PubPeer workflow

In order to manage the growing number of PubPeer allegations, the PubPeer Manager (PPM) will triage new posts and determine the correct investigation route.

Triage

PPM receives an alert to new allegations, logs it on the Google sheet, and checks whether a formal Correction has been made. If so, marks it as Resolved on the Google sheet. Otherwise, determines next steps as described below.

Image manipulation or duplication allegations

Preflight Editor involvement is required. PPM gathers the files from the archive and places them in a folder on Dropbox for Preflight Editor to access.

1. If the author has acknowledged an error on PubPeer and stated that they will submit a Correction

• Check with the Managing Editor to see if the author has reached out to the journal.

• If the author has not contacted an Editor, email the author (email template 4) to confirm their PubPeer post and that they do indeed want to issue a Correction.

• Request high-resolution replacement files and source data. 

• Ask Preflight Editors (see email template 5) to preflight the new figure(s) and perform a quick scan of all figures published in the article. They should also run ImageTwin. 

• Preflight reports findings to PPM, who shares findings with the handling editor or Exec Editor and coordinates the Correction or awaits further investigation by the Editor. 

How old is too old?
If the article was published 10+ years ago, look for duplications but do not do a full forensic assessment (however, if something obvious and egregious is spotted – e.g., evidence of the clone stamp being used – alert the editor).

2. If the author acknowledged a mistake was made but did not mention issuing a Correction, or said a Correction is not necessary

• Check with the Managing Editor to see if the author has reached out to the journal.

• If not, email the author and ask if they would be willing to submit a Correction (email template 3). Copy the Scientific Editor who handled the paper, if possible. Otherwise, cc the journal’s Executive Editor.

• If the author says no, wait for guidance from the Editor.

• If the author agrees, request high-resolution replacement images and source data.

• Ask Preflight Editors (email template 5) to preflight the new figure(s) and perform a quick scan of all figures published in the article. They should also run ImageTwin. 

• Preflight reports findings to PPM, who shares findings with the handling editor or Exec Editor and coordinates the Correction or awaits further investigation by the Editor. 

3. If the author has not responded to the PubPeer allegation (email template 1) or denied that a mistake was made (email template 2)

• The Scientific Editor should review the comments and decide whether any further action is needed. If yes,

• Ask Preflight Editors (email template 5) to preflight the new figure(s) and perform a quick scan of all figures published in the article. They should also run ImageTwin. 

• If the allegations are validated, PPM will reach out to the corresponding author, cc’ing the handling or Executive Editor, for source data and explanation.

• If the authors do not have source data, the next steps will depend on the importance of the compromised figure to the findings in the article.  

  • Not important: issue an Expression of Concern. 

  • Important: issue a Retraction. 

  • Possible: Editorial dept. to determine whether to offer the author the opportunity to repeat the experiment to be included in a Correction to the article.

PubPeer allegations of missing/inappropriate citations or other text- or table-based errors

• PPM reviews the allegation and determines whether the alleged error was introduced in production/proof. If so, work with handling SE or Exec Editor and authors on issuing a Correction. 

1. If the author has acknowledged an error on PubPeer and stated that they will submit a Correction

• Check with the Managing Editor to see if the author has reached out to the journal.

• If the author has not contacted an Editor, email the author (email template 4) to confirm their PubPeer post and that they do indeed want to issue a Correction.

2. If the author acknowledged a mistake was made but did not mention issuing a Correction or said a Correction is not necessary

• Check with the Managing Editor to see if the author has reached out to the journal

• If not, email the author and ask if they would be willing to submit a Correction (email template 3). Copy the Scientific Editor who handled the paper, if possible. Otherwise, cc the journal’s Executive Editor.

• If the author says no, wait for guidance from the Editor.

3. If the author has not responded to the PubPeer allegation (email template 1) or denied that a mistake (email template 2) was made

• The handling or Executive Editor should review the comments and decide whether any further action is needed.

• If the allegations are validated, PPM will reach out to the corresponding author, cc’ing the handling or Executive Editor, for an explanation.

Other allegations

Other allegations that may appear on PubPeer include

• Plagiarism: PPM runs iThenticate

• Data fabrication or falsification: PPM sends directly to handling or Exec Editor

• Methodological concerns (inadequate experimental design; inappropriate statistical analysis; lack of proper controls; use of flawed or inappropriate reagents or tools): PPM sends directly to handling or Exec Editor

After evaluation

RUP should not comment on PubPeer. Authors are welcome to post comments and resolution details themselves. 

Any Corrections, Retractions, or Expressions of Concern resulting from PubPeer posts need not mention PubPeer in the text. If an author wishes to, they may.  

Email templates

All PubPeer correspondence should cc the EJP and JPS email loader addresses with ms id in the subject line:
rupjpsemail@gmail.com
jem.ejpress@gmail.com 

1)

Subject: Inquiry Regarding Your [JXX] Article: [Article #]

Dear Dr. [Author],

We are writing to you today regarding your article, "[Article Title]," published in [Journal Name] (DOI: [DOI]).

Our attention has been drawn to some comments posted on PubPeer concerning this article. As part of our commitment to maintaining the integrity of the scholarly record, we aim to address any questions that arise about published research.

We believe it's important to provide you with an opportunity to review the points raised and offer any clarification you deem appropriate.

Could you please take a look at the comments at the following link: [link to PubPeer comments]? We would appreciate it if you could share your perspective on the points raised.

Please let us know if you have any questions or if there is anything we can do to assist you.

Sincerely,

[Journal Name]

2) 

Subject: Inquiry Regarding Your [JXX] Article: [Article #]

Dear Dr. [Author],

We are writing to you today regarding your article, "[Article Title]," published in [Journal Name] (DOI: [DOI]).

We have noted your response to comments on the PubPeer platform [link to PubPeer comments], and we appreciate you taking the time to address the points raised there.

To help us fully understand the situation and ensure a comprehensive review, we'd be grateful if you could provide us with any additional information or context that you believe is relevant to the discussion. This could include, for example, more detailed explanations, original data or files related to the specific concerns, or anything else you feel would be helpful for us to consider.

Our aim is to support our authors and maintain the integrity of the scholarly record. Providing us with further details will assist us in this process.

If you have any questions or would like to discuss this further, please don't hesitate to reach out.

Sincerely,

[Journal Name]

3)

Subject: Inquiry Regarding Your [JXX] Article: [Article #]

Dear Dr. [Author],

We are writing to you today regarding your article, "[Article Title]," published in [Journal Name] (DOI: [DOI]).

We have seen your recent response on PubPeer [insert PubPeer link] where you've addressed the comments and noted that a mistake was made. We appreciate your transparency in clarifying this on the platform.

For the sake of the scholarly record and to maintain the highest level of accuracy for your published research, we want to confirm that the information you provided on PubPeer reflects the current understanding of your work. If it does, we kindly request that you formally submit a correction to [Journal Name].

A formal correction ensures that the updated information is clearly and permanently associated with your article for all future readers and databases. Please let us know if you intend to submit a correction or if you'd like to discuss this further.

Sincerely,

[Journal Name]

4)

Subject: Inquiry Regarding Your [JXX] Article: [Article #]

Dear Dr. [Author],

We are writing to you today regarding your article, "[Article Title]," published in [Journal Name] (DOI: [DOI]).

We noted your recent response on PubPeer where you acknowledge a mistake and indicate your intention to submit a correction to [Journal Name]. We appreciate your proactive approach in addressing this for the scientific record.

We haven't yet received a formal correction submission for this article. We wanted to reach out to confirm if your intention to submit a correction is still accurate, and, if so, to offer our assistance in guiding you through the submission process.

Please let us know if you still plan to submit a correction or if you have any questions about the process.

Sincerely,

[Journal Name]

5) 

Subject: Investigation: [Article #] 

Dear RUP Graphics,

Figure [No.] is being replaced in published article [Article #]. Please preflight the new figure, run ImageTwin, and perform a quick review of all other figures in this article.

The files are on Dropbox at [Dropbox link]. Please upload the prepared figure(s) there and let me know the results of your preflight review.

Thank you,

[PPM]