Chapter 4: Kotahi Production Features
IN THIS LESSON
Introduction to the Production Page.
The Kotahi Production interface is designed to radically reduce the cost and time for producing various formats such as HTML, PDF and JATS (XML). It can also be used for author proofing.
The interface is simple but powerful. In the production editor, you will see the manuscript displayed. This is entirely editable. On the right we see a download dropdown menu.
From this dropdown menu, you can select PDF, JATS and HTML. PDF is generated using Paged.js (see documentation). JATS is created automatically by Kotahi and validated. HTML comes straight from the content displayed in the editor.
If you wish to improve the granularity of the JATS files you produce, you can use the tools on the left menu (see JATS documentation in this manual).
You can also access the PDF (Pagedjs) editor, which can be used to alter the CSS or template before exporting to PDF. Although accessed at the manus cript level, changes here will reflect all manuscripts exported as aPDF.
Brand name - this enables you to set the name of the group. The group name is displayed in a dropdown menu at login time for installations with multiple groups
Title - is the title of your publication
Description - a brief summary outlining the purpose of your publication
ISSN - is an 8-digit code used to identify newspapers, journals, magazines and periodicals of all kinds and on all media–print and electronic
Contact - contact details can be inserted as plain text
Brand primary color - used for the left hand menu, some buttons, and title texts
Brand secondary color - used for additional highlighting
Logo - the logo for the group login page
Favicon - icon displayed on your browser tab
Workflow
Dashboard
In Kotahi, you can change the landing page for users as the first page they arrive at after they log in.
The Landing page settings allows you to choose from either the Dashboard or the Manuscripts page as the landing page. The Dashboard is probably the most common use case but in flatter hierarchies, the entire community may wish to have access to the manuscripts page. We have found this to be the case for small groups working together or some preprint review communities.
You can additionally choose which tabs are displayed on the Dashboard. Your choice here is also reflective of your use case. If you are a Journal group, then you probably want to select all three items. If you are a community that reviews preprints that are automatically ingested, you may wish to only display the ‘To Review’ item etc
Manuscripts page
Here you have some great options for configuring the Manuscripts page.
List columns to display on the Manuscripts page - you can configure the columns displayed on the Manuscripts page. This is actually more powerful than you might think. It is possible, for example, to create a form element in the submission form builder for the selection of workflow status from a dropdown. This can then be displayed as a column on the Manuscripts page and effectively functions as a workflow tool. There are many other possibilities and experimentation is key. Columns are added using the comma-separated internal fieldname fields for each form element added in the submission form (you can hide these elements from submission and review forms if required via the form builder controls).
Number of manuscripts listed per page on the Manucripts page - this controls the number of items displayed as a list (pagination controls).
Hour when manuscripts are imported daily (UTC) - this is a setting for the AI importing of preprint metadata. Currently set up for the AI integration requires a developer but you can use these settings to control how it works once set up.
Number of days a manuscript should remain in the Manuscripts page before being automatically archived - if you are auto-ingesting manuscripts, you might get a lot of ingested items and not be able to get through them all in the time window you desire. This option gives you the ability to auto archive those ‘expired’ items if required.
Import manuscripts from Semantic Scholar no older than ‘x’ number of days - when auto-ingesting preprints via AI you can specify the maximum age of the preprint. This helps preprint review communities discover the latest preprint materials for review.
'Add new submission' action visible on the Manuscripts page - displays the button to start a manual submission from the Manuscripts page. This is useful for many use cases, it has been used to enable preprint review communities that have automated ingestion of preprints to also add an item manually.
Display action to ‘Select’ manuscripts for review from the Manuscripts page - ‘Select’ is a triaging feature, especially useful in conjunction with bulk imports. It changes the 'label' field to ‘Ready to evaluate’. Filtering and bulk deletion can be used in conjunction with these labels. It is also used for feeding AI selection criteria in some use cases.
Import manuscripts manually using the 'Refresh' action - this will put a ‘Refresh’ button on the Manuscripts page so you can manually start the auto ingestion process.
Control panel
This setting group enables you to configure various items on the Control page.
Display manuscript short ID - each research object has a unique ID given to it by Kotahi. This is an ‘internal’ identifier largely just used so users can discuss or find the item easily. Checking this item will display the relevant manuscript ID on the Control Panel for each research object.
Reviewers can see submitted reviews - set if you wish reviewers to see each others’ reviews. If not checked, reviewers can see only their own review.
Authors can see individual peer reviews - if checked, authors can see the entire review for each reviewer.
Allow authors to participate in proofreading rounds - if checked, editors will be able to assign authors to a round of proofing.
Editors can edit submitted reviews - if checked, editors can edit submitted reviews from the Control panel>Reviews page.
Control pages visible to editors - you can hide various tabs if they are not relevant to your use case.
Submission
There is one item - Allow an author to submit a new version of their manuscript at any time. This setting determines if an author/submitter needs to wait until the beginning of a new review round to submit a new version of their manuscript and metadata, or alternatively, if checked, the author can submit at any time (even mid-review). This has been used by preprint review communities where the review process (Kotahi) and submission system (a preprint server) are decoupled.
Review page
This setting determines whether Reviewers can see the decision/evaluation information.
Task manager
Here you can set the timezone for the date picker when setting tasks.
Reports
Settings to show or hide the reports page from the menu.
User management
One interesting user setting and a misplaced API key setting
All users are assigned Group Manager and Admin roles - essentially gives you a flat community hierarchy in which all users can access all pages in the menu and see all parts of the process.
Production
Settings relevant to the Production page include controls to configure output when using the ‘Reference’ parser.
Integrations and Publishing Endpoints
Semantic Scholar
A checkbox setting to enable/disable the import of preprints from Semantic Scholar. Group Managers can select servers to import preprints/journals from. This feature is only implemented on the prc archetype. This is because import queries are most commonly associated with a publish, review and curate workflow, and an existing query will need to be in place to use this feature.
Hypothesis
Settings related to some specific publishing endpoints. This may or may not be relevant to you. Essentially, if you are publishing preprint reviews to some external services the way in is via the hypothesis API.
Crossref
API information and controls for accessing Crossref.
Webhook
This section enables you to set a webhook for publishing to an external endpoint.
Publishing webhook URL - the endpoint or target for the publishing action supplied as a URL
Publishing webhook token - the secret token used to authenticate the exchange
Publishing webhook reference - data sent to the target to know how to process the information
Kotahi API tokens
Input a token to access the unreviewedPreprints API and no other queries.
COAR Notify
Kotahi can receive messages from COAR's Notify service. Authors can submit a manuscript to a 3rd party server and request a review from a group in Kotahi. Selected server IP addresses can be inserted (as comma-separated variables) and whitelisted - Kotahi can only receive requests from servers that are whitelisted.
A request results in a manuscript being imported and displayed on the Manuscripts page. Manuscripts imported via COAR Notify are identifiable by the Notify logo in the title text.
AI Design Studio
Utilize the studio to tweak page layouts, adjust image placements, manage widows and orphans, refine content with ease, or come up with completely new designs using the studio. Read more here; https://www.robotscooking.com/redefining-document-design-unveiling-our-ai-powered-pdf-designer/
Select an area (element) on the screen and insert a prompt into the AI chat editor and see the result! Add your OpenAI credentials on the Configuration>Integrations and Publishing Endpoints>OpenAI access key to activate the service.
Task manager
Here you can set the timezone for the date picker when setting tasks.
Notifications and E-mails
Emails
Configuration for the account information through which Kotahi will send emails. Currently, only Gmail is supported. These instructions outline the correct Gmail password to use when configuring your account.
Event notifications
Configuration options for sending email notifications. Each workflow type has supporting events, and the option to assign an email notification template.
Reviewer rejects an invitation to review - choose from the email templates for the email to be sent to the reviewer when they reject an invitation to review.
Reviewer invitation - set the email to be sent to the reviewer when they are invited to review.
*Submitted review - set the email to be sent to the author when the editor has submitted a decision (accept, revise or reject) .
*Submitted manuscript - choose the email to be sent to the submitter when a research object is submitted.
Author proof assigned invitation - choose this email sent to the author when invited to participate in a round of proofing.
Author proof completed and submitted feedback - choose this email if you wish an editor (editor role assigned) to receive a notification that the author has submitted proofing feedback.
Unread discussion message - choose the email to be read when messages are remaining to be read in a chat for all users.
Immediate Notification for users @mentioned in a message - choose the email template to be sent when a user is @ mentioned in the chat.
*****Currently, only available when using the journal workflow (instance archetype)