Identifying publications in questionable journals in the context of performance-based research funding

Joshua Eykens; Raf Guns; A. I. M. Jakaria Rahman; Tim C. E. Engels

doi:10.1371/journal.pone.0224541

Peer Review History

Original SubmissionMay 24, 2019
17 Jul 2019 Decision Letter - Sergio A. Useche, Editor PONE-D-19-14700 Identifying publications in questionable journals in the context of performance-based research funding PLOS ONE Dear Mr. Eykens, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Two experts in the field have commented your paper, but they suggest to perform an exhaustive revision on it before considering its acceptance. Thus, my advice to the authors is to respond to each one of their queries and carry out all the improvements suggested by them. Personally, I believe this is a good paper, and might help scientists to improve their practices and standards in scientific publication. 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Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 5) We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere. Please clarify whether this conference proceeding was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This is an important topic to examine for public trust in scientific research. More specifically, a critical point the authors make is: whether initiatives to raise awareness about POA publishing have the adverse effect of ranishing all open access journals with the same brush." I was left wondering why more 'predatory' publishers are active in the field of biomedical research and why POA is a serious problem in the neurosciences and related field. Tell me more about what is going on here. This is a worrisome finding. How does prestige come into play with respect to the findings that "the proportions of senior authors in POA publications is in 8 out of 13 of the publication years higher than in other peer-reviewed publications"? Do senior authors need prestigious journals less? The authors do a good job of following up on the research questions by addressing the implications of the answers to the research questions in the conclusion. Specifically, the emphasis on mentoring, and tools like ThinkCheckSubmit. In the U.S., university libraries are playing an educational (and non-judgemental role) in this space. Perhaps another recommendation could be, as part of dossier prep, that outlets are checked or verified. Certainly the conclusion that international citation databases screen for POA journals is an excellent step. I think reaching out to professional associations, such as AEA, COSSA, AMA, etc would also be helpful. The suggestions for future studies, namely contacting authors to address questions about motivation and providing a comparative quantitative investigation of national and regional bibliographic databases, are valuable as well. Reviewer #2: This is an important paper, as many have called for more action on the part of research funders with respect to this issue. Overall, this is a well-written paper. In particular, section 2.2 is really quite fascinating and relevant, as it excellently demonstrates some of the problems with relying on “white” and “black” lists, and the inconsistencies across the lists. My comments are primarily on areas that I feel could either use additional clarification or areas that I think would benefit from additional discussion. Areas for additional discussion: • In the introduction: why did you opt to focus on the SSH fields? • In the discussion, regarding the generalizability of the data: Do you feel that your findings are reflective of other fields, particularly the medical sciences (which as you note, seems to be more affected by “POAs”?) What about other countries/geographic regions? In general, your findings regarding the decrease in researchers publishing in POA journals seems to be at odds with findings in other fields/locations. Why do you think this is? • Following up on the last point, do you think that the decision by the GP to begin doing analyses of publications in POA journals by Flemish authors could be part of the reason for the drop-off in more recent years? (i.e. authors who may have been knowingly publishing in POA journals to boost their publication history lose some of their incentive because these publications will not be included in the VABB-SHW?) • You note the huge discrepancy between using Beall’s list versus the CJB. Why do you think this is? Is the CJB not as comprehensive a list as Beall’s, or was it that Beall’s had several journals/publishers on it that were not actually POA? • With regard to your findings on authorship (senior versus junior authors), I note that for junio researchers you have targeted those who are primarily pre-doctoral or early post-doctoral – presumably many of these researchers are still under the supervision of an experienced research mentor who may be helping them decide what journal(s) to publish in. Do you think this plays a role? Additionally, do you think you might see any differences if you further separated the “senior” researchers into the group of researchers that are late stage post-doctorates or have just recently been appointed to their first professor position (and looking to establish themselves and win grants), versus more experienced tenured professors that are possibly not under as much pressure to publish? Areas for additional clarity: • In the abstract, I suggest clarifying that this analysis was specific so the SSH fields. • The introduction is quite comprehensive and provides good information, however, the literature review is quite lengthy and, in some places, it could be more concise. At times, the wordiness detracts from clarity. • In Table 1, row 1, it appears that there are more journals on the blacklist than publications in the journals? (62 vs 59). I am also unclear whether the whitelist journals were used by ECOOM (and if so, how did they end of classifying journals that appeared on both white and black lists) or was the whitelist portion of the analysis was performed only by the authors of this paper? • I would appreciate more clarity regarding how the list of POA journals was generated since, as the authors have noted, this is far from straight-forward. For example, since the list included journals over several years, what happens to a journal that is on a blacklist one year, but was removed from the list in a later year (or vice versa)? Or a journal that was on Beall’s list but not the CJB? What was the role of the whitelists in making this list? What if a journal was on both a black and a white list? • In Table 2, and throughout the Results, I found it confusing what the difference is between the DOAJ-indexed publications and journals versus the “Peer-reviewed” publications and journals. Are peer-reviewed the total number of submissions to the VABB-SHW? • I find the sentence beginning on line 409 and ending on 412 to require several read-throughs to be able to process. Is there a simpler way to say this? • I found the heat map (Figure 4) to be a bit confusing. I assume one direction (i.e. column or row) corresponds to the field in which the authors work and one direction refers to the field in which the journal is classified, but its not clear which is which. I suggest better labeling on the figure and possibly re-phrasing the text. Furthermore, were there no journals that did not fit into a single classification (i.e. journals that accept all or multiple fields of research, etc.)? • The line that begins on 496 – is this for POA journal articles or for all articles? Finally, the article contains quite a few statements that would be stronger and/or more helpful if citations were provided to support them or for those who might want to seek further information. Examples of statements that would benefit from citations are those starting on the following lines: • Line 47 • Line 48 (I also suggest elaborating on this as not all readers will be familiar with what this is referring to). • Line 53 (what sources?) • Line 64 (suggest providing citations for papers that document some of the unethical practices of “POAs”) • Lines 225 – 230 • Line 485 ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0224541.r001
Revision 1
2 Sep 2019 Author Response Subject: Revision and resubmission of manuscript PONE-D-19-14700, Identitying publications in questionable journals in the context of performance-based research funding, PLoS ONE Dear Dr. Useche, Dear reviewers, We are pleased to read that our manuscript will have merit for PLoS ONE. The suggestions offered by the reviewers have been very helpful; we appreciate the constructive and critical comments. We have included the reviewer comments in this letter, together with a description of how we addressed each concern. For each comment, we indicate where changes have been made. The revised manuscript as well as the marked-up copy with tracked changes were submitted via the editorial manger platform. Although most of the revisions prompted by the reviewers were addressed by making (often substantial) alterations to the text, we would like to further highlight an addition made to Table 1. In this table we present the results of the different screenings that were carried out over the past period. In the first row, indicating the screening for articles published between 2003 and 2012. For the numbers presented there, one of the reviewers has correctly noticed that the number of journals found on the blacklist was higher than the number of publications which appeared in the journals and were found in VABB-SHW. We have added a brief footnote to the figure which also refers readers to the corresponding report, but we here detail how this difference came about. A screening round is typically done on the basis of a journal list which is compiled from the raw bibliographical data we receive from the five Flemish universities. However, after compiling this list several operations happen that may cause differences between the list and the corresponding final version of the VABB-SHW (e.g. record consolidation, validation, corrections of publication year of some other variable, etc.). This may lead to such – at first sight at least – inaccuracies. A question raised by one of the reviewers regarding ‘predatory’ publishers active in the field of (bio)medical research and neurosciences has also been addressed in the text, but we wish to share some additional thoughts which might be out of scope of the manuscript but of interest for the reviewer. It is indeed worrisome finding that these fields suffer more from questionable publishers. This might have to do with, we believe, three things. First, the relative size and popularity of these fields. Second, differences in publishing practices between fields, and third, more potential interest of organizations and businesses in such fields to publish their findings regardless of their scientific value. With regard to the first aspect, it is reasonable to assume that predatory publishers are only interested in making ‘easy money’. The most efficient way to accomplish this, is to look for the largest market potential. Given the relative size of fields like biomedicine and the rapid growth of the neurosciences, these fields are interesting areas to operate in. This might be one of the reasons why prevalence is higher. Whereas we only briefly touched upon this in the literature overview, other authors have already shown that predatory publishers are targeting these fields intensively. The second aspect closely relates to the former. These fields are known to differ in their publishing practices compared to, let’s say fields in the social sciences and humanities. Whereas SSH scholars are prone to publish, for example, more books, scholars from medicine related fields almost exclusively publish journal articles. In addition, within the medical fields, there is a greater prevalence of open access publishing in general. This is especially true for the preferred format of predatory publishers: the Gold Open Access model. Third, and this is again (much like the previous two aspects) speculative but has been shown by investigative journalists; employees of pharmaceutical and other companies have been publishing in predatory journals and sponsor predatory publisher’s conferences. Beall and colleagues also suggested that some pharmaceutical companies have an interest in publishing their findings, regardless of their scientific value. They do not really care where their research gets published, as long as it is out there and shows to potential new ‘costumers’ that their products are ‘beneficial’. As noted in the manuscript, this article elaborates considerably on an earlier conference proceeding. In the conference paper, we report on the yearly results of the screenings for POA journals and shortly address the architecture of the Flemish PRFS. It was presented as a research in progress paper and presented at the Science and Technology Indicators conference in Leiden, September 2018 (STI2018). The article has undergone external peer review and has been published in the conference proceedings. The proceedings book can be found here: http://sti2018.cwts.nl/proceedings and the paper can be found here: https://openaccess.leidenuniv.nl/handle/1887/65285. In the current paper however, we expand this description considerably. Table 1 of the current manuscript is copied from the conference proceedings, as it gives an overview of the results from our previous five screenings. In addition, we present a lot of new information, including novel bibliographic analyses, which haven’t been published or presented elsewhere. The other comments will be addressed below. We hope the revised manuscript will better suit PLoS ONE’s publishing standards. We would like to thank you for your continued interest in this study. Sincerely, Joshua Eykens ECOOM – University of Antwerp Middelheimlaan 1 2020 Antwerp, Belgium Reviewer comments, author responses and manuscript change Reviewer 1 Comment 1 I was left wondering why more 'predatory' publishers are active in the field of biomedical research and why POA is a serious problem in the neurosciences and related field. Tell me more about what is going on here. This is a worrisome finding. Answer: Besides the short note presented in the guiding letter above, in the discussion we have added some findings from a study by investigative journalists. See lines 507 – 513 Comment 2 How does prestige come into play with respect to the findings that "the proportions of senior authors in POA publications is in 8 out of 13 of the publication years higher than in other peer-reviewed publications"? Do senior authors need prestigious journals less? Answer: This is a very interesting question and something we haven’t looked into. It is a reasonable assumption, but should be studied by making use of qualitative methods. We have added this in the limitations section and refer interested readers to studies which present more qualitative insights into the motivations of scholars who have published in questionable journals. See lines 562 - 565 Comment 3 Perhaps another recommendation could be, as part of dossier prep, that outlets are checked or verified. Certainly the conclusion that international citation databases screen for POA journals is an excellent step. I think reaching out to professional associations, such as AEA, COSSA, AMA, etc would also be helpful. Answer: Thank you for bringing this up, we didn’t think of including such suggestions but have done so now. This is indeed an important action which could certainly lead to greater awareness. See lines 531 - 541 Reviewer 2 Comment 1 In the introduction: why did you opt to focus on the SSH fields? Answer: This relates to the database at hand. VABB-SHW has been set up to better account for research in the SSH and as such offers a unique opportunity to study these fields in a comprehensive manner. We have made this more explicit in the abstract. See line 25 Comment 2 In the discussion, regarding the generalizability of the data: Do you feel that your findings are reflective of other fields, particularly the medical sciences (which as you note, seems to be more affected by “POAs”?) What about other countries/geographic regions? In general, your findings regarding the decrease in researchers publishing in POA journals seems to be at odds with findings in other fields/locations. Why do you think this is? Following up on the last point, do you think that the decision by the GP to begin doing analyses of publications in POA journals by Flemish authors could be part of the reason for the drop-off in more recent years? (i.e. authors who may have been knowingly publishing in POA journals to boost their publication history lose some of their incentive because these publications will not be included in the VABB-SHW?) Answer: We belief the decrease in the number of POA publications has to do with (1) awareness raising in general as well as targeted awareness raising by Higher Education institutions. We have added some lines on these aspects. And (2) Cabells’ blacklisting service is relatively young and under continuous development. Publishers like Frontiers, which were included on Bealls list, are not present on Cabells’ Blacklist. This leads to quite large differences. In sum, we do think the screenings for publications in POA outlets have indeed increased awareness and may have lowered the prevalence. With regard to the possibility of authors who are knowingly using these journals to boost their CV’s; we have not found any alarming numbers of POA articles authored by a single individual. In the manuscript, we cannot disclose any information on the individual level, as this could be at odds with researchers’ privacy. See lines 187, 374 - 376 Comment 3 You note the huge discrepancy between using Beall’s list versus the CJB. Why do you think this is? Is the CJB not as comprehensive a list as Beall’s, or was it that Beall’s had several journals/publishers on it that were not actually POA? Answer: As noted above, this might have to do with the relative ‘newness’ of Cabells’ black list. Publishers like Frontiers, for example, are not present on Cabells black list, but many of their journals were listed on Bealls lists. We have added this example to illustrate this. See line 187 Comment 4 With regard to your findings on authorship (senior versus junior authors), I note that for junior researchers you have targeted those who are primarily pre-doctoral or early post-doctoral – presumably many of these researchers are still under the supervision of an experienced research mentor who may be helping them decide what journal(s) to publish in. Do you think this plays a role? Additionally, do you think you might see any differences if you further separated the “senior” researchers into the group of researchers that are late stage post-doctorates or have just recently been appointed to their first professor position (and looking to establish themselves and win grants), versus more experienced tenured professors that are possibly not under as much pressure to publish? Answer: With regard to mentoring; we have emphasized the importance of mentoring and other initiatives targeted at junior researchers. This has been done in the discussion. Regarding further differentiating between academic positions of authors; unfortunately we do not have any detailed information available on these aspects. We have added a brief note about this in the ‘Limitations and future research section’. See lines 531 – 541, 560 – 566 Comment 5 In the abstract, I suggest clarifying that this analysis was specific so the SSH fields. Answer: Thanks for pointing this out. We have made this more explicit in the abstract. See line 25 Comment 6 The introduction is quite comprehensive and provides good information, however, the literature review is quite lengthy and, in some places, it could be more concise. At times, the wordiness detracts from clarity. Answer: We have substantially altered both the introduction and the literature overview to increase readability. See section 1 and 2.3 Comment 7 In Table 1, row 1, it appears that there are more journals on the blacklist than publications in the journals? (62 vs 59). I am also unclear whether the whitelist journals were used by ECOOM (and if so, how did they end of classifying journals that appeared on both white and black lists) or was the whitelist portion of the analysis was performed only by the authors of this paper? Answer: Regarding the discrepancy in table 1; besides the note presented in the guiding letter, we have added a footnote to the table further detailing how this difference came about. With regard to the whitelist used by ECOOM; we have further detailed how this list is being curated in the methods section. See lines 132 – 135, 271 - 283 Comment 8 I would appreciate more clarity regarding how the list of POA journals was generated since, as the authors have noted, this is far from straight-forward. For example, since the list included journals over several years, what happens to a journal that is on a blacklist one year, but was removed from the list in a later year (or vice versa)? Or a journal that was on Beall’s list but not the CJB? What was the role of the whitelists in making this list? What if a journal was on both a black and a white list? Answer: Thank you for pointing out this rather confusing aspect. We have included some more details on this procedure in two places in the methods section. See lines 271 – 283, 295 – 300 Comment 9 In Table 2, and throughout the Results, I found it confusing what the difference is between the DOAJ-indexed publications and journals versus the “Peer-reviewed” publications and journals. Are peer-reviewed the total number of submissions to the VABB-SHW? Answer: We have further detailed this in the methods section. See lines 295 - 300 Comment 10 I find the sentence beginning on line 409 and ending on 412 to require several read-throughs to be able to process. Is there a simpler way to say this? Answer: This sentence has been rephrased. See lines 430 - 435 Comment 11 I found the heat map (Figure 4) to be a bit confusing. I assume one direction (i.e. column or row) corresponds to the field in which the authors work and one direction refers to the field in which the journal is classified, but its not clear which is which. I suggest better labeling on the figure and possibly re-phrasing the text. Furthermore, were there no journals that did not fit into a single classification (i.e. journals that accept all or multiple fields of research, etc.)? Answer: Indeed, some journals did not fit into a single category. These are indicated by the label ‘General/very broad’ (last row). The heatmap has been relabeled and the caption has been rephrased. See figure 3, lines 463 - 464 Comment 12 The line that begins on 496 – is this for POA journal articles or for all articles? Answer: Thanks for pointing this out, this has been clarified in the text. See lines 526 - 527 Comment 13 Finally, the article contains quite a few statements that would be stronger and/or more helpful if citations were provided to support them or for those who might want to seek further information. Examples of statements that would benefit from citations are those starting on the following lines: Comment 13.1 Line 47 Answer: This sentence has been omitted, since after all it does not add any value to the introduction. Comment 13.2 Line 48 (I also suggest elaborating on this as not all readers will be familiar with what this is referring to). Answer: We have added some information about the report to the introduction. See lines 50 – 54 Comment 13.3 Line 53 (what sources?) Answer: Here we were referring to statements by public opinion makers in Flanders, shared primarily on social media. After reconsideration, these do not add context or value to the manuscript, so we have omitted these lines. Comment 13.4 Line 64 (suggest providing citations for papers that document some of the unethical practices of “POAs”) Answer: A citation has been added here. See line 65 Comment 13.5 Lines 225 – 230 Answer: Reference has been added. See line 226 Comment 13.6 Line 485 Answer: This sentence has been altered and a reference has been added. See lines 507 Attachments Attachment Submitted filename: Response_reviewers_v2.docx https://doi.org/10.1371/journal.pone.0224541.r002
17 Oct 2019 Decision Letter - Sergio A. Useche, Editor Identifying publications in questionable journals in the context of performance-based research funding PONE-D-19-14700R1 Dear Dr. Eykens, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. 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Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The author has adequately address my concerns and those of the other reviewer. The manuscript provides solid work on an important question. Reviewer #2: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No https://doi.org/10.1371/journal.pone.0224541.r003
Formally Accepted
31 Oct 2019 Acceptance Letter - Sergio A. Useche, Editor PONE-D-19-14700R1 Identifying publications in questionable journals in the context of performance-based research funding Dear Dr. Eykens: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Sergio A. Useche Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0224541.r004

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