Manuscript Management Systems: Understanding the Workflow from Submission to Publication

Manuscript Management Systems:
Understanding the
Workflow from Submission
to Publication
1st PAMJE Convention
Journal Editing and Management 101
AMADO O. TANDOC III, MD, FPSP
Research Institute for Tropical Medicine
*Journal of the ASEAN Federation of Endocrine Societies
**Philippine Journal of Pathology

FROM TO
Non peer-reviewed Peer-reviewed
Occasional publication Regular & timely publication
Limited article submission Active solicitation of articles
from Endo both local
and international
Limited subscription Increased readership
Non-indexed Inclusion in international
journal indexes (ISI, Scopus,
WPRIM)
No online presence 24/7 online
presence for correspondence
and submissions

https://library.uwinnipeg.ca/scholarly-communication/index.html

Pre-Publication
PublicationPost-Publication
https://library.uwinnipeg.ca/scholarly-communication/index.html

Manuscript
submission
Article
Publication
A B
Screening and
Peer Review
Production

Screening and Peer Review as QC mechanism
https://images.theconversation.com/files/31778/original/

https://www.editage.com/insights/peer-review-process-and-editorial-decision-making-at-journals

Screening
• Non-technical initial check
• Quality of writing
• Compliance with journal’s instructions
• Technical check
• Fit to journal’s scope and aim
• Interest to readers

Desk Rejection
Declined without
review
Peer Review

STEP 1: Initial Check
• Usually performed by the non-scientific staff
of the journal. It may include for example:
• Checking for missing or broken files.
• Checking compliance with length requirements,
if any.
• Checking central formatting requirements, e.g.,
line numbers, if required by the journal.
• A plagiarism check.
• Excluding manuscripts of very low quality, such
as automatic translations or manuscripts with
very poor language.
https://academia.stackexchange.com/questions/55665/what-does-the-typical-workflow-of-a-journal-look-like

Usual Requirements
• Cover letter
• Authorship declaration
• Disclosure of conflicts of interest
• Copyright agreements
JAFES experience:
• Compliance to EQUATOR checklists
• ORCID registration of authors

STEP 2: Editor assignment
• Based on the topic of the
manuscript and/or suggestions
by the authors, an editor is
assigned to handle the
manuscript.
• Depending on the journal, the
assignment may be done by
technical staff, the journal's chief
editor, or automatic by
submission category or author
suggestion. With some journals,
editors are invited and not
assigned.
https://www.nature.com/news/predatory-journals-recruit-fake-editor-1.21662

STEP 3: Editorial Assessment
• Editors decide whether the paper should enter
the review process or should be rejected
directly
• Journal scope and requirements, intended audience
• Request for more data, clearer figures
• Also known as: with editors, waiting for
potential reviewer assignment, under
review, assigned to the editor

STEP 3: Editorial Assessment

STEP 4: Peer Review
• Reviewer selection
• Dependent on a deep pool of
reviewers with expertise
• Mechanics vary:
• Blinded or open
• 1-round or multiple rounds
• 2 or 3 reviewers
• Support reviews: statistics,
radiology, pathology
https://blogs.plos.org/absolutely-maybe/2017/10/31/the-fractured-logic-of-
blinded-peer-review-in-journals/

STEP 5: Editorial Decision
• Based on the reviews, the
editors decide whether:
• The manuscript shall be rejected.
• The manuscript needs to be
revised by the authors before it
can possibly be accepted.
• The manuscript shall be accepted
as it is.
• A decision requires further
reviews.
• Template response

Steps 1-5: Summary
https://www.editage.com/insights/a-look-at-the-conventional-journal-publishing-workflow

• Copyediting
• Ensure article conforms
to the journal’s house
style/standards
• Correctness of
references, figures and
lables
• Consistency of text,
grammar, spelling,
punctuations,
capitalization
• Requests to authors
• In-house or outsource
STEP 6: Copyediting
and Typesetting

• Typesetting
• Layout
• Preparation of
galleys/proofs
https://www.elsevier.com/editors/article-layout

STEP 7: Proofreading
• Proof correction (with authors)
• If corrections are necessary, it goes
back to copy editing and
typesetting.
• In-house or outsource
https://link.springer.com/article/10.1007/s11192-017-2310-5

STEP 8: PUBLICATION!
• Options:
• Immediate publication online
• Queue up the publication for collation into a
journal issue with other articles.
• The time before this issue is published depends
on the size of the journal’s publication backlog
and can range anywhere from a few weeks to
several years.
• Many journals with an issue-based delay provide
“online early” access to articles so that they are
available to the community before the final issue
date. Articles thus often acquire two publication
dates: one for online and one for print
publication.

Operational timelines
https://www.nature.com/news/snail-s-pace-nature-readers-on-their-
longest-wait-to-get-published-1.19375

Manuscript
submission
Article
Publication
A B
Screening
Peer
Review
Declined
without review
Peer
Review
Author
Revisions
Rejection
NOTE: Timelines depend on the
journal’s level of operations,
copyflow, reviewer “efficiency”,
author revision
Operational Timelines
Production

Process Typical Duration
Step 1: Initial Check A few workdays.
Step 2: Editorial
Assignment
A few days to several weeks
Step 3: Editorial
Assessment
This strongly depends on the journal: With some journals, it is less than
a week; with others it may take a month, in particular if several people
are involved in the decision or the initial quality hurdle is high.
Step 4: Peer Review Depends on the field and journal. It typically ranges from a few weeks to
several months, but in some cases (particularly for highly theoretical
work where intense proof-checking is expected), it may be as long as one
to two years.
Step 5: Editorial Decision A few workdays to a week. This may take longer with some journals, in
particular if several people are involved in the decision.
Step 6: Copyediting and
typesetting
Depends on the journal copyflow. Backlogs may take a few weeks to
months
Step 7: Proofreading Most journals request proofs to be returned within a certain time,
usually between 48 hours and a week.

Journal Management Tips
• Set up an office with dedicated staff and equipment
• Establish the editorial policies based on international
standards
• Journal compliance checklists to facilitate screening
• Establishment of a deep peer reviewer pool
• Standard peer reviewer templates to focus review
• Set timelines (deadlines) for screening, peer review, author
revisions
• Attend APAME, PAMJE! Be on the lookout for innovations
• Go online!
• Consider automation to facilitate editorial management

Journal Management Solutions
• Consider automated editorial
management systems
• Commercial, proprietary software
(EM)
• Open-source software (OJS)
In 2016, JAFES migrated to Public Knowledge
Project.
Options:
Editorial Manager [5000 USD/year]
Public Knowledge Project [2700 USD/year]
Locally developed

OJS Experience
• Streamlined the processes
• Customized templates
• Customized timelines
• Capture of metadata
• Audit trail
• Tracking of manuscripts
• Journal performance
• Factored into the Scopus
indexing of the journal and
PubMed score

Thank you for your attention!
Contact me at:
Amado.Tandoc@ritm.gov.ph
JAFES.editor@gmail.com
Philippinepathologyjournal@gmail.com

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