For our SNPedia project, we will write up a description for a SNP then post it on SNPedia, which is a wiki focusing on human genetics. A wiki is a collaborative project that is gradually improved by contributions from its users. Anyone who visits can create new pages or edit existing ones.
Like most wikis, SNPedia runs on the MediaWiki software. This means that it shares it shares the same interface and most of the same syntax with other wikis, including Wikipedia. Many of Wikipedia’s help pages are very detailed and apply to SNPedia as well.
With wikis, you don't really create a page, you just sort of start writing in one and it exists. For instance, if you wanted to make a page for rs123, you'd just go to http://www.snpedia.com/index.php/Rs123, and then click edit and start writing. When you submit the changes, the page will be created.
The basic idea behind editing a wiki is very simple. On any page, click the “Edit” button in the top right to open the edit window. Make your changes, then click “Save page,” and the changes will be applied immediately. To make a new page, type the name of the page you want in the search bar (also in the top right), and if the page does not exist you can create it.
After you select a topic (make sure that it doesn’t already have an article), complete your writeup with the software of your choice. For references and formatting, see “References” and “Formatting.” Then sign in as gene210/stuart, create the page as described above, and copy and paste your text. If the page name is an rs number, the page will already have three default lines of text, and your text goes below this. The three lines are what create the “infobox” on the right-hand side of the page, and a number of entries will be filled in by one of the SNPedia bots within about 24 hours.
1. To make a new SNPedia entry for rsxx, login as gene210/stuart. Then go to http://www.snpedia.com/index.php/Rsxx.
In this case, the SNP is rs1711437. So the new webpage is http://www.snpedia.com/index.php/Rs1711437.
Then click on "edit this page".
Then copy your text below.:
A genomic convergence approach was used to show that rs1711437 in MMP20 is correlated with kidney aging .....
The syntax to add formatting (such as bold and italics) is described at http://snpedia.com/index.php/Edit_Pages. For example, to make a link to another page in the same wiki (an “internal link”), you put [[double square brackets]] on either side. You can also add formatting using the toolbar in the edit window.
2. To cite a publication, find the pubmid ID for your paper and then add {{PMID|198xx}} at the appropriate place in your page where 198xx is the pubmed ID for the paper.
3. Add a summary for your page.
4. The SNPedia bot will fill in a number of entries at the top of your page within about 24hr.
5. While not essential, it is helpful to also fill in the genotype. For 1711437, the genotypes are A;A, A;G and G;G. Three new pages should be created for this.
There are 2 ways to do this. For the 1st technique, notice on the page
http://snpedia.com/index.php/Rs1711437
where it now says 'Make rs1711437(A;A)' and click on that. You will be taken to
http://snpedia.com/index.php/Special:FormEdit/Genotype/rs1711437(A;A)
repute indicates whether that genotype is desirable. So the risk genotypes should be bad and the protective genotypes should be good.
http://snpedia.com/index.php/Repute
and the magnitude indicates how interesting this SNP is (10 is really interesting and 3 is worth your time).
http://snpedia.com/index.php/Magnitude
The 'Make ...' text was present, because the bot had already specified the 3 genotypes.
For the 2nd technique, if you don't want to wait for the bot to make the genotype pages for you, then create each genotype page by yourself. For the G;G genotype of rs1711437, go to this page:
http://snpedia.com/index.php/Rs1711437(G;G)
save the page, then click "edit with form". This lets you make the genotype page immediately. Do the same for the A;A and the A;G genotypes.
Links:
05/09/2013