How to Curate a Disease Page

CCGA Disease curation guidelines: How to curate a Disease page in CCGA

Summary:

TO BE WRITTEN, IF NECESSARY EG: Steps in the curation process.

After you have decided to become a curator, contact ???, read this tutorial, watch the tutorial and sign your Honor Agreement.
Contact your editor and gain permission to the CCGA site
Chose or be assigned a DISEASE page to curate
Curate the page by reading suggested reading materials and authoring content on the DISEASE page (DO NOT PLAGIARIZE!)
Contact Editor upon completion of DISEASE page curation.

Introduction:

Thank you for volunteering to help curate the Compendium of Cancer Genome Aberrations (CCGA)! Your help will make this resource a valuable tool for users of the CCGA, including researchers, clinicians and others. This short, written description will help you get started and should serve as a collection of best practices and content style as you curate. Please sign and date and return your “Honor Agreement” before starting your curation, which is available here: . (TO DO: make link to Honor Agreement, downloadable by PDF, if possible).There is also a video that should be very helpful to show you how to curate, and is required before you start to curate. It can be seen here:

TO DO: create a tutorial video based on this script

The basic logic for CCGA pages is that there is basic Gene and Protein (and mutation) molecular biology-type information on the “Gene Pages”, and that there is Disease and clinical-type information type on the “Disease pages”. The CCGA is especially interested in the curation fusion genes/mutations that arise in disease, esp. in the hematological cancers. However, the dividing line between "Gene/Protein/Mutation" information and "Disease" information is sometimes hard to determine (For example, in the case of describing fusion gene's value in diagnostic or prognostic tests i a specific disease). Basically, this type of "cross over" Molecular Disease information can be included IN ABBREVIATED form on the GENE pages, and will be addressed more fully on the DISEASE pages. These guidelines will help you determine what information goes where. Please note that you should plan to spend between 4-8 (???) hours in curating the information onto a single gene page, more if you are unfamiliar with the gene.

Editor:

Your curation of the DISEASE information will be aided and edited and reviewed by an “EDITOR”. Your assigned Editor will be your go-to person to help you curate and review your curated information after you are done curating. Please note that this written document and the curation tutorial cannot cover all the questions and decisions your will be faced with as you curate. Therefore, PLEASE feel free to contact your editor with any questions. You will need to contact your assigned editor to get “write” permissions to the CCGA so that you can create and edit pages in the Wiki.

Wiki Pages:

The CCGA web site is based on wiki pages and can be accessed here : http://www.ccga.io/index.php/Main_Page. please ask your editor for write permissions.

The functionality of the wiki pages are described in brief, at MediaWiki, see here: https://www.mediawiki.org/wiki/MediaWiki.

There are also short videos available on youtube that describe MediaWiki functionality here: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l. Others are available, by searching youtube for "MediaWiki tutorial".

Disease Pages:

You will be asked to curate a Disease page. This may be a full disease or a "sub-disease": See list here: (Do we have a list of Disease that are priority???) A “Gene specific Template” has been produced which provides you with very nice Media Wiki Template to fill in with information you have curated. It is shown here. http://www.ccga.io/index.php/Disease_Category_Overview_Template

Note that the Template already has the markup language you will need for headers, links, and other syntax to be used in the Disease Paes. Please do not change the syntax of the template, so users of the CCGA pages will want to see the same format from page to page.

NOTE: When you do large edits on a Wiki page, the security makes sure you are a human with test at the top of the page and a simple mathematical formula you must complete, as below. YOU MUST answer the mathematical equation for your edits to be saved.

Your edit includes new external links. To protect the wiki against automated spam, we kindly ask you to solve the following task below and enter the answer in the box in order to save your edit (more info): 45−1 =

Disease curation using the “Disease Category Overview Template” MediaWiki Template in CCGA

In most cases, the Disease you will curate has already been created, based on the Disease Category Overview Template. However, if not, you will need to copy the Disease Category Overview Template to a new page.

Go to the disease specific template (http://www.ccga.io/index.php/Disease_Category_Overview_Template)
Click “edit source” link at top center-right of page
Copy the entire page (eg on a Mac, “command (cmd) a”, and then “cmd c”
Open in another browser window the gene page you will curate
Paste in the template (cmd v) and then save (at bottom of page)

The template provides an easy "fill in the blanks" WikiMedia page which already has formatted markups (for headers) and has examples for you to follow. The Template is described briefly, below.

Sections:

Primary Authors
General Disease Overview / Description of Cancer Category
WHO Classification Pages (Includes Links to Content)
Other Related Pages (Includes Links to Content)
Additional Information
References

The sections of the Template are for ease of reading for the USER: HOWEVER, as a curator, you will want to curate and load information in the WIKI in a non-linear fashion. This is the suggested workflow:

1. Primary Authors

By adding your name to the PRIMARY AUTHORS section you can make sure that no-one else is curating this gene now, and so you will get credit for curating this information by your peers.

3. WHO Classification Pages (Includes Links to Content)

To familiarize yourself with recent information you are curating, “Your Disease of Interest” (designated YDI throughout), please start with reading the relevant section in the Book "2017 World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues"

(Is this correct? If not correct, what is the place to start?)

(Is this where an author would also go to PubMed, for a review and/or key articles?)

EXAMPLES

PLEASE NOTE: DO NOT PLAGIARIZE. You can borrow phrases here or there without attribution. Yo can even use a sentence here and there if you attribute the quote directly ( eg: "From NCBI"). However, you CANNOT cut and paste whole paragraphs from other resources into the CCGA pages.

4. Other Related Pages (Includes Links to Content)

(Description)

EXAMPLES

5. Additional Information

(Description) EXAMPLES

2. General Disease Overview / Description of Cancer Category