Help:Annotation Jamborees

From GONUTS

Annotation Jamboree pages are used to compare the annotations of sets of genes of interest. GONUTS allows you to create Category pages that can automate the comparisons. This page describes how to set up a Jamboree page in GONUTS, and gives advice for using it.

Contents 1 Quick overview 2 Quick Guide to July Jamboree tables 3 Setup 3.1 Create the Jamboree Category page 3.2 Add genes to the Category 3.3 Add a live chat (optional) 4 Annotate the individual gene pages 5 View the summary on the jamboree category page 6 Examples

Quick overview

1. Create a jamboree category page, e.g. Category:xx
2. Create gene pages using the 'create new gene page' on the left hand menu, add the uniprot ID (or refseq protein ID)
3. Wait for the site to be created
4. The annotations are downloaded automatically
5. Newly created annotations need to be added manually to this gene page
6. Use the 'edit table' link at the bottom of the annotation table
7. Add row (using button at bottom of editing annotation table)
8. Save row edits
9. Save table when you have finished editing
10. Add [[Category:xx]] to the 'notes' section of the gene page, using 'edit' for that section.

Quick Guide to July Jamboree tables

All the required gene pages are already created on the 2 jamboree gene category pages. These gene pages have already imported any old annotations that were available. However, new annotations need to be added manually, and old ones can be deleted if necessary see below.

1. Open the jamboree gene category page (this may take a while to download)

ETFDH SLC11A1/2

1. Open the appropriate gene page using the link 'edit table' at the bottom of the jamboree gene category page NOT the 'edit' option on the right
2. Edit/delete/copy existing rows
3. Alternatively, add row (using button at bottom of editing annotation table) and edit as necessary (note reference format would be PMID:12070036)
4. Save row edits
5. New rows appear at the bottom of the table
6. Save table when you have finished editing using the button at the bottom of the page 'Save Table to wiki page:xxx'
7. Other editing options are available at bottom of page, such as revert to saved table if you want to start again!

Setup

Create the Jamboree Category page

You can use the inputbox below (for RefGenome jamborees the one on Category:Refgenome_Electronic_Jamborees preformats the PAGENAME)

Create a new Electronic Jamboree page:

Alternatively, if you don't like that format, you can add the <GOsummary />tag to any category page.

Add genes to the Category

Find the genes you want to include in the Jamboree. You can create gene pages as needed from UniProtKB ids using Special:GoPageMaker.

Add a live chat (optional)

For RefGenome Jamborees, we typically embed a live chat using CoverItLive

<iframe_embed> coveritlive altcast code < iframe_embed >

See Help:Embedding iframes for more info.

Annotate the individual gene pages

Use the table editor to add annotations to each gene page in the category. The jamboree page should automatically update (you may need to reload your browser) to reflect changes in the annotations assigned to each gene.

View the summary on the jamboree category page

An extension finds all the gene pages assigned to this category, filters out the IEAs and builds a comparison table. It also generates images to show how the annotations are distributed among the ontologies.

If you would like to bulk load your annotation data, the format of the input file is:

Qualifier||GOID||GO term name||reference (e.g.PubMed ids) ||evidence code||with data||aspect||notes|| ||

e.g. ||GO:0006919||activation of caspase activity||18082289 ||IDA|| ||P|| || || ||GO:0015684||ferrous iron transport||18082289,17109629,17293870,12734107 ||IDA|| ||P|| || ||

Examples

• Refgenome jamborees. Before July 2009, a different setup was used. The earlier Jamboree pages are individual articles. Starting in July 2009, the Jamboree pages are subcategories.
• Category:Complement_comparison
• Category:Insulin_signaling