Changes

<big>CCGA Gene curation guidelines:  How to create a page in CCGA

<big>CCGA Gene curation guidelines:  How to create a page in CCGA

</big>

</big>

Summary:

== Summary: ==

Introduction:

== 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:

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

 

''TO DO:  create a tutorial video based on this script''

 

The basic logic for CCGA pages is that there is basic Gene and Protein molecular biology-type information on the “Gene Pages”, and that there is Disease and clinical-type information type on the “Disease pages”.  However, the dividing line between these types of information is sometime hard to determine.  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.

The basic logic for CCGA pages is that there is basic Gene and Protein molecular biology-type information on the “Gene Pages”, and that there is Disease and clinical-type information type on the “Disease pages”.  However, the dividing line between these types of information is sometime hard to determine.  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:

 

== Editor: ==

Your curation of the gene and protein 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.   

Your curation of the gene and protein 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:

 

== Wiki Pages: ==

The CCGA web site is here : http://www.ccga.io/index.php/Main_Page The CCGA is based on wiki pages.  The functionality of the wiki pages are described in brief, at MediaWiki, see here:  https://www.mediawiki.org/wiki/MediaWiki.   

The CCGA web site is here : http://www.ccga.io/index.php/Main_Page The CCGA is based on wiki pages.  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

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

Gene Pages:

 

== Gene Pages: ==

You will be asked to choose from a number gene pages that you would like to curate. See list here: http://www.ccga.io/index.php/List_of_Gene_Pages

You will be asked to choose from a number gene pages that you would like to curate. See list here: http://www.ccga.io/index.php/List_of_Gene_Pages

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/Gene-Specific_Template  

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/Gene-Specific_Template  

Gene curation using the “Gene specific Template” MediaWiki Template in CCGA

== Gene curation using the “Gene specific Template” MediaWiki Template in CCGA ==

Copying the Template to a new gene page.

Copying the Template to a new gene page.

In most cases, the Gene you will curate has been created, based on the Gene specifc template. However, if not, you will need to copy the Gene specifc template to a new page.

 

In most cases, the Gene you will curate has been created, based on the Gene specific template. However, if not, you will need to copy the Gene specific template to a new page.

 

1. Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_Template )

1. Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_Template )

2. Click “edit source” link at top center-right of page  

2. Click “edit source” link at top center-right of page  

3. Copy the entire page (eg on a Mac, “command a”, and then “command a”

3. Copy the entire page (eg on a Mac, “command a”, and then “command a”

5. Paste in the template (cmd v) and then save (at bottom of page)

5. Paste in the template (cmd v) and then save (at bottom of page)

   

   

 

=== Curating the Template with Gene Information ===

Curating the Template with Gene Information

==== Describing the Template information. ====

Describing the Template information.

The template seeks to provide  

The template seeks to provide