Help:Browsing and Searching the GO wiki

The GO wiki is meant to be used as a GO browser and a GO usage guide. 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.

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.

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.

Adding references

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.