Compendium of Cancer Genome Aberrations

How to Curate a Gene Page: Difference between revisions

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<big>CCGA Gene curation guidelines:  How to curate a page in CCGA
==Steps in the Curation Process==
</big>
==Summary:==


TO BE WRITTEN, IF NECESSARY
#To become a curator, contact ccga@cancergenomics.org to request access to the CCGA site.  You will also be connected with an Associate Editor.
EG:
#Choose or be assigned a few gene pages to curate.
Steps in the curation process.
#Read this tutorial and curate the page by reviewing appropriate related literature and authoring content on the gene page (DO NOT PLAGIARIZE!)
 
#Contact the Associate Editor for questions and upon completion of gene page curation.
#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 few GENE pages to curate
#Curate the page by reading suggested reading materials and authoring content on the GENE page (DO NOT PLAGIARIZE!)
#Contact Editor upon completion of GENE page curation.


==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.  
 
''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 sometime 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 wil 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 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:==
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 premissions.


The functionality of the wiki pages are described in brief, at MediaWiki, see here:  https://www.mediawiki.org/wiki/MediaWiki.   
The 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 “Disease Pages”.  The CCGA is interested in the curation of genes/mutations that arise in cancer.  However, the dividing line between "Gene/Protein/Mutation" information and "Disease" information is sometimes hard to determine (For example, in the case of describing a fusion gene's value in diagnostic or prognostic tests in a specific disease). Basically, this type of "crossover" Molecular Disease information can be included IN ABBREVIATED form on the GENE pages and will be addressed more fully on the related 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 on a single gene page, and more if you are unfamiliar with the gene.


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".
==Associate Editor:==
Your curation of the gene and protein information will be aided and reviewed by an assigned Associate Editor. Please note that this written document cannot cover all the questions and decisions your will be faced with as you curate.  Therefore, PLEASE feel free to contact your Associate Editor with any questions and upon completion of a page.


==Gene Pages:==
==Gene Pages:==
'''''QUESTION: do we need to designate Genes as Drivers vs. passengers?'''''
You will be asked to choose the gene pages you wish to curate from this list: http://www.ccga.io/index.php/List_of_Gene_Pages.
A “Gene specific Template” has been added to these pages for you to use to add your curated information.


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
Note: The gene pages template already has the required headers, links and other syntax.  Please do not change the syntax of the template so there is consistency between similar 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. 


Note that the Template already has the markup language you will need for headers, links, and other syntax to be used in the Gene 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: Save edits to your page frequently or produce content in a Word format of the template and add it into the wiki site subsequently.  For a Word document template for authoring a <u>'''gene-specific page'''</u> before transferring content online please see [[File:Gene-Specific Template Word Version (9-28-21).docx|none|thumb|Gene-Specific Template]].  


NOTE:  When you do large edits on a Wiki page, the security makes sure yo 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.
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 =''
''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 =''


==Gene curation using the “Gene specific Template” MediaWiki Template in CCGA==
==Gene Curation Using the “Gene-Specific Template” in CCGA==
In most cases, the Gene you will curate has already been created, based on the Gene specific template. However, if not, you will need to copy the Gene specific template to a new page.
 
#Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_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.  
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:   
Sections:   
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===2. SYNONYMS Section===
===2. SYNONYMS Section===
As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp. NCBI Gene and GeneCards.  Please italicize the alternative gene names (synonyms).  Please source your information, for example by putting "(from GeneCards and NCBI Gene)" after the information.
As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp. NCBI Gene and GeneCards.  Please italicize the alternative gene names (synonyms).   


===3. GENOMIC LOCATION Section.===
===3. GENOMIC LOCATION Section.===
This information is most easily obtained from GeneCards, in the GeneCards section "Genomics" and subsection "Genomic Locations for YFG" and subsection "Genomic View for YFG"and sub-subsection "Cytogenetic band".  Please source your information, for example by putting "(from GeneCards)" after the information.
This information is most easily obtained from GeneCards, in the GeneCards section "Genomics" and subsection "Genomic Locations for YFG" and subsection "Genomic View for YFG"and sub-subsection "Cytogenetic band".   


===5. GENE OVERVIEW Section===
===5. GENE OVERVIEW Section===
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The example of RUNX1 is shown below.
The example of RUNX1 is shown below.


*'''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_and_Related_Precursor_Neoplasms Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms]'''
*'''[http://www.ccga.io/index.php/HAEM4:Acute_Myeloid_Leukemia_(AML)_and_Related_Precursor_Neoplasms Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms]'''


--- '''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_t(8;21)(q22;q22.1);_RUNX1-RUNX1T1 Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1); RUNX1-RUNX1T1]'''
--- '''[http://www.ccga.io/index.php/HAEM5:Acute_myeloid_leukaemia_with_RUNX1::RUNX1T1_fusion Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1); RUNX1-RUNX1T1]'''


--- '''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_Mutated_RUNX1 Acute Myeloid Leukemia (AML) with Mutated RUNX1]'''
--- '''[http://www.ccga.io/index.php/HAEM4:Acute_Myeloid_Leukemia_(AML)_with_Mutated_RUNX1 Acute Myeloid Leukemia (AML) with Mutated RUNX1]'''


The frequency of ''RUNX1'' mutations is between 5-18% of all AML patients tested [3]. The most common chromosomal translocation is t(8;21)(q22;q22)resulting in RUNX1-RUNX1T1 fusion in ''de novo'' AML, at approximately 7% [2,6].  This translocation confers a favorable prognosis in AML and other neoplasms [2,5,6].  Another ''RUNX1'' alteration is the t(3;21)(q26;q22), in which the RUNT domain of ''RUNX1'' is fused to the entire ''EVI1'' gene.  This translocation is rarely found in patients diagnosed with ''de novo'' AML and is more common in those with therapy-related myelodysplastic syndrome (MDS)/AML [9].  Other mutations in ''RUNX1'' include deletions, missense, splicing, frameshift, and nonsense alterations (mostly loss-of-function or decreased function), and occur at a frequency of approximately 10% in AML patients [6]. These mutations are mechanistically distinct from the chromosomal translocations and confer a worse prognosis [2,5,6].
The frequency of ''RUNX1'' mutations is between 5-18% of all AML patients tested [3]. The most common chromosomal translocation is t(8;21)(q22;q22)resulting in RUNX1-RUNX1T1 fusion in ''de novo'' AML, at approximately 7% [2,6].  This translocation confers a favorable prognosis in AML and other neoplasms [2,5,6].  Another ''RUNX1'' alteration is the t(3;21)(q26;q22), in which the RUNT domain of ''RUNX1'' is fused to the entire ''EVI1'' gene.  This translocation is rarely found in patients diagnosed with ''de novo'' AML and is more common in those with therapy-related myelodysplastic syndrome (MDS)/AML [9].  Other mutations in ''RUNX1'' include deletions, missense, splicing, frameshift, and nonsense alterations (mostly loss-of-function or decreased function), and occur at a frequency of approximately 10% in AML patients [6]. These mutations are mechanistically distinct from the chromosomal translocations and confer a worse prognosis [2,5,6].
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'''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphoblastic Leukemia]'''
'''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphoblastic Leukemia]'''


'''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_BCR-ABL1 Acute Myeloid Leukemia (AML) with BCR-ABL1]'''
'''[http://www.ccga.io/index.php/HAEM5:Acute_myeloid_leukaemia_with_BCR::ABL1_fusion Acute Myeloid Leukemia (AML) with BCR-ABL1]'''


'''[http://www.ccga.io/index.php/Mixed_Phenotype_Acute_Leukemia_(MPAL)_with_t(9;22)(q34.1;q11.2);_BCR-ABL1 Mixed Phenotype Acute Leukemia (MPAL) with t(9;22)(q34.1;q11.2); BCR-ABL1]'''
'''[http://www.ccga.io/index.php/HAEM5:Mixed-phenotype_acute_leukaemia_with_BCR::ABL1_fusion Mixed Phenotype Acute Leukemia (MPAL) with t(9;22)(q34.1;q11.2); BCR-ABL1]'''


See the '''[http://www.ccga.io/index.php/BCR "BCR gene"]''' for additional details of the BCR-ABL1 gene fusion.
See the '''[http://www.ccga.io/index.php/BCR "BCR gene"]''' for additional details of the BCR-ABL1 gene fusion.
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#“WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” Download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf
#“WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” Download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf


==<big>FAQ (Frequently Asked Questions)</big>==


 
'''''QUESTION:  Do we need to designate Genes as Drivers vs. Passengers?'''''
==<big>FAQ (Frequently Asked Questions)</big>==
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