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How to Curate a Gene Page (view source)
Revision as of 16:09, 5 December 2018
, 16:09, 5 December 2018→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 specific template. However, if not, you will need to copy the Gene specific template to a new 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.
#Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_Template )
#Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_Template )
Sections:
Sections:
# Primary Authors
# Synonyms
# Genomic Location
# Cancer Category/Type
# Gene Overview
# Common Alteration Types
# Internal Pages
# External Links
# 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.
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:
# Atlas of Genetics and Cytogenetics in Oncology and Haematology
# COSMIC
# CIViC
# St. Jude ProteinPaint
# Precision Medicine Knowledgebase (Weill Cornell)
# Cancer Index
# OncoKB
# NCBI Gene
# My Cancer Genome
# UniProt
# Pfam
# GeneCards
# OMIM
# LOVD(3)
# 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).
<big>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.</big>
3. SYNONYMS Section
As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp.