Storing images and supplementary files using the 'Object Store'
This week we released our first iteration of the Kotahi 'Object Store'. The Object Store organises images and supplementary files for access in the Wax word processor as well as scaling images for export to various endpoints.
On submission; all images inserted into Word documents (JPEG, PNG, SVG, TIFF, EPS & GIF) will be retained in the original format in the Object Store. On conversion to HTML, images are converted to "medium" size format (JPEG or PNG) for access in the Wax word processor. Images will be also accessible in multiple quality formats (size "small", "medium" and "original") for export to the web, print-ready PDF or JATS XML (as a zipped file component).
All supplementary files (submission, review and/or decision form attachments) are stored and accessible for export to a defined endpoint e.g. Flax (static website builder and publishing frontend) or Pagedjs.
We are currently working on an Asset Manager which caters for the management of image files. You'll be able to use the Asset Manager to insert images in the Wax word processor after our next release.
Export print-ready PDFs from Kotahi
This week we release we released an integration with Pagedjs. You can now export print-ready PDFs from the Wax Production editor with a single click.
Word comments imported into Kotahi are converted to HTML using XSweet pipelines. Content is edited in the Wax word processor, with the option to export as PDF, JATS XML and HTML in the Production editor.
Manuscript metadata such as title, abstract, author names, date accepted, date released, corresponding author email address etc. are captured in the submission form and made available to Pagedjs via graphql. A graphql endpoint also provides the CSS used to style the PDF. For now, each instance will utilise a single stylesheet. In the future, when exploring multitenant workflows we'll incorporate support for multiple stylesheets.
Creating customisable Review and Decision forms
Currently, the Review page feedback and Control panel>Workflow Decision fields are hard-coded. Reviewers are able to submit public feedback to the author or confidential feedback to the editorial team with a recommendation; 'Accept', 'Revise' or 'Reject'. Editors are able to submit feedback to the author in conjunction with a decision of either 'Accept', 'Revise' or 'Reject'.
The Form builder has been utilised to create dynamic and easily editable submission forms. We'll be applying the same solution to the Review and Decision components. Soon system administrators will be able to create Review and/or Decision forms that are tailored to your needs across both traditional/PRC workflows
All current form field types will be available in both Review and Decision form builders; Supplementary Files, AbstractEditor, VisualAbstract, Authors Input, Links Input, Text Field, Checkbox Group, Select & Radio button Group options. Along with various advanced settings for 'required fields' or 'DOI validation' etc.
Capturing of Review and Decsion form data in a structured manner offers an opportunity for more versatile and innovative publishing actions. With the added ability to select and send feedback components to select endpoints as desired.
PRC workflows and supporting editor-author feedback loops
The publish, review, curate (PRC) preprint review workflow requires that the editorial team shares individual reviews or a summary report with the author. The author should have the opportunity to not only update their manuscript content but also submit a formal response regarding changes implemented.
This week we have started conceptual work on a new form field type. System administrators will be able to select and add a 'threaded discussion' form field to a Review and/or Decision form. This will allow a reviewer to share an individual review, or an editor to share a summary report and leave the opportunity for author response.
Editors will be able to QA (edit) reviews/responses on behalf of the reviewer/author. As a handling editor, you'll have the ability to publish review summaries and author responses separately. We're still in the process of refining the specifications for this feature and welcome your feedback.
New features added to the chat panel
This week we released enhancements to the chat (discussion) function in Kotahi in support of the following use cases;
- Improve the quality of synchronous and asynchronous engagement through the use of enhanced text styling/formatting and video chat capabilities.
- Support Curator triage and selection of preprints for review (in the case of a PRC workflow) through the use of an Admin discussion panel added to the Manuscripts page.
New discussion features;
- A simple Wax editor; supporting styling, formatting, Math, tables, lists special characters etc. added to the Editorial and Admin discussion panels.
- A link to video chat within the Admin and Editorial discussion panels.
- A collapsable Admin discussion viewport.
Enhancements implemented over the last 10 months
- bioRxiv covid-19 search specific API call
- Pubmed API call
- Manually submit PDFs and supplementary files (using an Object Store)
Login and general usability;
- Improve log in page instructions
- New user prompt upon first login to complete/edit profile details
- Including user profile images, preferred username and ORCID across views
- Control panel; splitting-out workflow (notifications & assigning role, reviewers etc.), manuscript (content) and metadata (form) views Adding drag and drop functionality to the form builder
- Advanced settings to parse and/or validate metadata e.g DOIs
- Ability to hide/view form fields from Author and Reviewers in support of specific workflows
- Updated Wax word processor to the latest version (multiple smaller UI/UX upgrades); highlighting text, adding comments and notes & headings are now tagged import
- Copyediting work can be done in Wax using a browser plugin e.g. Grammarly
- Added component tagging to Wax editor in support of exporting valid JATS
- Integration with Pagedjs for exporting print-ready PDFs (using an eLife journal article as a default CSS template)
- Access submission data as well as editing/publishing manuscripts and/or evaluations
- Use labels in support of triage and specific/unique workflow status updates
- Filtering manuscripts view by status, ad hoc labels and/or topics
- Sorting of Manuscripts by title, date etc.\
- Hide/show metadata fields as required using a config file
- Discreet vs shared reviews
- Public vs anonymous reviews (single-blind reviews)
- Video chat added to Manuscripts page and Editor discussion chat viewport
- Added email notification and templating subsystem; including user/role field mapping as well as automated notifications linked to specific workflow triggers
- Enhancements to the Wax editor to include component annotations (semantic tags) for exporting valid JATS XML
- Export a print-ready-PDF
- Publishing to Kotahi’s homepage
- Developing and publishing to Flax (including a notification indicating successful publishing status)
- Registering peer review and journal article DOIs via Crossref (including a notification indicating successful publishing status)
- Publishing to a spreadsheet
- Publishing to Hypothe.is
Reports; filter and view system-wide, manuscript and role-specific performance data
Instances in production;
- eLife (included work done to include a CI pipeline)
- Novel Corona Virus Research Compendium (included work done to include a CI pipeline)
- Aperture Neuro Journal
- Biophysics CoLab PRC
Queued for development in Q1 into Q2…
Production editor enhancements;
- Adding additional component annotations e.g acknowledgements
- Also to Include a metadata placeholder component in Wax - indicating where data is being pulled from the submission form
- Built-in DTD/XSD XML validation tool
PRC workflow focus;
- Handling of editor-author response feedback loops -Building a customisable Review form, including the ability for the author to provide inline responses to specific Review form comments
- Curation team (admin) synchronous and asynchronous chat features
- Select and publish specific editor and author peer review feedback to an endpoint
- Linking a new user to a review in Kotahi
Multi-tenancy; planning for the inclusion of features such as groups/teams of users and support publishing to multiple journals
UX/UI improvements; we’re working through a backlog of incremental improvements
The form builder is now even easier to use
This week we added 'drag & drop' functionality to the form builder. Making it even easier to add and reorder form fields to best suit your desired author submission form workflow.
'Successfully published' notifications added to the Control panel
This week we included external system status feedback in the Control panel when publishing manuscripts to an endpoint e.g. a static website (Flax), Crossref, Hypothesis etc.
With the example of Crossref, we can display errors related to;
- Server configuration e.g. Publishing to Crossref failed: Unrecognised DOI prefix "http://examplebrokendoiprefix"
- Submission form misconfiguration e.g. 'Publishing to Crossref failed: Manuscript has no title'
- User error e.g. 'Publishing to Crossref failed: Issue year "1234" does not appear to be a valid year'
- System bugs e.g. 'Publishing to Crossref failed: Manuscript has no submission object'
These notifications support the Editors, providing reassurance that publishing to a given endpoint has been successful and useful context in the event the post is unsuccessful.
Leave/reply to comments in the manuscript text
As an editor, you can now leave inline comments to the author in the manuscript text (Wax word processor) view. Editors can use the comments feature to suggest content changes and authors can reply. Authors are able to implement content changes in a new version of the manuscript (copy) in Kotahi - there's no need to edit and re-upload the original file.
Export JATS XML from Wax word processor
It's still early days in the development of this tool, but we have a working production editor exporting valid JATS XML markup from Kotahi.
The 'Production page' provides editors/production roles with tools to add semantic annotations (tags) in Wax. The system applies the correct conversion from HTML to JATS XML and the following markup is downloadable as an XML file.
Journal metadata, such as author names, captured in the submission form are automatically inserted into the XML markup.
Based on the 'single source publishing' principle; the canonical format for content in Kotahi is HTML. The short term goal for the Production editor is to export HTML, print-ready PDFs and JATS XML from the system.
Automated email notifications
This week we released automated email notifications in support of 3 critical journal workflow engagement points on Aperture's instance of Kotahi. Email notification templates are customised per instance and triggered by user behaviour related to submission or status actions;
- Email is sent to an Author from a Handling Editor when a 'accept', 'revise' or 'reject' decision is submitted.
- Email is sent to an author confirming their manuscript submission was successful.
- Email is sent to a Handling Editor when a Reviewer assigned to a manuscript 'rejects' (declines the invitation) to review.
Templates include field mapping for Manuscript specific data e.g. Author/Handling Editor name, manuscript title, number etc.
Improving the notifications subsystem drives timeously engagement within Kotahi, alerting the right users to specific actions at the right time.
Editorial team-specific Metadata can now be included in a submission form and remain hidden from the author
Aperture would like the Journal Manager to be able to view and edit selective manuscript metadata. In this case, the journal volume (year) and issue (number) need to be captured for registering article DOIs with Crossref when publishing.
In support of this use case, we've added an advanced setting in the form builder allowing system administrators the ability to easily select a yes/no checkbox to 'hide field from author'.
This flexible solution gives the editorial team the ability to include additional metadata to use as required when publishing.
Workflow, Manuscript text and Metadata specific views added to the Control panel
This week we've decoupled the Control panel 'Submission form' and 'Manuscript text' views as follows;
- Workflow; the editorial can send email notifications, assign editors, manage reviewers, capture peer review feedback ('Recommendations' and 'Decisions'), and publish articles.
- Manuscript text; is the Wax word processor used to edit content imported from MS Word.
- Metadata; capturing, displaying or modifying submission form and publishing specific information.
This enhancement will improve the overall user experience and better serve the organization of editor tools added to Kotahi moving forward.
White Paper: Kotahi Current State (15 Sept 2021)
The Kotahi workflow is very configurable and can support very linear, to very concurrent, workflows. In addition, the submission types supported are configurable. These two features together mean that Kotahi can support a wide variety of use cases and workflow models.
This document outlines Kotahi as it is configured for a typical Journal workflow. Please note that this is just one configured pathway and many parts of what you will see in this document are configurable to meet your needs.
Here's the link to the 'White Paper: Kotahi Current State (15 Sept 2021)'; https://coko.foundation/kotahi-current-state/
Reviewer names now visible in the control panel
With a lot of larger projects on the go, this week we released the following enhancement; to easily identify reviewers and access a user profile from the control panel.
In an effort to improve the user experience for the editorial team evaluating peer reviews; a user's ORCID has now been replaced with the user's profile image, name, surname, username and link to the user's profile page. All appearing within the context of the peer review in the control panel.
A reminder that settings to 'hide review' or 'hide reviewer name' are also possible when publishing and sharing peer review feedback with the author.
Manuscript headings tagged on import
This week we improved the import of content into Kotahi.
XSweet handles the conversion on Docx file into an HTML format that the Wax word processor understands. Heading structure (H1 - 6) and tagging will now be retained for all imported manuscripts.
We also neatened up the Wax toolbar by adding a dropdown menu to optimise page real estate.
A lot on the go at the moment, you'll be seeing more updates in the days to come.
Reviewers can view selective manuscript metadata prior to accepting a review
Today we introduced a feature offering reviewers the opportunity to view selective manuscript metadata prior to accepting a request to conduct a peer review. This 'pre-review' step gives the reviewer insight into the subject matter and their suitability to provide a review.
To include a field on the 'pre-review' page we've added an advanced setting in the form builder allowing system administrators to easily select a yes/no checkbox per form field (element). The manuscript and all submitted metadata are accessible upon accepting a review.
As the Journal Manager, you can now invite multiple reviewers and provide a context for the review.
Adding the 'Include in reviewers' preview' setting to each individual form field is a versatile solution that can be leveraged in a number of other use cases as well.
Email notifications added to control panel
This week we introduced the ability to send customized email notifications from the control panel.
The Biophysics-Colab team wanted to reach out to authors notifying them that an article they have published is being considered for peer review. In support of this request, the notification subsystem will store email templates, offering editors/system administrators the option to select an email notification template and designate a receiver.
If the user is not yet registered in the system an email containing a special link (token) will pair the new user with the manuscript upon log in to Kotahi. Notifications sent from the system will be recorded and displayed as log entries in the control panel 'Editorial discussion' chat window.
Again, we've designed this solution to be as flexible as possible to suit as many of our current use cases as possible.
Form builder enhanced to support manuscript table filtering
We added dropdown filtering to the manuscripts view this week. Here's a bit more information on how we used Kotahi's form builder to implement the solution.
The form builder captures all imported or submitted manuscript metadata, author submission and peer review contribution.
The form builder is accessed by clicking on the Forms link in the menu. Form fields are highly configurable. Here's an example; we recently added DOI validation as an advanced settings option in support of eLife's evaluation workflow.
The form builder also integrates with Wax, Coko's premium web-based word processor. Text captured in form fields can be formatted and styled with the HTML retained for publishing purposes.
This week on the NCRC instance we've enhanced the form builder in support of triage making the ‘Topic’, ‘Status’ and ‘Label’ form fields accessible as dropdown menus on the Manuscripts page. This allows editors to easily filter and sort the imported article list for review, or locate articles by state that require action.
Here are a few other features we added in support of triage;
-API integration; articles can be imported from bioRxiv (medRxiv), Pubmed and soon EuropePMC.
-Manuscripts page; clicking on 'select' assigns a label.
-Manuscripts page; selecting 'bulk delete' allows editors to easily remove articles from the Manuscripts list. These articles although deleted, still remain in the database.
In NCRC's existing system; importing, filtering, sorting and selecting articles was a major time-waster for the team. Kotahi not only solved this problem but using the form builder, the solution is robust enough to support future use cases as well.
Aperture is joining the Kotahi community!
We are happy to announce that Aperture is joining the Kotahi community!
Today we are very happy to announce that Aperture – An Open Publishing Platform of the Organization for Human Brain Mapping – is joining the Kotahi community.
Aperture is an open-access peer-reviewed online publishing platform powered by the Organization for Human Brain Mapping to share and promote research beyond the traditional PDF and enhance, innovate, and advance neuroscience. Aperture publishes articles (research reports and reviews) and other research objects, including tutorials, workshops, processing pipelines, software, simulations, computational notebooks, and datasets.
We have known the Aperture folks for many years and we are very happy that they are joining the Kotahi community and have chosen Kotahi for their publishing platform.
Kotahi is a community as much as it is a publishing platform, and we welcome the kind people at Aperture to this growing community. The community drives Kotahi and we look forward to the new ideas and energy Aperture brings to the table.
Stay tuned for more updates!
New news page
This page added to Kotahi today. More news to come!