGA Knowledgebase workgroup or Genomic Resources Development Committee (GRDC) may provide access immediately if requested to do so by an individual. However, typically accounts will be created by the Technical Editor following receipt of a completed Volunteer Form.
*<u>'''After Editorial Review Completed Process'''</u>:
+
#The person who provides access will add the new contributor information into the user access log at [[User Access Log|<u>User Access Log</u>]].
 +
#It is encouraged that ABMGG trainees, pathology residents or other post-graduate trainees collaborate with a mentor/sponsor who can help curate their work.
 +
#Individuals will be required to review and agree with the “Honor Code for CCGA Content Contributor” which is part of the initial [https://mms.cancergenomics.org/members/form.php?orgcode=CGC&fid=3830649 <u>Volunteer Form</u>].
 +
#The CCGA leadership reserves the right to deny CCGA site authorship/editorial access to any applicant and to remove access as deemed appropriate.
  
#Add Categories to the page to link searching functions on the homepage (see "How to Add Categories to a Page" section below).
+
==Technical Editorial Review Process==
#Add the WHO copyright permission information for any disease overview page that shows WHO classification structure 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): <nowiki>*</nowiki>The hierarchical tumour classification structure displayed on this page is reproduced from the [https://tumourclassification.iarc.who.int/welcome/ WHO Classification of Tumours] with permission from the copyright holder, ©International Agency for Research on Cancer.
+
Each Associate Editor is responsible for regularly determining the appropriateness of their author edits and approving the final changes. The instructions below will provide a guide to (1) perform editing in the CCGA site, and (2) set up and configure the features built into the site to streamline the editing process. The basic process for monitoring and approving changes will utilize two main functions:
#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 {{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}, <nowiki>https://www.ccga.io/index.php/Myeloid_Sarcoma</nowiki>.  See this in action at the bottom of [[Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms|<u>Example</u>]].
 
##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.
 
  
[[File:Citing page image.png|center|thumb|alt=]]
+
'''Revision Tracking'''
  
*<u>'''Technical Issue Troubleshooting'''</u>:
+
This feature prevents author edits from moving to the live ("stable") version of a page until the Associate Editor has approved the changes (Note: the pending revised version is actually visible to anyone in a separate tab from the stable version, and once changes are approved, the two tabs collapse back down to the one "stable" version).
  
#Be a direct liaison with [[mailto:sevastian82@gmail.com <u>IT Support</u>]] to resolve technical issues noted by the other Associate Editors and authors in a timely manner.
+
'''Watchlist'''
  
*<u>'''Streamlining and Automating Site'''</u>:
+
The watchlist is a list of pages chosen by the Associate Editor which will help keep them notified of changes made to those pages as well as provide a single webpage where they can view all altered pages with pending changes. An initial setup and configuration of the watchlist is required.
 +
<br />
  
#Help develop ideas for process improvement and automation of the CCGA site.
+
===Watchlist===
#Communicate the technical language for implementation of the improvements when possible.
 
#Provide technical review as processes are being developed and implemented.
 
  
==How to Create a New User Account==
+
====Essential steps:====
  
#Sign into your personal CCGA account
+
*Log in! You cannot see your watchlist if you are not logged in.
#On left side of the homepage, click on “Special pages”
+
*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 (figure below).
#Under the subheading Long/create account, click on “Create account”
+
**Make sure your watchlist filter isn’t removing pages! For instance, in the example below, any changes older than 1 day would not appear in the watch list (set to a longer time period).
#Fill out form such as the example below and click "Create account"
+
**Make sure email notification is enabled and at what frequency you wish to receive notifications of changes pending approval (suggested timeframe is weekly).
#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.
 
#IMPORTANT: Add the information to the [[User Access Log|<u>User Access Log</u>]].[[File:Create account example.jpg|none|thumb]]
 
  
==How to Add Categories to a Page==
+
<br />[[File:Editor01.png|frameless|800x800px]]
  
#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.
 
#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.
 
#Click on the hamburger icon on the upper right and select "Categories" from the drop down menu (see image below).
 
#In the box, add in categories appropriate to the page using the exact language of the options available here: [[All Categories|<u>All Categories</u>]].
 
#Save changes.
 
#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.
 
  
[[File:Inserting Categories.jpg|none|thumb|871x871px]]
+
====Approving Revisions:====
 +
 
 +
#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 Associate Editor needs to approve/disapprove the edits.  <br />[[File:Editor02.png|frameless]]      <br />Note, as the FlaggedRevs system was recently implemented, all pages are currently listed as “no reviewed versions”.  <br />[[File:Editor03.png|frameless|600x600px]] <br />
 +
#As an Associated Editor, click on “review pending changes”, which will allow you to see the differences between the original and the suggested revised page.  You can review changes in two modes: Visual or Wikitext. '''The default view is Wikitext, but once you click on Visual, the site should remember your last setting.'''  <br />[[File:Editor-selection.png|frameless]] <br />
 +
##<u>Visual mode (likely preferred method)</u> <br />[[File:Editor04.png|frameless|900x900px]]    <br />''Red text'' means removed and the ''Green text'' means added.  The functionality will be similar to popular document creation software.
 +
##<u>Wikitext mode</u>  <br />There is more functionality in this mode to manipulate the wiki syntax (for advanced editors this may be the best way to review long pages and also to spot syntax errors)
 +
#To approve/disapprove edits, go to the “Review this revision” box at the bottom of the page (see image below). 
 +
##IMPORTANT NOTE: You can only accept or reject all the new revisions that were saved together at once (cannot accept some and reject some) – if only some changes are desired, the Associate Editor will need to reject the revision and then manually re-edit the page to add in the new wanted changes or accept all the changes and manually remove the new ones that are not desired.
 +
##Associate Editors can choose the quality/style of the revision (accuracy, depth and readability).
 +
##If an Associate Editor chooses to disapprove the revision, a comment can be made for the reasoning.  <br />[[File:Editor07.png|frameless|600x600px]]      <br />'''<u>Until revisions are approved, they will not appear as the default view for a page.</u>'''  <br />
 +
#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.
 +
 
 +
====Book Conversion (Moving Content to a New WHO Book; HAEM4 to HAEM5 as an example):====
 +
 
 +
*Content moved from a prior page will be present beneath a purple instructional box (see example image below).  The author should use that content and other current sources to update the content in the related section above it.  You can then have the authors or you delete the old content and purple instructional boxes.
 +
**Note: The purple instructional boxes can be TRICKY to remove and so if you need help, please don't worry about it and just email CCGA@cancergenomics.org when the page is complete to get help on the removal.
 +
**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 were performed with the following page conversion types:
 +
 
 +
#Note: HAEM4 content have been assigned to HAEM5 counterparts when possible.
 +
##New disease entity in HAEM5 - no prior content to convert (add content from scratch).
 +
##Disease entity only in HAEM4 and not in HAEM5 - no content was converted.
 +
##Same disease entity exists in HAEM4 and HAEM5 but no prior content added into HAEM4 page - no content to bring over to HAEM5 page (add content from scratch).
 +
##Same disease entity exists in HAEM4 and HAEM5 with prior content added into HAEM4 page - content brought in from HAEM4 page (update content).
 +
##Disease entity in HAEM5 represents multiple diseases in HAEM4 - Content from most completed HAEM4 page added to HAEM5 page with notes in conversion instructions on the HAEM5 page indicating all the relevant HAEM4 pages to consider for content (update content).
 +
##Disease entity in HAEM4 is now split into multiple disease entities in HAEM5 - Notes in conversion instructions on each relevant HAEM5 page indicate the relevant HAEM4 page to consider for content (update content).
 +
##Note: The automated process has also attempted to convert older template structure to the current template on all HAEM5 pages 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 sections.
 +
 
 +
[[File:HAEM4 content example.png||frameless|900x900px]]
 +
 
 +
If a HAEM5 page has one or more HAEM4 pages, see example below of the contents of one of the pages being automatically transferred and that all the relevant pages HAEM4 pages are listed in the Conversion Notes box at the top of each page. The first indicated page is the one that had its contents transferred. If relevant pages were empty or if no relevant pages were identified, there will not be a Conversion Notes box.
 +
 
 +
[[File:HAEM4 conversion example.png||frameless|900x900px]]
 +
 
  
==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.
 
  
#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.
+
<u>Extra functionality if of interest</u> - Browsing history interactively (see image below): 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:  <br />[[File:Editor06.png|frameless|900x900px]]  <br />
#The person who provides access will add the new contributor information into the user access log at [[User Access Log|<u>User Access Log</u>]].
 
#It is encouraged that ABMGG trainees, pathology residents or other post-graduate trainees collaborate with a mentor/sponsor who can help curate their work.
 
#Individuals will be required to review and agree with the “Honor Code for CCGA Content Contributor”.
 
#The GRDC reserves the right to deny CCGA site editorial access to any applicant and to remove access as deemed appropriate.
 

Latest revision as of 12:08, 10 March 2024

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 and instructional text (in blue color) 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 (further technical details in "Technical Editorial Review Process" below):
  1. Approve the page using the FlaggedRevs system.
  2. Ensure the page has been added 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.
  • 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 New Version of a WHO Classification of Tumours book:
  1. Content from any pertinent prior page will be automatically pulled into the new book page, with any conversion notes highlighted in boxes with purple headers.
  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.

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. Any member of the CCGA Knowledgebase workgroup or Genomic Resources Development Committee (GRDC) may provide access immediately if requested to do so by an individual. However, typically accounts will be created by the Technical Editor following receipt of a completed Volunteer Form.
  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.

Technical Editorial Review Process

Each Associate Editor is responsible for regularly determining the appropriateness of their author edits and approving the final changes. The instructions below will provide a guide to (1) perform editing in the CCGA site, and (2) set up and configure the features built into the site to streamline the editing process. The basic process for monitoring and approving changes will utilize two main functions:

Revision Tracking

This feature prevents author edits from moving to the live ("stable") version of a page until the Associate Editor has approved the changes (Note: the pending revised version is actually visible to anyone in a separate tab from the stable version, and once changes are approved, the two tabs collapse back down to the one "stable" version).

Watchlist

The watchlist is a list of pages chosen by the Associate Editor which will help keep them notified of changes made to those pages as well as provide a single webpage where they can view all altered pages with pending changes. An initial setup and configuration of the watchlist is required.

Watchlist

Essential steps:

  • Log in! You cannot 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 (figure below).
    • Make sure your watchlist filter isn’t removing pages! For instance, in the example below, any changes older than 1 day would not appear in the watch list (set to a longer time period).
    • Make sure email notification is enabled and at what frequency you wish to receive notifications of changes pending approval (suggested timeframe is weekly).


Editor01.png


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 Associate Editor needs to approve/disapprove the edits.
    Editor02.png
    Note, as the FlaggedRevs system was recently implemented, all pages are currently listed as “no reviewed versions”.
    Editor03.png
  2. As an Associated Editor, click on “review pending changes”, which will allow you to see the differences between the original and the suggested revised page.  You can review changes in two modes: Visual or Wikitext. The default view is Wikitext, but once you click on Visual, the site should remember your last setting.
    Editor-selection.png
    1. Visual mode (likely preferred method)
      Editor04.png
      Red text means removed and the Green text means added. The functionality will be similar to popular document creation software.
    2. Wikitext mode
      There is more functionality in this mode to manipulate the 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 this revision” box at the bottom of the page (see image below). 
    1. IMPORTANT NOTE: You can only accept or reject all the new revisions that were saved together at once (cannot accept some and reject some) – if only some changes are desired, the Associate Editor will need to reject the revision and then manually re-edit the page to add in the new wanted changes or accept all the changes and manually remove the new ones that are not desired.
    2. Associate Editors can choose the quality/style of the revision (accuracy, depth and readability).
    3. If an Associate Editor chooses to disapprove the revision, a comment can be made for the reasoning.
      Editor07.png
      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.

Book Conversion (Moving Content to a New WHO Book; HAEM4 to HAEM5 as an example):

  • Content moved from a prior page will be present beneath a purple instructional box (see example image below). The author should use that content and other current sources to update the content in the related section above it. You can then have the authors or you delete the old content and purple instructional boxes.
    • Note: The purple instructional boxes can be TRICKY to remove and so if you need help, please don't worry about it and just email CCGA@cancergenomics.org when the page is complete to get help on the removal.
    • 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 were performed with the following page conversion types:

  1. Note: HAEM4 content have been assigned to HAEM5 counterparts when possible.
    1. New disease entity in HAEM5 - no prior content to convert (add content from scratch).
    2. Disease entity only in HAEM4 and not in HAEM5 - no content was converted.
    3. Same disease entity exists in HAEM4 and HAEM5 but no prior content added into HAEM4 page - no content to bring over to HAEM5 page (add content from scratch).
    4. Same disease entity exists in HAEM4 and HAEM5 with prior content added into HAEM4 page - content brought in from HAEM4 page (update content).
    5. Disease entity in HAEM5 represents multiple diseases in HAEM4 - Content from most completed HAEM4 page added to HAEM5 page with notes in conversion instructions on the HAEM5 page indicating all the relevant HAEM4 pages to consider for content (update content).
    6. Disease entity in HAEM4 is now split into multiple disease entities in HAEM5 - Notes in conversion instructions on each relevant HAEM5 page indicate the relevant HAEM4 page to consider for content (update content).
    7. Note: The automated process has also attempted to convert older template structure to the current template on all HAEM5 pages 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 sections.

HAEM4 content example.png

If a HAEM5 page has one or more HAEM4 pages, see example below of the contents of one of the pages being automatically transferred and that all the relevant pages HAEM4 pages are listed in the Conversion Notes box at the top of each page. The first indicated page is the one that had its contents transferred. If relevant pages were empty or if no relevant pages were identified, there will not be a Conversion Notes box.

HAEM4 conversion example.png


Extra functionality if of interest - Browsing history interactively (see image below): 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:
Editor06.png