Changes

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

==Gene curation using the “Gene specific Template” MediaWiki 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.

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.

#Open in another browser window the gene page you will curate

#Open in another browser window the gene page you will curate

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

#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.  

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:

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. ====

=== 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.

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.

==== 8. EXTERNAL LINKS Section. ====

=== 8. 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:

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:

<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>

<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>

==== 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).

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"

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 ===

This is where you will be compelled to find and read journal articles and books text.  You may have found some relevant articles listed at some of the EXTERNAL LINKS sites (esp. Uniprot and NCBI Gene), but you will have to search for new, relevant articles in PubMed and also from the Hematological Cancer resource "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf).  Note that you will be finding information that will fit in other sections of the gene template, like CANCER CATEGORY TYPE and COMMON ALTERATION TYPES and REFERENCES.  This section should describe in 1 paragraph (approx 5-7 sentences):

This is where you will be compelled to find and read journal articles and books text.  You may have found some relevant articles listed at some of the EXTERNAL LINKS sites (esp. Uniprot and NCBI Gene), but you will have to search for new, relevant articles in PubMed and also from the Hematological Cancer resource "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf).  Note that you will be finding information that will fit in other sections of the gene template, like CANCER CATEGORY TYPE and COMMON ALTERATION TYPES and REFERENCES.  This section should describe in 1 paragraph (approx 5-7 sentences):

# the molecular function of the gene/protein

# the molecular function of the gene/protein

We suggest when writing in the wiki, that you use as "placeholder" with the authors last name (in parentheses) to denote the reference at the end of the sentence, and write the reference used in to the REFERENCE Section (section 9) using the proper syntax suggested for either book, article or internet source.  When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.

We suggest when writing in the wiki, that you use as "placeholder" with the authors last name (in parentheses) to denote the reference at the end of the sentence, and write the reference used in to the REFERENCE Section (section 9) using the proper syntax suggested for either book, article or internet source.  When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.

==== 4. CANCER CATEGORY/TYPE Section ====

=== 4. CANCER CATEGORY/TYPE Section ===

NOTE:  this section crosses over into the "Disease Pages" in CCGA, and is meant to be a short summary or introduction to the information that is already on the Disease information pages, or will be written there in the future.  This section is to be a list of cancer types important to CCGA, and for the most part, already created cancer disease pages in CCGA.  As you read journal articles and abstracts from Pubmed and content in "World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues" and OMIM, you should be filling in content on this section.  As you come across cancer types that are associated with YGI, you should search CCGA for those diseases (or subclasses of disease) and read the content there.  You should link YGI to the Disease page in CCGA (see examples, below).  You may be able to summarize the content you have found in CCGA disease pages.  The extent of the content should be a short paragraph for each cancer type (1-7 sentences).  The content should include:  the frequency of YGI mutations or fusion genes associated to patients with that specific disease, whether the mutation is a common mutation in that specific disease (if it is uncommon, you are likely NOT to reference that fact), interesting information having to do with drugs, therapy, prognosis and/or outcome.  In some cases, you will find that some CCGA Diseases/Cancer Types have not yet been created.  Please do NOT create a disease page.  Instead, create a new sub heading and write the content in that new section. As CCGA grows, we will add new Diseases/Cancer types and link to the Gene pages later (see example of CML, below).

NOTE:  this section crosses over into the "Disease Pages" in CCGA, and is meant to be a short summary or introduction to the information that is already on the Disease information pages, or will be written there in the future.  This section is to be a list of cancer types important to CCGA, and for the most part, already created cancer disease pages in CCGA.  As you read journal articles and abstracts from Pubmed and content in "World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues" and OMIM, you should be filling in content on this section.  As you come across cancer types that are associated with YGI, you should search CCGA for those diseases (or subclasses of disease) and read the content there.  You should link YGI to the Disease page in CCGA (see examples, below).  You may be able to summarize the content you have found in CCGA disease pages.  The extent of the content should be a short paragraph for each cancer type (1-7 sentences).  The content should include:  the frequency of YGI mutations or fusion genes associated to patients with that specific disease, whether the mutation is a common mutation in that specific disease (if it is uncommon, you are likely NOT to reference that fact), interesting information having to do with drugs, therapy, prognosis and/or outcome.  In some cases, you will find that some CCGA Diseases/Cancer Types have not yet been created.  Please do NOT create a disease page.  Instead, create a new sub heading and write the content in that new section. As CCGA grows, we will add new Diseases/Cancer types and link to the Gene pages later (see example of CML, below).

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/Acute_Myeloid_Leukemia_(AML)_and_Related_Precursor_Neoplasms Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms]'''  

==== 6. COMMON ALTERATION TYPES Section ====

=== 6. COMMON ALTERATION TYPES Section ===

==== 7. INTERNAL PAGES Section ====

=== 7. INTERNAL PAGES Section ===

After you have completed the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES, you will be more knowledgeable about the other INTERNAL PAGES that are relevant to information on YGI page.  These will include links to diseases, and links to fusion partner genes.  In fact, these links will essentially collect all the related INTERNAL PAGES from the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES sections, all in one place.

After you have completed the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES, you will be more knowledgeable about the other INTERNAL PAGES that are relevant to information on YGI page.  These will include links to diseases, and links to fusion partner genes.  In fact, these links will essentially collect all the related INTERNAL PAGES from the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES sections, all in one place.

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.''

==== 9. REFERENCES section ====

=== 9. REFERENCES section ===

When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.

When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.