Submitting suggestions to GO using SourceForge.net

The SourceForge Tracker

This system allows GO users to submit suggestions for changes to the gene ontologies to the GO curators. Changes can be anything; from suggestions for new terms to spelling mistakes you may have noticed. This system allows the submitter to track the status of their suggestion, both online and by email, and allows other users to see what changes are currently under consideration.

Setting up a SourceForge account

Setting up your own SourceForge account allows you to track your submitted requests by email and online.

To set up an account, access the SourceForge homepage and click on New User via SSL in the left hand side bar.

Once you have registered you will be sent two e-mails. One will be a 'New Account Confirmation Letter' and the second will give you instructions and a URL to complete your registration process and activate your new account.

Once registered, you can log on to the SourceForge site by clicking Login via SSL in the left hand side bar.

Submitting a suggestion to GO

Access the Gene Ontology Curator Request page.

This page displays a list of all submitted requests. Clicking on a specific request summary will bring up more detailed information about that request.

At the top of the page you can navigate to various parts of the Gene Ontology project on SourceForge. To enter a new request, click 'Submit New'. Choose from the category options 'New term request' and 'Other term related request' according to the nature of your suggestion. In the 'Summary' field, enter the subject of your suggestion; this text will appear in the "Summary" field of the requests list. Ignore the 'Group' field, but fill the details of your request in the 'Detailed Description' field. If you are requesting a new term to be added to the ontology, it is useful for GO curators if you include as much of the following information as possible:

• the term name
• a suggested definition
• a suggestion of where it should appear in the GO hierarchy
• any pertinent literature references
• any possible synonyms of the new term

Requests can be submitted separately if you want to track each suggestion individually. Alternatively, you can upload a file with many requests in the one submission by pressing the browse button at the bottom of the page and selecting the path to the appropriate file.

When you are satisfied, click on 'SUBMIT'.

Keeping track of your requests

Once your request is submitted there are several ways to keep track of it.

• You can receive specific emails about a single request by signing up for the monitor. To do this, click on the summary of your request to access all its details. At the top of the page there is a grey 'Monitor' button; you can monitor and un-monitor your request item by clicking on this button. You will be sent an additional email for any changes, e.g. status change, additional comments etc. that are made to this request item.
• Any open requests will be visible in My Personal Page in the left hand side bar after you have logged in. When your request has been dealt with by a curator, its status changes from 'open' to either 'closed' or 'pending'. Only open requests are visible from your personal account page.
• You can use the request ID number or any free text in the search facility in the left hand tool bar. Search 'curator requests'.
• If you want notification of new entries, modifications and comments to all requests, you should subscribe to the geneontology-term-request mailing list.

Browsing requests

All requests remain in SourceForge indefinitely, but by default only open suggestions are displayed. You can view suggestions with a different status by selecting one of the options from the "Status" pulldown menu on the Gene Ontology Curator Request page and clicking "Browse".