PONE-D-22-08328Semi-automated socio-anthropologic analysis of the medical discourse on Rheumatoid arthritis: potential impact in public healthPLOS ONE

Dear Dr. Nardini,

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.

 We have received comments from two independent reviewers (please see below) and they have raised some important methodological issues. Please carefully assess these comments and make the necessary changes to your submission. 

Please submit your revised manuscript by Sep 08 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

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• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Carla Pegoraro

Division Editor

PLOS ONE

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CN was partially funded by the iPC project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 826121. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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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: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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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: No

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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: No

**********

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: The authors have presented their study related to semi-automated socio-anthropologic analysis of the medical discourse on Rheumatoid arthritis. The goal of the study is quite interesting and the results of the presented well. Some of the following concerns in the manuscript, if addressed could make the manuscript more consistent and further strengthen the author's conclusions:

1. Technically, the abstract could be slightly revised and made more precise for the users to understand the overall study.

2. Introduction explains more insights related to the study but requires few revisions and changes. For Example sentences such as “biology and biochemistry to medical research or practice” [12], including by now bioinformatics, computational and systems biology [13] as well as network medicine [14,15], …” needs revision.

3. Minor changes such as terms “data base” needs to be changed as “database”.

4. Careful revision of manuscript is required for easy understanding of the readers.

5. In the methods section, kindly modify the following sub-headings:

“Materials – reviews, Materials – Variables, Methods Analysis.”

6. In methods section, describe the unsupervised learning technique used in this study. Techniques used in this study such as unsupervised clustering is not well explained in the manuscript. Only one sentence explains it, in the discussion part.

7. This study has certain limitations such as only 28 articles are used in the analysis both for textual and automated analysis. Can this approach be implemented for other studies with a large dataset (articles)?

Search terms used for the article selection from PubMed can also be included in the methods section.

8. Careful editing of the sentences such as

“modulators of the ANS, which coincides to date with vagus nerve stimulation (VNS), which jointly represent novel experimental therapies (EXP)”

“In the following: variables represents also the dimensions of the socio-anthropological space, ..”

will make the manuscript more readable for the users.

Reviewer #2: The authors have presented a view interesting work on medical discourse related to rheumatoid arthritis. Their study is an interdisciplinary biomedical research work that need expertise in anthropology, sociology, and medicine.

Major revisions

1. Introduction section is very long. Specifically, the authors have presented a detailed note on the three stages or parts of their work in the introduction section. Instead, they can provide a summary that will motivate the readers to look into the methods immediately.

2. The authors have provided the limitations of their work in the introduction itself. This has to be moved to discussion, probably with a sub-heading, “Limitations”.

3. The definition for each variable is helpful. However, it could be short. A detailed description on each variable in the methods section may take the readers away from the main research information.

4. The authors use only six variables for the automated learning (page 12). Why? A brief note in he manuscript will be useful.

5. The automated learning section need to be elaborated for better understanding of the method implemented by the authors. How did the authors implement the automated learning? Which package did they use?

6. The results section must include the results or findings. Rest can go to the discussion section. The authors should try to present the results in Tables or Figures, not just the text (see the sub-heading, “Textual analysis – individual variables). The result section must be revised completely.

7. The authors must revise the sub-headings in such a way that the sub-heading provides or summarizes the content in the paragraphs within it.

8. Why the authors performed supervised learning on some variables and unsupervised learning on other variables? What is the reason? Can they apply either one? What happens if the learning approaches are swapped?

Minor revisions

1. “(level I) the modulators of the GIP [19],” should be “the modulators of the GIP [19] (level I),”

2. The sub-heading “Materials – Variables” should be within “Materials and Methods”. The font size must be similar to “Materials – Review”.

3. The sub-headings with Materials and Methods (e.g. Materials – Variables, Materials - Review) could be renamed for better clarity.

4. In table 1, the variables under Low and High levels is unclear.

5. Methods Analysis could have a better name.

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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

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[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.]

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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PONE-D-22-08328R1Semi-automated socio-anthropologic analysis of the medical discourse on Rheumatoid arthritis: potential impact in public healthPLOS ONE

Dear Dr. Nardini,

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.

The reviewers have identified a number of outstanding concerns that will need to be addressed before the manuscript can be accepted for publication. Please respond carefully to all of the points they have raised when preparing your revision.

Please submit your revised manuscript by Oct 29 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Jamie Males

Editorial Office

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

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2. 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: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

**********

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: No

**********

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: Overall, the content and language has been improved by the authors with several changes, but there are still issues with syntactical constructions and formal scientific writing (e.g. in the added/extended text sections). Modification of subtitles and its content is more helpful for the readers to gain better insight of your research. If the manuscript is finally accepted, it should be looked at carefully for language check and sentence simplifications.

Some of the minor corrections are as follows:

1. Abstract has Background followed by Aim. In my opinion, abstract does not require the ‘aim’ section. Usually background followed by methods, results and conclusion would make it.

2. Some sentences needs simplification for readers to understand, (For example: “Our aim with this study is to contribute from yet another viewpoint, i.e. by analyzing how NCDs’ management is currently conceived and presented, using as proxy to gain insight into this issue an interdisciplinary analysis of the medical discourse.”)

3. Is ‘automated’ and ‘automatic’ learning the same in the manuscript. Kindly maintain the consistency throughout the manuscript.

4. Does this sentence explain the methodology used or the manuscript?

“Therefore, we chose a graphical approach to visualize up to six dimensions (variables) on the bidimensional space of the manuscript”. Could this sentence be modified for more clarity.

5. Conclusion section is quite long. If this could be precise, it would be appreciated.

Reviewer #2: 1. The paragraph that starts as “First, our analysis is run from the biomedical standpoint,” in page 49 and the paragraph that starts as “An overview of our approach is shown in Fig 1.” In page 50 include text on the author’s approach. The content is too long as well as clarity is missing. In the introduction, the authors should try to highlight the advancements they made. Their approach or pipeline should be presented as a summary. It must be clear and easy to understand.

2. Fig 1 can be cited in the beginning of methods. An overview of the approach (if required) can be presented withing the methods section.

3. Is the subheading “Variables” come under “Materials”? The font size shows that they both are independent subheadings. The authors should check the instructions on the subheadings allowed in the journal.

4. The authors should recheck the language in the entire manuscript. For example, “Unsupervised Second, to search for emergent properties” is not grammatically correct.

5. The authors can’t give the same subheading names within Methods and Results.

6. The authors can present the results in a better way. Current version includes only text.

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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

**********

[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.]

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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PONE-D-22-08328R2Semi-automatic socio-anthropologic analysis of the medical discourse on rheumatoid arthritis: potential impact in public healthPLOS ONE

Dear Dr. Nardini,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has satisfied our scientific requirements for publication.

However, our editorial team have significant concerns about the grammar, usage, and overall readability of the manuscript. PLOS ONE requires that published manuscripts use language which is 'clear, correct, and unambiguous', see our criteria for publication at https://journals.plos.org/plosone/s/criteria-for-publication#loc-5. We therefore request that you revise the text to fix the grammatical errors and improve the overall readability of the text.

We suggest you have a fluent English-language speaker thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can do this, you may wish to consider employing a professional scientific editing service.

Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (https://www.aje.com/go/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services. If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free.

Please note that we will not be able to proceed with publication of your manuscript until the concerns above are addressed.

Upon resubmission, please provide the following:

• The name of the colleague or the details of the professional service that edited your manuscript
• A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a supporting information file)
• A clean copy of the edited manuscript (uploaded as the new manuscript file)

We look forward to receiving your revised manuscript.

Kind regards,

Jamie Males

Editorial Office

PLOS ONE

Journal Requirements:

Please 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.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. 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: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

**********

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: No

**********

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: (No Response)

Reviewer #2: Major revisions:

1. The authors have improved the language much better than the last version. However, they need to pay more attention to correct the language. For example, “Our aim with this study is to contribute to explore” could be “We aim to contribute” or “We aim to explore”. Many sentences are too wordy and can be simplified further. This comment is applicable to the entire manuscript.

2. Introduction has improved a lot when compared to the previous version. However, the authors introduce their approach in three paragraphs. The authors should condense this to one paragraph and focus on the significant contributions they made in this current work.

3. The authors highlight the merging of manual curation into a table in the last paragraph of the introduction. It is not necessary to cite Table 2 here. Table 2 should be pushed to methods or results section.

4. In general, the introduction section does not include table or figure. Sometimes, it is okay to include a figure or a table in the introduction. However, citing a figure and two tables in the introduction is not appropriate.

5. The authors still use the same sub heading (ex. Digitalization) in methods and results. In methods, they explain their approach. In results, they present their findings. The sub heading should match this. It can’t be the same in both the sections.

Minor revisions:

1. The authors have changed the phrase to “semi-automatic” in the title. However, the phrase, “semi-automated” is the right one.

2. The authors should avoid very long sentences. For example, the following sentence is too long: “In particular, the pharmacological gold standard therapy (from now on PHA) includes drugs that aim at the symptomatic control of inflammation like non-steroideal anti-inflammatory drugs (NSAIDS), and paracetamol or morphine(-derived) analgesic drugs; corticosteroid which operate beyond symptoms and attempt to contrast the degeneration associated with the disease; and finally disease modifying anti-rheumatic drugs (DMARDs) able to interfere and block on more (biologic, bDMARDs) or less (conventional, cDMARDs) specific targets, the activity of pro-inflammatory molecules (cytokines) or cells, once the disease has been diagnosed [16–18].” The authors should try to split the content in multiple sentences such that it will be clear to the readers.

**********

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

**********

[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.]

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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Semi-automated socio-anthropologic analysis of the medical discourse on rheumatoid arthritis: potential impact on public health

PONE-D-22-08328R3

Dear Dr. Nardini,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. 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.

Kind regards,

Dario Ummarino, PhD

Staff Editor

PLOS ONE