ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES Scholarly journals: present and future Emma Van Burns, PhD Matteo Cavalleri, PhD Patricia Johnson, PhD

2 What is the purpose of a scholarly journal? Dissemination Spreading the word through publishing platforms But also indexing and generally organizing knowledge Registration Precedence of discovery can be established based on a paper’s submission date to a journal Archival Safeguarding and preserving knowledge Publishers play an important role preserving the scientific record Certification Peer-review is still the gold standard for certifying articles This is not the same as quality-control! ➕ Peer-review management, Curation, Infrastructure, Ethics, & much, much more. Here’s a list of 96 things publishers do: https://bit.ly/2UW3rKX

3 < 1600s Scientists share their results by writing letters (and sometimes books) and mailing them to each other mid-1600s Small groups begin to meet in person, becoming the first scholarly societies 1665 The first scientific journal, Philosophical Transactions of the Royal Society, publishes its first issue 1730s The Royal Society of Edinburgh begins publishing Medical Essays and Observations, probably the first fully peer-reviewed journal 1800s Modern publishing companies Wiley (1807), Springer Nature, Taylor & Francis, and Elsevier are founded mid-1900s Peer review by external reviewers becomes a standard component of the publication process 1975 Journal Impact Factors are first released The origins of scholarly publishing

4 1987 The first open access journal, Flora Online, begins publishing on the internet 1990 Postmodern Culture becomes the first online journal to publish with no printed version 1991 arXiv, the first online preprint database, is launched 2008 Predatory journals are identified in the first edition of Beall’s List of Predatory Journals and Publishers 2012 ORCID (Open Researcher and Contributor ID) issued its first alphanumeric codes to uniquely identify researchers 2018 A consortium of European funding agencies launches the Plan S initiative requiring research funded by them to be published in open access journals 2019 Wiley and German institutions sign the first Projekt DEAL transformative agreement Recent developments in scholarly publishing

5 Author(s) The peer review process Write manuscript (Prescreening) Initial assessment Peer review time First decision Revise manuscript + respond to reviewers Reject (Final) Decision Reject Initial submission Editor assignment Reviewers invited Feedback submitted Reviewers invited Revised manuscript submission Revision request Copy editing, typesetting, etc. Accept Review + edit proofs Proofs sent Proofs approved (payment sent) Online and/or print publication Journal staff Journal editor Reviewers

6 What are the differences between editors and reviewers? Reviewers Editors −Are formally affiliated with the journal −Have general expertise covering the overall scope of the journal −Make final decisions on whether to publish submitted manuscripts −Represent the journal to the scientific community and to the public −Have no formal affiliation with the journal −Have specific expertise on the exact topic of the manuscript −Provide specific feedback on submitted manuscripts, including suggestions for improvement, and recommendations on whether to publish them

7 Who are the editors? External / academic Internal / “in-house” − Employed full-time by the publisher − Have a background in the field − More general expertise − Employed part-time by the publisher and full-time by a university (or other institution) − Are active researchers, authors, and experts in the field − More specific expertise

8 How are manuscripts assigned to a specific Editor? Automatically Manually − Papers selected individually by each editor − Editor chosen by the author upon submission − Individual assignment by the Editor-in- Chief or other lead Editor − Random assignment − Sequential (round robin) assignment − Assignment based on sections/subject areas selected by the authors − Assignment based on manuscript type (article, review, editorial, etc.) …or a combination of both Initial assignment to a Deputy Editor based on subject area, then the Deputy Editor manually assigns to an Associate Editor

9 Author(s) Journal staff Journal editor Reviewers The peer review process Write manuscript (Prescreening) Initial assessment Peer review First decision Revise manuscript + respond to reviewers Reject (Final) Decision Reject Initial submission Editor assignment Reviewers invited Feedback submitted Reviewers invited Revised manuscript submission Revision request Copy editing, typesetting, etc. Accept Review + edit proofs Proofs sent Proofs approved (payment sent) Online and/or print publication * time

10 What happens during pre-screening? Staff and/or editors check for: − Plagiarism − Duplicate submissions − Journal-specific requirements (word count, figure formatting, supplementary files, ethical approval for animal experiments, etc.) Editors check for: − Scope − Legibility − Technical/presentation quality − Soundness − Novelty (most journals)

11 The pre-screening plagiarism check Inevitable and harmless Tolerable Some overlap in the experimental section can be tolerated. Many papers use the same standard experimental methods. Questionable The red overlap is harmless (hundreds of papers have already been published on this topic) but the purple overlap is highly questionable. The text was probably lifted intentionally from the source paper and only minimally modified.

12 The pre-screening plagiarism check Plagiarism Outrageous plagiarism

13 Rejection before peer review (desk/editorial rejection) Out of scope Failure to meet specific journal requirements Ethical concerns (plagiarism, data/image manipulation, authorship issues) Results are not supported Results are presented too poorly for reviewers to evaluate Flawed methodology Lack of originality, novelty, impact, or significance Authors can avoid many editorial rejections by carefully reviewing the journal’s scope, requirements, ethical guidelines, and previously published papers before submission. Insufficient results presented

14 Author(s) Journal staff Journal editor Reviewers The peer review process Write manuscript (Prescreening) Initial assessment Peer review First decision Revise manuscript + respond to reviewers Reject (Final) Decision Reject Initial submission Editor assignment Reviewers invited Feedback submitted Reviewers invited Revised manuscript submission Revision request Copy editing, typesetting, etc. Accept Review + edit proofs Proofs sent Proofs approved (payment sent) Online and/or print publication * time

15 Who are the reviewers? It’s called peer review for a reason!

16 Who are the reviewers? Recently published on the topic Experts in the field Diverse representation

17 How do editors find reviewers? − Author suggestions − Reviewer suggestions − Cited papers, especially relevant reviews − Keywords − Web of Science − Scifinder − Online/public search engines − Publisher databases

18 How do editors choose reviewers? − Relevant recent publication record indicating expertise in the field − No obvious conflicts of interest (recent coauthorship, joint grants awarded) − Not affiliated with the same institution or city − Not currently occupied with other review assignments − Diversity of multiple reviewers (geographical, career level, etc.)

19 Author(s) Journal staff Journal editor Reviewers The peer review process Write manuscript (Prescreening) Initial assessment Peer review First decision Revise manuscript + respond to reviewers Reject (Final) Decision Reject Initial submission Editor assignment Reviewers invited Feedback submitted Reviewers invited Revised manuscript submission Revision request Copy editing, typesetting, etc. Accept Review + edit proofs Proofs sent Proofs approved (payment sent) Online and/or print publication * time

20 Common reasons for rejection after review (for most journals) Lack of originality, novelty, impact, or significance Unclear motivation/ not valuable to the field Ethical concerns (plagiarism, data/image manipulation, authorship issues) Claims/conclusions are not supported Unclear/illogical presentation Concerns that the conclusions are incorrect Too preliminary Flawed/improper methodology or statistical unsoundness Generally, the editor will request revisions if they believe the paper can be improved enough to meet the journal’s publication standards, and will reject the paper if they don’t.

21 What’s the difference between “major” and “minor” revisions? Major revisions Minor revisions − May involve changes to the manuscript itself, such as clarifying the arguments, updating figures, etc. − Authors expected to complete the revision fairly quickly − Generally not sent back to reviewers before the editor’s decision − May involve additional experiments and/or analysis in addition to changes to the manuscript itself − Authors may be given more time to complete the revision − Generally sent back to reviewers before the editor’s decision

22 Rejection letters come in different forms Simple rejection The paper will not be published in this journal. Suggestion to resubmit “Soft rejection” The editor would be willing to consider a new, revised submission in the future. Transfer offer The submission could be considered by a different journal.

23 Author(s) Journal staff Journal editor Reviewers The peer review process Write manuscript (Prescreening) Initial assessment Peer review First decision Revise manuscript + respond to reviewers Reject (Final) Decision Reject Initial submission Editor assignment Reviewers invited Feedback submitted Reviewers invited Revised manuscript submission Revision request Copy editing, typesetting, etc. Accept Review + edit proofs Proofs sent Proofs approved (payment sent) Online and/or print publication * time

24 Accept as-is Once accepted, the manuscript enters the production process and is published online and/or in print.

25 Author Corrections Early View Online Publication Issue Build and checking Issue Publishing and Distribution Typesetting Submission Peer review Copy-editing Peer Review Article Publishing (Early View) Issue Publishing What happens after acceptance?

26 What happens during post-acceptance editing? − Figure formatting/standardization − Formatting − Typesetting − Copy editing (minor spelling/grammar) − Author gets to approve final version abcdefg

ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES Trends in scholarly publishing

28 How are journals evaluated and compared?

29 What is a transfer offer? A rejected manuscript is recommended as suitable for a different journal (from the same publisher) If the author accepts the offer, the submission is moved to the new journal All files submitted to the original journal – including any reviewers’ reports – are shared with the new journal The author may also update or revise the manuscript between submissions An editor of the new journal begins evaluation of the manuscript If necessary, the manuscript will be re- evaluated by external reviewers

30 Why should authors accept the transfer offer? Benefits to authors Benefits to reviewers − Minimizes redundant reviews − Fewer total reviews are needed, lessening the load on the peer review community − Up to three times more likely to be accepted − Faster publication times − No need to re-enter submission information

31 The many models for peer review: reviewer anonymity “Single-blind” Editor Author Reviewers ✗ ✓ ✓ ✓ Editor Author Reviewers ✗ ✓ ✓ “Double-blind” Editor Author Reviewers ✗ ✗ ✓ “Triple-blind” Editor Author Reviewers ✓ ✓ ✓ Open

32 The many models for peer review: reviewer comments Transparent Reports are published along with the paper Confidential Reviewer reports are not published Open Readers may post additional reports after publication Independent Reader feedback published elsewhere (PubPeer, etc.) None Post-publication reader evaluation only ?

33 Different journal access/fee structures Gold Open Access Articles are freely accessible online, but authors must pay an Article Processing Charge (APC) Subscription Usually free to publish, but only subscribers can access the papers Copyright belongs to the publisher Authors retain copyright of their work

34 Transformative agreements between publishers and institutions A Transformative Agreement is a contract between an institution/consortium and a publisher allowing researchers to access subscription content as well as publish their work in Open Access journals. Gold Open Access Articles are freely accessible online, but authors must pay an Article Processing Charge (APC) Subscription Usually free to publish, but only subscribers can access the papers

35 The Open Science / Open Research movement … broad term, covering the many exciting developments in how science is becoming more open, accessible, efficient, democratic, and transparent. This Open Science revolution is being driven by new, digital tools for scientific collaboration, experiments and analysis and which make scientific knowledge more easily accessible by professionals and the general public, anywhere, at any time … - European Commission

36 Open Research Increasing accessibility of publicly funded research OPEN ACCESS Enabling reproducibility and verification of research data, methodology, and reporting standards OPEN DATA Embracing greater transparency throughout the research process OPEN PRACTICES Supporting inclusive and networked research practices OPEN COLLABORATION Helping to integrate researcher identification and evaluation tools OPEN RECOGNITION & REWARD

37 Impact & Integrity Through Open Research Make research more open, transparent & accessible More Open Create a more efficient landscape for conducting, funding & supporting research More Reproducible Protect the integrity & overall reputation of research More Accountable

38 The Open Researcher and Contributor ID (ORCID) − It is impossible to accurately distinguish researchers based on their full names. • Names are not always unique • Names are not always written the same way • Names may change throughout a person’s lifetime − Researchers are not always properly credited for their work, and Editors struggle to identify and invite reviewers. − ORCID issues researchers a unique alphanumeric code that resolves this name ambiguity problem. − Many journals now require authors to include their ORCID codes upon submission and publish them with the papers.

39 Advancements beyond simple pdf files Supplementary files Embedded video HTML article format Executable code

ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES Predatory journals

41 What is a predatory journal? Predatory journals profit by exploiting authors’ desire to publish their work. − Use the Open Access publication model and charge fees to publish and/or submit (but most Open Access journals are legitimate) − Do not provide legitimate peer-review and publishing services − May use names of real researchers without their consent − May falsely imitate well-known legitimate journals or publishers − May post false claims of being indexed or fake journal metrics, such as Impact Factors

42 How can we defend ourselves from predatory journals? Check lists of known/suspected predatory journals as well as indexing services for legitimate journals: − Beall’s List of Predatory Journals and Publishers: https://beallslist.net/ − Cabells’ Journal Blacklist: https://www2.cabells.com/about-predatory ($) − Useful appraisal tool: https://thinkchecksubmit.org/ − Directory of legitimate Open Access journals: https://doaj.org/ − Clarivate’s Master Journal list: https://mjl.clarivate.com/home Watch for warning signs that a journal may be predatory: − Has a low-quality/unprofessional website − Promises unreasonably fast publication times and/or high acceptance rates − Lacks transparent editorial and peer review policies − Lacks a well-defined scope or publishes papers far outside its stated scope − Accepts manuscript submissions by email − Sends frequent spam emails asking for submissions − Unfamiliar to you and your colleagues

ENABLING DISCOVERY | POWERING EDUCATION | SHAPING WORKFORCES Tips & best practices for manuscript writing

44 Common types of ethical misconduct in publishing − Plagiarism − Others' data + words − Your own data + words − Reuse of images – get publisher's permission to reuse! − Falsifying/fabricating: − Data − Images − Reviewer reports − Citations − Dual/duplicate submission − Fractured publication: “salami slicing”

45 Ethical misconduct: authorship misrepresentation Inclusion of non- contributing authors Exclusion of contributing authors Unexplained author addition or removal during revision Criteria for authorship: 1. planning and contribution to some component of the work or interpreting at least a portion of the results 2. writing a draft of the article or revising it for intellectual content 3. final approval of the version to be published

46 Search Engine Optimization (SEO) begins with keywords − Search engines typically focus on paper titles, abstracts, and section headings − Include 1-2 different keywords or phrases in the title, 2-3 in the abstract, 5-7 in keyword fields, and in section headings as needed − Use the keywords consistent with your field – if unsure, review the keywords used in recent publications − Test potential keywords on trends.google.com, Google Scholar, Web of Science, etc. − Avoid excessive keyword repetition, known as “keyword stuffing,” which will cause search engines to suppress or even un-index a web page − Post links to your paper across your social media, networking, and institutional sites

47 Further resources for Search Engine Optimization Search engine optimization: What is it and why should we care? - Cushman - 2018 - Research and Practice in Thrombosis and Haemostasis - Wiley Online Library The impact of metadata implementation on webpage visibility in search engine results (Part II) – ScienceDirect Academic Search Engine Optimization (ASEO) | Optimizing Scholarly Literature for Google Scholar & Co. (utpjournals.press)

48 Writing an effective, optimized title − An effective title accurately indicates the paper’s scope in ~15 words or less (consider moving longer phrases to the start of the abstract) − It states what was found, not what was done − It contains 1-2 related keywords, ideally at the beginning of the title − It encourages readers’ interest in clicking on and reading the entire paper − It does not include “Study on,” “Research on,” “Effect of,” “Investigation of,” “Characterization of,” etc… − It does not include unfamiliar jargon or acronyms

49 Improving a suboptimal title Effect of Metal Catalyst on the Outcome of Coupling Reactions with Aryl Alcohols X What effect? X Which metal(s)? X What type of coupling reaction(s)? X Which aryl alcohols? Ruthenium Trichloride: a High-Yield Catalyst for C–H Activation with 2,4- Disubstituted Aryl Alcohols ü Specific ü Concise ü Contains many keywords

50 Writing a good abstract (max. 250 words!) − Hypothesis − Explain keywords − Main findings − Main conclusions − Importance/impact − Unanswered questions 7-10 sentences No citations No abbreviations Findings first

51 A general procedure for designing successful charts: 1. Choose the appropriate chart type and plot the data. 2. Sequentially adjust every parameter of the chart — anything that can be changed from the defaults! (Fonts, colors, line widths, grid lines, axis increments, tick marks, key format/location…) 3. At each stage, consider: what setting communicates the most effectively to the audience? Consider the chart’s intended setting and audience. 4. Eliminate clutter and do not introduce new clutter. 5. Use consistent design for all figures in the same document. AaBb Data 1 Data 2 Data 3

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53 Journal Impact Factors: a simple but flawed metric − Used as a measure of journal prestige… unfortunately? − Field-dependent − Skewed by popular (or infamous) articles and reviews − Volatile − Doesn’t predict future citations − Not transparent arXiv:1906.02660 arXiv:1906.02660 @DuttonChemistry, Jason Dutton, Assoc. Prof. Latrobe University IF(2022) = # citations in 2022 to citable papers published in 2020 and 2021 # of citable papers published in 2020 and 2021

54 Different journal access/fee structures Green Open Access A subscription journal that allows authors to self-archive their papers Gold Open Access Articles are freely accessible online, but authors must pay an Article Processing Charge (APC) Hybrid A subscription journal that allows authors to make their papers Open Access by paying an APC Diamond Open Access Articles are freely accessible online with no charges to authors; costs are covered by a university or other institution Subscription Usually free to publish, but only subscribers can access the papers Copyright belongs to the publisher Authors retain copyright of their work