Submitting suggestions to GO using SourceForge
The SourceForge Tracker
This system allows GO users to submit suggestions for changes to the ontologies to the GO curators. Any sort of change may be proposed, from suggestions for new terms to correcting spelling mistakes you may have noticed. The submitter can track the status of a suggestion, both online and by email, and other users can 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. SourceForge provides detailed documentation on registering for an account.
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 GO curator requests tracker.
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', 'Other term related request', and 'Term obsoletion' 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 GO curator requests tracker and clicking 'Browse'.
Guidelines for Curators
All changes to ontology content and organization (terms, parent-child relationships, and definitions) should go on the SourceForge tracker. This will help reduce duplication of effort, improve record-keeping, and let any outsiders who check the tracker see what's being worked on.
Every member database whose curators have GO CVS write access should have at least one curator on the SourceForge list; Jane and Midori can add any GO curator to the list of possible assignees, and grant the necessary "tech and admin" privileges. Technicians can be assigned items; admins can make changes to items.
Anyone can enter new items even if they don't have the tech or admin privileges; the Curator Requests Help page explains how.
Effort should be made not to duplicate entries; check whether an open entry already exists for the topic of interest, and if so, comment on the existing entry rather than making a new one. This will help avoid having to keep multiple entries in sync.
General guidelines
- The SourceForge tracker is not meant to be a substitute for discussing complicated issues on the GO mailing list. There are a lot more people on the main GO mailing list than on the SourceForge request mailing list, so if an item turns out to be really complicated or to result in extensive changes, messages should be sent to the GO mailing list. In some cases curators will have to use some judgment to decide whether to post to the list or not. An item can be sent to the list at any time, not just when it's first posted. If in doubt, err on the side of going to the list.
- If the topic falls under the remit of one of the "interest groups", a member of that group should claim it. See the interest group documentation for more information, including current groups and members.
Step-by-step instructions
- Assign the item to yourself before you start work. Adding comments as you work is optional; sometimes it's helpful to keep track of your reasoning or to allow others to comment.
- Choose a group. The "group" selector has two different sets of options: the group options, such as "GO" and "SGD," indicate where the curator is; others, such as "developmental biology," indicate interest groups. For both types of group, more can be added if needed.
- As the first step implies, it is OK to comment on an item that someone else is working on. You can offer to help the assignee if you have relevant knowledge or are simply interested.
- Don't assign an item to anyone other than yourself unless the other curator has already agreed to it, or reassign an item without checking with the original assignee.
- Consider the GO content points made in documents such as the editorial style guide and the GO editor guides.
- Send the item out to the GO mailing list if it proves non-trivial.
- Before you close an item, add a comment that explains what you've done. The minimum is the new term ID and text string especially if the text is different from what was originally suggested. Other affected terms should also be mentioned: parents, children, etc., and any rearrangements fully described. If the work was complicated, also explain the reasoning behind the changes.
- Supporting material for a new entry or a comment can be put in an attached file. This is particularly useful if the comment is long or involved, or if you know of a relevant email or other document.
- When you've finished an item, change the status to "Closed" and choose a resolution. New term requests are usually either "Accepted" or "Rejected." Other requests can be assigned whichever resolution seems best.
