Compendium of Cancer Genome Aberrations

Associate Editor Instructions: Difference between revisions

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#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 their page is complete, '''<u>Perform Editorial Review</u>'''<u>:</u>
*After authors indicate their page is complete, '''<u>Perform Editorial Review (see further details in the "Editorial Review Process" section)</u>'''<u>:</u>


#Review the content for accuracy and appropriate completeness.
#Review the content for accuracy and appropriate completeness.
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#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 such as adding linking categories to the page.
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#Solicit original page authors or help find new authors to update pages in a timely manner.
#Solicit original page authors or help find new authors to update pages in a timely manner.
#Perform editorial review of the updated content.
#Perform editorial review of the updated content.
==Technical Associate Editor-Specific Functions==
*'''<u>Onboarding Process</u>''':
#Following receipt of the [https://mms.cancergenomics.org/members/form.php?orgcode=CGC&fid=3830649 <u>Volunteer Form</u>], 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.
#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>]].
*
*<u>'''After Editorial Review Completed Process'''</u>:
#Add Categories to the page to link searching functions on the homepage (see "How to Add Categories to a Page" section below).
#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): <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.
#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 [[HAEM4: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=]]
*<u>'''Page Conversion/Creation for New Versions of WHO Classification of Tumours Books'''</u>:
#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.
*<u>'''Technical Issue Troubleshooting'''</u>:
#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.
*<u>'''Streamlining and Automating Site'''</u>:
#Help develop ideas for process improvement and automation of the CCGA site.
#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==
#Sign into your personal CCGA account
#Go to [https://ccga.io/index.php/Special:CreateAccount Create account].
#Fill out form such as the example below and click "Create account"
#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==
#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]]


==Policy for Granting of CCGA Contributor Access==
==Policy for Granting of CCGA Contributor Access==
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#The CCGA leadership reserves the right to deny CCGA site authorship/editorial access to any applicant and to remove access as deemed appropriate.
#The CCGA leadership reserves the right to deny CCGA site authorship/editorial access to any applicant and to remove access as deemed appropriate.


<br />
==Editorial Review Process==
==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:
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:
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====Conversion Notes:====
====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.
 
**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:
For the HAEM4 to HAEM5 book conversion, several key automatic processes have been performed:
#HAEM4 pages have been assigned to HAEM5 counterparts when possible
#HAEM4 pages have been assigned to HAEM5 counterparts when possible
## 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.
##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.
## 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.
##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.
 
[[File:HAEM4 content example.png||frameless|900x900px]]
[[File:HAEM4 content example.png||frameless|900x900px]]
#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.
#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.
[[File:HAEM4 conversion example.png||frameless|900x900px]]
[[File:HAEM4 conversion example.png||frameless|900x900px]]


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