Dear Dr Ziemann,

Thank you very much for submitting your manuscript "Gene name errors: lessons not learned" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

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Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Christos A. Ouzounis

Associate Editor

PLOS Computational Biology

Ilya Ioshikhes

Deputy Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors have written a clearly readable paper with all relevant data and code made available.

It is beneficial to highlight how incorrect gene names continue to be published and how this can be an issue as they are difficult to check for.

It is unclear how useful the comparison between different publications is. It is unclear how many other users will see value in the provided software. It is also unclear whether it was necessary to spend time focusing on which organisms have gene names at risk, and the text devoted to gene name errors by year. Calling a correlation coefficient of 0.589 a strong association is somewhat optimistic.

This paper could be strengthened by offering more solutions to this problem, for example by emphasising using .csv rather than .txt format, and alternatives to spreadsheet software, such as RStudio.

A couple of minor points, it is possible to paste directly into Google Sheets without errors occurring. There appears to be an error with the automated reporting system, with four identical reports currently shown.

Reviewer #2: I applaud the hard work of the authors. Opening several thousand file by hand is a heroic task that nobody envies them for. My hat is off!

I liked the analysis and the writing very much. I have only four minor points, the last one is optional:

1. Ordering table 4 by highest to lowest „Proportion of publications affected” makes grasping the results much easier.

2. Show graph for the correlation between JIF and error rate and report R2. Such a graph is useful for visualizing the negative correlation of journal rank with reliability, consistent with similar graphs from other publications (see next point).

3. In the discussion (p14), the authors mention that the correlation of error rate with journal prestige may seem counterintuitive, but it is not only the 2016 analysis that their results are consistent with. See, e.g., https://doi.org/10.3389/fnhum.2018.00037 for a list of many other analyses that all suggest that work published in prestigious journals is more error prone than that of other publication venues. I fact, it would have been counter-intuitive had the authors found less errors in highly prestigious journals: the evidence predicts more errors in more prestigious journals.

4. The authors may consider inserting a few sentences into their discussion about a solution to this (and many other, related) problems with the data and code underlying our narratives: an infrastructure solution that integrates research data and code in a way that makes supplemental files unnecessary. Such a solution has been technically feasible for some years now and many people have suggested to use such solutions, e.g.:

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000117

http://www.theguardian.com/science/head-quarters/2015/may/12/will-traditional-science-journals-disappear

https://neuroneurotic.net/2015/07/17/revolutionise-the-publication-process/

https://micahallen.org/2015/03/20/short-post-my-science-fiction-vision-of-how-science-could-work-in-the-future/

Björn Brembs

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes: Björn Brembs

Figure Files:

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. 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.

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References:

Review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Dr Ziemann,

We are pleased to inform you that your manuscript 'Gene name errors: lessons not learned' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Christos A. Ouzounis

Associate Editor

PLOS Computational Biology

Ilya Ioshikhes

Deputy Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: I thank the Authors for addressing all of the comments. I am pleased with the additions, particularly Box 1. This article helps continue to strengthen the case for reproducible and transparent science, thank you.

Reviewer #2: The reivewers have addressed all my concerns adequately.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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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: Yes: Björn Brembs