Help:Curation Process

From Human Salivary Proteome Wiki

Curation Process

The Human Salivary Proteome Wiki is a collaborative effort to enrich the catalog of human salivary proteins through involvement of the entire scientific community. The diverse backgrounds and expertise of our contributors ensure the depth and breadth of the contents stored in the wiki. From taking part in a discussion to uploading MS/MS data to annotating a protein sequence, there are many ways to participate in the effort. One consequence of such an open-content approach is the potential high degree of variation in data quality. To ensure that we provide the most accurate content possible, with strong scientific grounding, a curation process is in place to gather community feedback and expert review before any changes can be officially incorporated. Here we will describe the entire process step by step.

Each user in the wiki can belong to one or more user groups. Each group may have a different set of permissions, which determine what operations the user can do. To see which group(s) you belong to, go to the my preferences page. Your groups are listed in the "Member of groups" field. The following user groups are relevant to the curation process:

Readers

Readers cannot add or modify pages in the wiki, except for talk pages, which are open to every registered user to participate in discussions.

Editors

Most users fall into the editor group. Editors have the ability to add annotations or make changes to pages with the "HSPW:" prefix (i.e. Proteins and Protein Clusters). Other pages, such as PubMed, Genes, and templates, are reserved pages that usually do not need to and should not be modified. You can tell whether you have the permission to edit a page by seeing if the "Annotate" or "Edit" tab shows up on top of the page (Figure 1). If you change a page, the page will be temporarily put into a basket (similar to a "shopping cart"), where you can confirm the change and submit it along with all your other changes as a single proposal (see details below).

Fig. 1: If you have permission to change a page, the "Annotate" or "Edit" tab should appear on top of the page. These tabs will take you to a form where you can insert data.

Designers

Designers are like editors in many ways. The only difference is that designers have the permission to change the layout and other underlying features (e.g. semantic properties) of a page, instead of its content. Users may belong to both the editor and designer groups.

Curators

Curators are responsible for reviewing and either approving or rejecting content changes suggested by editors. Users with curator role are well-recognized experts in the field. They use their own expertise and input from the community to determine whether a proposal should be accepted. Please also note that changes made by curators are effective immediately without the need to go through the curation process.

Submitting a Proposal

A proposal is a collection of changes made on one or more pages submitted for approval. If you are subject to the curation process, a message titled "Approval required" will be displayed when you attempt to save your changes. The page that you edited will be put into your proposal basket. You will then have the opportunity to make changes to other pages. Once you are done, you can go to the basket to see all the pages that you have edited, decide if any additional revisions are desired, and submit all the changes as one package or proposal. The curator who reviews your proposal will be able to consider all your changes as a whole because related changes may span multiple pages. The idea is similar to online shopping, where you can put multiple products in the shopping cart and check them out as one order.

A screen-shot of the proposal basket is shown in Figure 2. You can go to your basket from the link that is displayed along with the "Approval required" message when you save a page, or through the link from the navigation menu of top of any page. Items in your basket are locked to prevent other users from making changes on the same page at the time. Only you have the permission to edit the pages in your basket. However, to avoid situations in which the pages are being locked permanently, items not submitted for curation within 24 hours may be automatically removed from the basket.

Fig. 2: Your proposal basket displays all the pages that you have modified or added but not yet submitted. To submit your proposal, click the "Submit Changes" button to send it out for review.

To submit your changes, click the "Submit Changes" button, and the proposal will be sent out for review. A message will then be displayed to confirm that the proposal has been submitted, and provide you with a link to check the curation status as described below. Figure 3 is the proposal summary page that indicates the status of each page in the proposal submitted in Figure 2. If you are a curator, you can use the buttons appearing on this page to perform actions on individual pages or on the entire proposal. Otherwise, those buttons will be disabled.

Fig. 3: The proposal summary page displays the status of each page in a proposal. You can see what has been modified by following the page links. The action buttons at the bottom of the page are enabled if you have the permission to act on the proposal.

After a decision has been made on a page, the editor who submitted the proposal will receive an email notification with an optional explanation from the curator. If approved, the page will be updated to reflect the changes. If the changes are rejected, they will be included in the email notification so that revisions can be made and be submitted for reconsideration.

Curation Status

A proposal will go through a series of stages before it is either approved or rejected. Each status that a page can have in the curation workflow is described below. When you go to a page with pending changes, the page status will be displayed at the top of the page (Figure 4). In addition, next to the status message are links that you can follow to learn about the changes that have been proposed. The "Proposal Summary" link will display the status of other pages submitted in the same proposal (see Figure 3). The "View Proposed Changes" link will show the line-by-line differences between the current page and the proposed page.

Fig. 4: If there are pending changes on a page, a message will appear at the top of the page indicating its status in the curation workflow. In this example, the page status is Pending Review.

Pending Submission

The message under the page title appears as "Changes have been made to this page, but have not been submitted for review.". This means that a user has made changes to the page, and is currently holding it in his or her proposal basket. At this stage, only the editor who originally edited the page can make additional changes. Other users will not have the permission to edit. If the editor does not submit the page for review in 24 hours, the page will go back to the Reviewed status, at which time any editors can edit the page again.

Pending Review

The status indicates that the page has been submitted as part of a proposal for review. The message appears as "Changes have been proposed for this page, and are pending for review." At this stage, the proposal is waiting to be claimed by a curator, who then has the option to either approve or reject the changes. The page is locked completely so that nobody can make any further (potentially conflicting) changes before a decision on the existing proposal is made. The user community can see the proposal at this time and provide feedback that can influence the curation decision.

Under Review

After a curator has claimed a proposal but before a decision is made, the page has the status of Under Review. The message under the page title will show who the curator is. At this stage, the curator can make changes to the page if necessary.

Reviewed

After the curation decision is made, approved changes are added to the page, and the page returns to the Reviewed status, which indicates that there are no pending changes and editors are free to submit new proposals. There is no message under the page title. You can see different versions of the page over time by clicking the history tab on top of the page.