User:Eryk (Wiki Ed)/sandbox/genes and proteins

This is the draft text for a guidebook on genes and protein articles. The final draft has been published in paper form for US and Canadian students in higher ed; it can be seen as free, printable pdf. However, additional suggestions are welcome for future revisions!

This text is given to university and college students in addition to guidebooks on editing and evaluating Wikipedia articles. While there is some overlap, the focus of this guidebook is advice on writing articles about genes and proteins.

We are looking for advice from experienced Wikipedia editors would give to new editors coming from these classrooms. Feedback before Monday, December 21st will be the most helpful!

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Editing Wikipedia articles on genes and proteins

Editing Wikipedia can be daunting for newcomers, especially as a student editor contributing to Wikipedia for the first time as a class assignment. This guide is designed to help you create or expand articles about genes and proteins to Wikipedia.

Be accurate

You are contributing to a resource millions of people use to inform themselves about a cutting edge area of scientific research. Your work for this class will be read by thousands of people, so it is important to be accurate.

By documenting and sharing your knowledge about genes and proteins, you will help Wikipedia provide a wider spectrum of scientific knowledge. With great power comes great responsibility!

Understand the guidelines

Take time to read and understand the suggestions here to make the most of your contributions to Wikipedia. If you post something that does not meet these guidelines, it may take up valuable volunteer time that could have been spent making your contributions, or other content, even better. If you are not comfortable with these guidelines, talk to your instructor about an alternative off-wiki assignment.

Engage with editors

Part of the Wikipedia experience is receiving and responding to feedback from other editors. Do not wait until the last day to make a contribution, or you may miss comments, advice, and ideas. Volunteers from the Wikipedia community might respond or ask questions about your work. If they do, make sure to acknowledge it. Discussion is a crucial part of the Wikipedia process.

Watch out for close paraphrasing

Use your own words. Plagiarizing by copying-and-pasting, or close paraphrasing — when most of the words are changed, but the structure and meaning of the original text remains — is against the rules.

Plagiarism is a violation of your university's academic honor code. Plagiarism on Wikipedia will be caught by other editors, and there will be a permanent online record of it tied to your account. Even standard resources or authors, such as educational resources from organizations like the Chemical Safety Board and abstracts of articles in chemistry journals, are under copyright and should never be directly copied.

The best way to avoid this hassle is to make sure you really understand your material, and write about it in your own words. If you are not clear on what close paraphrasing is, contact your university's writing center.

Be bold!

Take the time to understand the rules and guidelines, and soon you will be contributing important knowledge to a resource you and millions of other people use every day.

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Using reliable sources

Wikipedia prefers "secondary sources." These sources summarize primary sources, and provide an overview of the topic. These include:

Literature reviews or systematic reviews from reliable journals, such as Biochemistry, the Journal of Biological Chemistry, or Cell.
Encyclopedias and specialist textbooks from reliable publishers, such as Oxford University Press, Cambridge University Press, or Wiley.

Exercise caution when using:

Primary sources, where authors documented firsthand experiences.
Nearly all papers published in medical journals.
Blog posts and popular press articles.

For more on good sources, see WP:SOURCE and WP:SCIRS.

What is a shortcut? (Pullout box)

WP:SOURCE is what is known on Wikipedia as a shortcut. You can type this text into Wikipedia's search bar to pull up specific pages.

Choosing an article

Once you have a variety of good sources, choose topics with lots of literature in peer-reviewed sources that do not have good coverage on Wikipedia. Check an article's Talk page for its rating: “Start-class” or “stub” articles need your help! Avoid “Featured” or “Good” articles.

Structuring your genes or proteins article

You can add, remove, or reorder sections for your own topic.

Infobox: If you use one, place it at the very beginning of the article (see next page).
Lead section: A short article summary.
Gene: Where is it located (i.e., which chromosome)? How is it expressed? Do not repeat what is in the infobox.
Protein: Specific information about the protein (describe splice variants, alterations, etc.).
Species, tissue, subcellular distribution: An optional section. What species have this gene? Where is the gene expressed? Describe subcellular compartments or organelles where you would find the protein (i.e., cytoplasm, nucleus, mitochondria, cell membranes).
Function: What does the transcribed protein do?
Interactions: What does the protein interact with, if anything?
Clinical significance: List diseases or conditions that result from a mutation in the gene, or a deficiency or excess of the expressed protein. See Wikipedia's sourcing requirements for medical information at WP:MEDRS.
History section: An optional section describing key aspects of the protein's history. (See next page for details).

Good references for gene and protein articles include Protein C, Gonadotropin-releasing hormone, or Rubisco.

What is a lead section? (Pullout box)

What is a lead section? The lead section is the first section of a Wikipedia article. Good leads summarize the entire article, offering context for important aspects of the topic. Names should come from the UniProt database (free, online) and include the approved HUGO (Human Genome Organisation) symbol, like this:

(UniProt Name) is a protein that, in humans, is encoded by the (HUGO gene symbol) gene.

For more tips, see WP:MCBMOS.

What is MEDRS? (Pullout box)

ANY statement, in any article, that relates to human medical or psychological health must follow a strict set of sourcing guidelines. See WP:MEDRS.

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What is a Protein Infobox? (Pullout box)

What is a infobox? An infobox gives an overview of a protein's (or enzyme or RNA) properties at a glance.

One or more of the following infobox templates as appropriate should be included at the top of each article:

template	description / suggested use	example article containing this template	template filling tool
{{Infobox GNF protein}}	for genes/proteins for which an ortholog is present within the human genome (articles containing this template were created as part of the Gene Wiki project)	Reelin	GeneWikiGenerator (input: HUGO gene symbol)
{{Infobox protein}}	smaller box appropriate for protein family articles where more than one protein is discussed in the same article (e.g., paralogs)	Estrogen receptor	Wikipedia template filling (input: HGNC ID)
{{Infobox nonhuman protein}}	for proteins without a human ortholog	Uterine serpin	—
{{Infobox protein family}}	for protein families (evolutionary related proteins that share a common 3D structure) that are listed in Pfam	T-box	—
{{Infobox rfam}}	for RNA families (evolutionary related non-coding RNAs that share a common 3D structure) that are listed in Rfam	U1 spliceosomal RNA	—
{{Infobox enzyme}}	for enzymes based on EC number (more properly refers to the reaction catalyzed by the enzyme rather than the enzyme itself)	Alcohol dehydrogenase	—

If there is only one human paralog assigned to a given EC number (the ExPASy database maintains EC number to protein mappings), then in addition to a protein infobox, it may be appropriate to also add the corresponding enzyme infobox. Likewise, if there is only one human paralog that has been assigned to Pfam family, then including a protein family infobox may also be appropriate.

Never delete anything from the template — just skip fields you do not know. Add what you can to the right of the equal sign on each line. Most acronyms are explained, with links to sources, on the Template page mentioned above. These include the Mendelian Inheritance in Man (OMIM) database, and Protein Databank (PDB). Cite these sources just like any other fact.

The Image line contains only the file name of the image from Wikimedia Commons. For example:

Image = ChymotrypsinA1.jpg

For templates and links to all relevant databases, see Template:Infobox protein.

Writing history sections

Do not mention research groups or institutions that conducted a study. However, you may list those who made key discoveries relayed to the gene or protein in this section. For example, the scientist or group that first cloned the gene, determined its function, linked it to a disease, or won a major award for the discovery, etc.

Cite your sources

You must have the PubMed ID (PMID) or Digital Object Identifier (DOI) for every journal article you cite, and the ISBN and page number of any book you cite. This enables other editors to verify the accuracy of the information you added.

To add a citation using wiki markup:

Move your cursor to the end of the first sentence you want to cite that source for.
Click the “Cite” tab in the top of the edit box.
In the dropdown Templates menu, select “Cite journal” or “Cite book”, as appropriate.
Type in the PMID, DOI, or ISBN with the page number/s, and then click on the magnifying glass icon (as shown below). The cite tool will automatically process the details.

To add a citation using VisualEditor:

Move your cursor to the end of the block of text you want to cite a source for.
Click “Cite” in the toolbar.
For a book, add the ISBN. For an online source, add the DOI. (There are extra options if you do not know the ISBN or DOI.)
Add any other key information, such as the page number(s) for a book, and insert the citation.

To add a citation using the Wikipedia Template Filling Tool:

Access the tool from this link.
Check the "Add ref tag" and optionally "Pad parameter names and values" boxes.
Paste in the PMID into the "PubMed ID" box.
Press the submit button.
Copy and paste the citation template into the Wikipedia article.

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Useful tips

As you start writing, keep these guidelines in mind:

Never offer medical advice. This includes information about genes related to diseases or treatments. If your work includes any statements about human health, you must follow a very strict set of sourcing guidelines. See more at WP:MEDRS.
The abbreviations of genes follows the HUGO Gene Nomenclature Committee and written in italic font style (the full names are also written in italic). Use abbreviations instead of the full name. For a style guide on gene/protein articles, check out WP:MCBMOS.
When mentioning technical terms for the first time, provide a short plain-English explanation in parentheses, if possible.

Final thoughts

Do not procrastinate! Writing good, reliable Wikipedia articles takes time. Do not wait until the last minute. If you get stuck, always ask your instructor for extra time, rather than adding content to Wikipedia that doe not meet these guidelines.
Check back on your page. It can be interesting to see how your article grows, but you may also have comments and suggestions from other editors, and want to get involved in new developments.
Do you have more questions? You can always ask the Wikipedia Content Expert listed on your course page. You can also post a question to Wikipedia volunteers at the Teahouse: WP:TH