How to Curate a Gene Page

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CCGA Gene curation guidelines: How to create a page in CCGA

Summary:

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 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:

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 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

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

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

Copying the Template to a new gene page.

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.

  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
  3. Copy the entire page (eg on a Mac, “command (cmd) a”, and then “cmd c”
  4. Open in another browser window the gene page you will curate
  5. Paste in the template (cmd v) and then save (at bottom of page)

Curating the Template with Gene Information

Describing the Template information.

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:

  1. Primary Authors
  2. Synonyms
  3. Genomic Location
  4. Cancer Category/Type
  5. Gene Overview
  6. Common Alteration Types
  7. Internal Pages
  8. External Links
  9. 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 section. 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. 2. EXTERNAL LINKS Section. To familiarize yourself with the latest information on the Gene you are curating, “Your Gene of Interest” (designated YGI throughout), please start with one of the last sections of the Template, the EXTERNAL LINKS Section. The listed resources will provide exhaustive (but not necessarily recent) molecular information about YGI, its mutations and its place in disease and cancer and treatment. The resources suggested as EXTERNAL LINKS as of Dec 2018 are as follows:

  1. Atlas of Genetics and Cytogenetics in Oncology and Haematology
  2. COSMIC
  3. CIViC
  4. St. Jude ProteinPaint
  5. Precision Medicine Knowledgebase (Weill Cornell)
  6. Cancer Index
  7. OncoKB
  8. NCBI Gene
  9. My Cancer Genome
  10. UniProt
  11. Pfam
  12. GeneCards
  13. OMIM
  14. LOVD(3)
  15. TICdb

Please note that some genes may have special resources devoted to them. An example is the International Agency for Research on Cancer page devoted to TP53 (see http://p53.iarc.fr/). This is unusual, but P53 is the most studied gene and protein on earth, so in this case, a specialized resource is justified. TO find if there are any special resources for YGI, perform a google search and/or

Please note that not all the external resources have links to YGI, and then please curate “NO entry for YGI at resource”. For example, the gene MEMCOM is not present in the OncoKB site, nor the CIViC site. In these cases, please write in "No Entry for YGI at Resource" in place of the hyperlink to that site. Please check all links after you have curated them, as some of the link syntax can be changed as you curate. As you read through each of the EXTERNAL LINK resources, note information that you can use. For example, the NCBI gene site and the GeneCard site are especially rich in Synonym information. Either note the information directly in the wiki page for YGI, or in a text document that you keep on your computer (and can cut and paste easily into the Wiki page later), or you can take notes by hand and re-write into the wiki page later (not suggested, very error-prone).

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.

3. SYNONYMS Section As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp.

  Appendix

Resources:

  1. Gene-Specific-Template: http://www.ccga.io/index.php/Gene-Specific_Template
  2. MediaWiki Help: https://www.mediawiki.org/wiki/MediaWiki
  3. YouTube videos for how to use MediaWiki: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l
  4. The CCGA web site is here : http://www.ccga.io/index.php/Main_Page
  5. Download “WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf
  6. Search for your YGI to see which cancer is associated with mutations in YGI. Read and collect annotations for YGI.


  FAQ (Frequently Asked Questions)

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