GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.
REMEMBER, any annotations to "____ BINDING" or "RESPONSE TO _____" will be marked as unacceptable for CACAO students according to the CACAO rules.
Tips for adding and editing content to GO wiki pages. Add your questions to the discussion for this page.
- 1 Browsing and Searching the GO wiki
- 2 Wiki Markup
- 3 Working with GO terms
Browsing and Searching the GO wiki
The GO wiki is meant to be used as a GO browser and a GO usage guide. Annotators can use the wiki to find appropriate GO terms by browsing or searching the wiki. Each GO term page includes links to the parents and children of that term, and a graphic showing where the term fits in the overall ontology, courtesy of QuickGO at the EBI. Users can follow links up and down the GO hierarchy, or can search for terms containing combinations of words that could lead to the right GO term. The standard Mediawiki search system will return a list of pages that match the words you enter in the search box. The search engine looks for full word matches, but is less sensitive than AmiGO to word order. For example, compare the results when you enter "cAMP protein kinase" into the GO wiki vs AmiGO.
Another way to find an appropriate GO term is to look for the terms associated with other genes you already know about. The gene pages from each of the organisms included have many synonyms for gene names, which are also searchable. The gene pages are also categorized using taxonomy terms, so that you can search, for example, for genes with a particular GO term from Metazoa, for example.
What makes the GO wiki different from the many other ontology browsers available from the Gene Ontology Consortium and others is that the GO wiki allows registered users to mark up pages for GO terms and for gene associations with notes to provide guidance about choosing the right annotations.
A brief guide to wiki markup is below. For more on editing, see the How to edit a page on Wikipedia and the Wikimedia Meta-wiki pages for editors. Go ahead and edit without worrying about having to know everything about wiki markup; one of the cool things about wikis is that more experienced users can fix your markup, and as you become more comfortable with wikis, you can fix the markup of others. The most important thing is to share your ideas...making them look pretty is secondary.
Entering and styling text
To enter or edit text on a GO page, just click on the link that says Edit. You'll get a web form, where you can modify the section for the consensus about how a node should be used. Often, you may want to post to the discussion page for a GO page first. To do this, click on the discussion tab, and then on the edit tab for the discussion page or on any internal edit link on the page if you just want to edit a subsection.
The wiki software allows you to preview what you entered by using the "Show preview" button. For the most part, you can just type in the space and the desired text will show up. However, here are some basic ways the text can be modified using wiki markup (intentionally or unintentionally!) to change the appearance of text on the page.
|italics||''italics'': two single quotes on each side of the italic text|
|bold||'''bold''': three single quotes on each side of the bold text|
Different levels of headings can be made by flanking text with different numbers of = signs, like ==heading== or ===heading===. To show as headings, these must be at the start of a new line. Headings create new editable subsections, and also generate table of contents links.
Text on a line that starts with blank spaces will be put in a box.
- Text on a line that starts with a colon ":" will be indented.
- Different numbers of :'s give different levels of indentations
One important thing in this wiki is to be able to add links to other pages, or to external websites. It's also useful to be able to assign new pages to the categories that correspond to GO nodes. Linking to another page in the wiki can be as simple as putting text between double square brackets. For example, the Sandbox is a page that users can use to play around with wiki markup. This link was generated like this:
For example, the [[Sandbox]] is a page that users can use to play around with wiki markup.
Double brackets are used to link to pages inside the wiki, or to another wiki using Interwiki links. If the linked page exists, then the link will take a reader there when it's clicked. However, you can also create a link to a page that doesn't exist yet. This will show up on the page in red, and clicking on it will take the reader to an edit page where new content can be created.
Here is an example of a link to an external website: The GO consortion website is at geneontology.org
The GO consortion website is at [http://geneontology.org geneontology.org]
The link is surrounded by single square brackets. Inside the brackets there is the URL, a space, and then the linked text. If you leave out the linked text, it will look like this . If there is no URL (no "http://"), it will look like this: [geneontology.org]
Sometimes you want to link to a page using different linked text than the page name. For example, this links to the Sandbox page: The Sandbox is a page for trying out wiki markup. This is made using a vertical line (a pipe, above the backslash on US keyboards)
The Sandbox is a page for [[Sandbox|trying out wiki markup]].
Linking to a GO node
The pages for GO nodes in this wiki are special pages called Category Pages. This means that [[GO:0008150_!_biological_process]] links to a nonexistent page. You can link to a GO node without assigning the page to that node, using [[:Category:GO:0008150_!_biological_process|GO:0008150_!_biological_process]], like this:GO:0008150_!_biological_process. Note that here I am linking to the page for a GO term, but I don't want this Help page to be considered as a Biological process.
Creating new pages
As noted above, you can create a new page by linking to a new page title.
Working with GO terms
Assigning an article to a GO term
To assign an article to a GO term, use [[Category:<PageTitle>]] where <PageTitle> is the title of the page for the GO term. This will be invisible in the display of your page, but you will see the GO term in the list of Categories for the page containing this tag, and the page for the GO term should now show your page as an article for this Category. I'm adding this page to the Articles in the GO top level category, by adding [[Category:GO]] to this page. To make a visible link to the GO term page in addition to the Categories link at the bottom, use [[:Category:<PageTitle>]]. This is useful when writing why a GO term is being associated with a gene based on an Evidence Code and a Reference.
We use a modified version of the Cite extension for MediaWiki to allow you to put references on each page. To add a citation to an article in PubMed, put <ref>PMIDXXXXXXXX</ref> where XXXXXXXX is the PubMed ID number. Cite will automatically add this citation to the references list at the bottom of the page where there is a section with the <references/> tag.
Where to put comments and questions about GO terms
Discussion and questions about the proper use of a GO term should be added to the discussion page for that term. For example, see: this discussion page. But what if the issue you want to discuss involves multiple terms? In the spirit of wikis, there isn't a single right answer, but issues that apply to more than one term should probably be discussed at the highest relevant node. You may want to create a new page and include links to multiple pages that are related.
Suggesting changes to the GO consortium
Part of the goal of this wiki is to provide a discussion trail so that new people working with GO can understand how the consortium decides when certain terms and relationships should be used or not used within the ontology. A corrolary to that is that users of this wiki can discuss possible changes to the GO ontology before formally requesting new terms or changes to existing terms. While we hope that the ontology consortium members will participate here, the hope is that we can hash out many issues among ourselves on the wiki and only forward things we can't resolve here to the GO development team.
To help keep this organized, we can tag specific pages as being either under active discussion or being ready to suggest a change to the consortium. Two category tags can be added to a page to flag a page.
- Category:GO:Discussion should be used for pages where active discussion is underway (however slowly), and issues are being considered that might lead to a suggestion to change the ontology, but where a consensus has not been reached on what should be suggested.
- Category:GO:Change_request should be used to flag discussions that have reached a consensus where an ontology change suggestion is ready to send to the consortium
Note that these flags can be set on existing pages or on new pages created by users.