Author Instructions

Introduction

Thank you for your interest in contributing to this community effort.

• Please complete the Volunteer Form and the Editor-in-Chief will be happy to discuss your interests and next steps.

1. Pages in need of authors can be found here: Volunteer Assignments and Opportunities (see “Authors” column and look for any that are not assigned; every attempt is made to keep this updated).
2. Trainees are highly encouraged and welcome to participate in this effort. Trainees are asked to work with a mentor to help review their page content before completion. If the trainee needs help identifying a mentor, one can be provided upon request.
3. We will be creating content for all entities with genetic findings in the current WHO Classification of Tumours books. This content is meant to be multi-sourced, including referencing the latest literature, guidelines, etc.
4. For diseases that are present in multiple WHO books, our goal is to have one page for a disease entity from a primary book (the primary book is selected based on being the most relevant for that disease), with related content from other body sites also added to that page.

• For pages that do not yet have any content, authors will be connected by the Editor-in-Chief with an Associate Editor based on their disease section(s) of interest. 

• Authors will be given a username and password by the Technical Associate Editor after they complete the Volunteer Form.  
• Author names will be added to the top of any page(s) that they wish to complete so others know they’re in process.

• Pages are based on current WHO entries and contain pre-loaded templates. Authors can work directly on the CCGA site. Authors can instead use a Word template (see section below to download; please track references by PMIDs as the site allows for automatic input of references based on PMIDs) and then copy/paste the content into the wiki site.
• There are two types of pages currently needing authors:

1. Disease category overview pages (for example see Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms), which are summaries of a group of diseases with links to all other relevant content. These will often be completed by Associate Editors but can be authored by others if interested.
2. Disease-specific pages (for example see any links on the AML page), which is for individual disease entities and much more detailed.
3. Gene-specific pages (these pages are in the process of being automated for data import and not requiring new authors at this time).

• For more details on how you use the site to be an author, please watch an instructional video (see section below).
• Content inclusion details:
  • Populate all the tables (i.e., for immunophenotype, chromosomal rearrangements, genomic gain/loss/LOH, etc) when applicable (DO NOT delete tables).
  • Insert N/A into sections or tables when there is not applicable content; for tables, delete the examples.
  • Use HUGO-approved gene names and symbols (italicized when appropriate), HGVS-based nomenclature for variants, as well as generic names of drugs and testing platforms or assays if applicable
  • The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged.
  • Additional section-based instructions can be found in the Word templates.

• For the timeline, there’s some flexibility and please work with your Associate Editor to set a target date.
• Once a page is complete, please:

1. If present at the top of the page, delete the statement "This page is under construction. We need you help! Please consider joining in the project and submitting a review".
2. Email the appropriate Associate Editor that the page is complete.

• For technical issues or any additional questions, please Contact us. If applicable, 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.

• Can you modify a page that has already been completed by other authors? Yes! The CCGA is a wiki-based platform with the intention that contributors can modify any page at any time if something is not accurate or new evidence and references would be beneficial to share. This will allow up-to-date accurate content to be available to the community. Primary authorship will typically be listed as those individuals that initially completed the page content, and inquiries can be made by Email if a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section.

Highlights Based on Recurrent Questions

1) Anyone who contributes significant effort can be an author (trainee or experienced, academic or industry position, CGC or non-CGC member, lab director, bionformatician, pathologist, various trainees, etc).

2) Please include images whenever possible (not copyrighted material; credit will be given to your image submissions in the figure legend).

3) Please DO NOT delete sections or tables; insert N/A into sections or tables when there is not applicable content; for tables, also delete the examples so the page looks completed. We keep all sections and tables for continuity of content and for the opportunity to add to those areas in the future if more information becomes available.

4) References can be added anywhere in the text or within tables (please DO NOT add references to the section titles).

5) While a subset of content from the WHO book page can be included and referenced, please DO NOT directly copy any content. Also, the goal of CCGA is not to replicate the WHO book content but rather to include all sources of relevant clinical information (PubMed articles, links to other sites with helpful content, data visualizations, etc) for diseases present in the WHO books.

6) The information to be included in CCGA is focused on clinically relevant content on the genetics of each disease (i.e., what would you want to know to write a clinical report).

7) While there is other information on the page such as morphologic features to give an overview of each disease, the main focus is to write a thorough summary of the clinically relevant genetic information.

8) Even if you're not a primary author on a page, please do update any page that has an inaccuracy or for which you've found additional useful content. This is a living crowdsourced wiki!

Video Tutorial

• A video tutorial on how to author in real-time an overview or disease entity-specific page is available: Video Tutorial. Revised videos for the recently updated templates will be available in the near future.

Word Version Templates

• For a Word document template for authoring a disease-specific page before transferring content online please see File:Disease or Entity-Specific Template Word Version with Instructions.docx.

• For a Word document template for authoring an overview page before transferring content online please see File:Disease Overview Template Word Version with Instructions.docx.

• For a Word document template for gene-specific page File:Gene-Specific Template Word Version with Instructions.docx.

• Note: Additional helpful information and instructions are provided in these Word templates. If applicable, please do use the provided tables.

Policy for Inclusion of Figures on the CCGA Site

Use of illustrative figures on the Compendium of Cancer Genome Aberrations (CCGA) is encouraged. This policy defines the process for inclusion of a figure.

1. For figures created by an individual or provided from their lab, the PHI must be removed and the submitter’s name and institution included in the figure legend.
2. For figures from any other source (such as a website or published paper), a link to the image content, if openly accessible, can be used on the CCGA page.  If such a link is not possible, written permission must be obtained by the person creating the CCGA page before addition to the page.  This written permission should be shared with the Associate Editor of the related section and copied to ccga@cancergenomics.org.  The figure legend should include the appropriate reference and confirmation that permission was obtained.

How to Cite CCGA Pages

• Citation for a CCGA page on an Author's CV:

1. Naeini Y, Quintero-Rivera F. “Myeloid Sarcoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), created 06/23/2018, https://www.ccga.io/index.php/Myeloid_Sarcoma.

• Citation in Reports or Other Media:

1. Naeini Y, Quintero-Rivera F. “Myeloid Sarcoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated 01/02/2020, https://www.ccga.io/index.php/Myeloid_Sarcoma.