It is now the 3rd CHALLENGE Period for CACAO Fall 2017! It will end on Sunday October 22, 2017 at 11:59 pm CDT
This is your chance to challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.

Have any questions? Please email us at


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This page is intended to be a reference for setting up a new session for CACAO on GONUTS FOR INSTRUCTORS.

Things you'll need

A class roster or list of participants
Each student needs to have a username (either chosen or assigned) and a valid email address.
A (tentative) schedule of your class
You can set up CACAO in a variety of ways, see the discussion below for more information.
Topic(s) for annotation
CACAO can operate using any scientific literature, but it sometimes easier to focus upon a particular area

Setting up a CACAO session

Some definitions:

  • Session: We define a CACAO session as a group of annotation activities. These are typically a semester long, but can be of any arbitrary length.
  • Inning: A session is divided into one or more innings. An inning is divided into one or more parts based on the allowed activities
    • Annotation - Participants make annotations. Challenges are blocked
    • Challenge - Participants challenge annotations made by members of other teams. New annotations are blocked
    • Open - Both annotations and challenges are allowed.

A CACAO session involves several different kinds of pages on GONUTS.

Session scoreboard pages

Each CACAO session has a main scoreboard page with a name like Category:CACAO_Spring_2017. This organizes the teams in a CACAO session and is a central hub for the scoreboards and assessments. The schedule of innings is also set from the Session page.

The Session page name must start with a "Category:" prefix to place it in the Category namespace (this is required for various features like assigning teams to a Session)

Making an new session page

To create a new CACAO session,

  • make an empty page with an appropriate page name.
  • Put {{subst:CACAO page}} in the content and save it. The first time you save it the Scheduling table won't show up.
  • Click Edit and save it again.
  • Edit the schedule table to set up the innings.

Players and teams

While it is possible to set up players and teams manually, it is much easier to send us the information in a tab-delimited text file so we can use a script on the server to set everything up automatically.

If you don't know which users are going to be in which groups, don't worry - this is a wiki, it's quite flexible.

Picking team names

We try to have all team names start with the word Team, which distinguishes CACAO teams from other Mediawiki category pages. A list of previously used team names can be found at Category:CACAO_Participation

Organize users into groups

Some of the organization was done in the previous step. If you are not sure which students will be in which teams, you can defer this step until later. It is possible to edit any page at any time, and you can easily add a user to a category (a team) at a later date.

At this point in our tutorial the students have been arranged into teams, but the actual Category: pages for those teams do not have any content. You can edit each team's page by following links from users' pages (the containing categories are listed at the bottom of a page), or by browsing to them. For example, if you look at the example user-page above you will see Daniel is in Team Aggies. This means you will want to go to Aggies.

Even though each user has a <cacao></cacao> table on their page it is sometimes useful to see an entire group's annotations. GONUTS is smart enough to show all annotations from all members of a group if you put a <cacao></cacao> tag on a category page. For example, Category:Team Aggies might look something like this:

Hello! We are TEAM AGGIES! Welcome to our team's page!

==Our Group's Annotations==
session = Texas A&M Sample CACAO 2011
==Our favorite links==

Each group must be put in the top-level category to be part of that Cacao. Just like we put the users into groups using categories, we will put the groups into a cacao using categories. In each group page add a Category: tag for the Cacao you would like to use. For example, we'll add our sample group to Texas A&M Sample CACAO 2011. The group's page would then look like this:

Hello! We are TEAM AGGIES! Welcome to our team's page!

==Our Group's Annotations==
session = Texas A&M Sample CACAO 2011

==Our favorite links==

[[Category:Texas A&M Sample CACAO 2011]]

This must be done for each group.

Ambox notice.png To be part of CACAO a groups page must include a single <cacao></cacao> set of tags with one parameter in-between them:
  1. session = session
    The session/class the user is in, with or without the Category: prefix.

==See Also==
*Help:Gene Ontology

Where to go for Help

If you have any questions or none of this makes any sense to you, then please email us at Someone from our team would love to help you get started using GONUTS. We can also set up some training via phone-conference on everything from using GONUTS to "what is the Gene Ontology." Please don't hesitate to contact us.


The code for CACAO is written as an extension to Mediawiki. It is written in object-oriented PHP and is free for download. Please email us for more information.

See Also