Learning important common data elements from shared study data: The All of Us program analysis

Craig S. Mayer; Vojtech Huser

doi:10.1371/journal.pone.0283601

Peer Review History

Original SubmissionDecember 27, 2021
9 Feb 2023 Decision Letter - Jake Michael Pry, Editor PONE-D-21-40725Learning important common data elements from shared study data: the All of Us program analysisPLOS ONE Dear Dr. Mayer, 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. Please see attached comments from two reviewers attached. While reviewer one confirms that the work is a valuable addition to the literature I would suggest focusing on addressing the feedback from reviewer two. We thank you for your time and hope that you choose to submit a revision given the reviews provided. Please submit your revised manuscript by Mar 26 2023 11:59PM. 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If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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: N/A Reviewer #2: N/A ****** 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: The authors have examined the common data elements from the All of Us program data. The data is available at our project repository https://github.com/lhncbc/CRI/tree/master/AoU/CDE This publication is in a combination of present and past tense. Even though the All of US program maybe continuing to enroll participants, the data for this study was obtained at a specific timeline (late 2021), and the analyses performed retrospectively, and hence could be described in past tense. Overall the paper is well written. Increased CDE usage in large studies like the All of Us program would better facilitate the usability of the data. Reviewer #2: Summary The authors analyze the All of US (AoU) program with respect to common data elements (CDEs) which are standardized across multiple clinical studies. AoU uses the OMOP Common Data Model for standardization. The authors investigate the frequency of CDEs as compared to unique data elements (UDEs), defined specifically for AoU. Among other details, the origin of the CDEs is described. General The manuscript deals with an important topic for the medical research infrastructure. I have a few comments but overall the manuscript merits publication. Comments 1) Several typos and grammar errors. Please correct. 2) Abstract: Abbreviation PPI not defined. “originated from a previous data collection initiative, such as PhenX (17 CDEs) and PROMIS (15 CDEs)” plr: data collection initiatives 3) 2.1 All of Us program Missing is the aim of the initiative and the planed follow-up. Is biomaterial collected by AoU? Is genetic data available? Please add. 4) The structures of the data elements and values are rather complex and not easy to grasp. Add figures which present the data structures and hierarchies and also add examples in the text. 5) Table 2: Why is the column “CRF” blank for some elements? Explain in legend to table 2. 6) Element ‘Current State’: Please explain what that means. 7) l 233: GROR: It is not explained what that is. 8) l 245: Brackets not consistent. 9) Table 6: Add the event counts. Why do the “Percent of Element Values” not add up to 100%? Please explain what the percent refers to. Please additionally use such a reference population that the percentages add up to 100%. 10) 5.1 EHR and research data integration: “An example of this can be seen with cigarette smoking quantification (OMOP concept_id: 40766929) which may be established by research questionnaire (in 97.2% of instances) but later updated via EHR import (in 2.8% of instances).” Discuss the possibility of bias because of the low follow-up percentages which might result in selective, biased information. 11) l. 388f: grammar error 12) 5.3 Types of CDEs: Please illustrate the two axes and the number of elements contained in the four sets by a table or Venn diagram. ****** 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.] 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. 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Revision 1
16 Feb 2023 Author Response Dear Dr. Jake Michael Pry, We thank you and the reviewers for the input and constructive comments on our manuscript. We have thoroughly reviewed each comment and our manuscript and have edited our paper taking into account each comment. We are now submitting the edited and improved version of our manuscript. See below our response (in bold font) to each reviewer comment. Our response follows the reviewer’s comments (shown in regular un-bolded text). Thank you, Craig Mayer and Vojtech Huser Reviewer #1 This publication is in a combination of present and past tense. Even though the All of US program maybe continuing to enroll participants, the data for this study was obtained at a specific timeline (late 2021), and the analyses performed retrospectively, and hence could be described in past tense. Thank you for the comment. We have changed the portions where we discuss our analysis, results and conclusions, to conform to past tense. For the purposes of describing the All of Us program and their data collection practices we maintain the text in present tense since we are describing the ongoing methodology of the program itself. While our analysis and the results we found were done in the past and therefore in the past tense, the All of Us program is ongoing, and we feel should be described in present tense for that reason. Reviewer #2 1) Several typos and grammar errors. Please correct. Thank you for your comments. We have corrected typos and grammar mistakes throughout the manuscript. 2) Abstract: Abbreviation PPI not defined. We have defined PPI in the Abstract where the acronym first appears. “originated from a previous data collection initiative, such as PhenX (17 CDEs) and PROMIS (15 CDEs)” plr: data collection initiatives We have made the term data collection initiative plural in the text of the Abstract to conform with the multiple initiatives discussed. 3) 2.1 All of Us program Missing is the aim of the initiative and the planed follow-up. Is biomaterial collected by AoU? Is genetic data available? Please add. We added the aims and a brief description of additional data types. However, it would be out of scope to further discuss these data types and process as the manuscript is focused on CRF and EHR data and the presence of common data elements. The addition of these data types beyond just mentioning them do not contribute to the conclusions as they are not part of the common data model structure. The further details regarding the All of Us program was added to this section (2.1). 4) The structures of the data elements and values are rather complex and not easy to grasp. Add figures which present the data structures and hierarchies and also add examples in the text. Figure 1 along with an explanation was added to section 3.2 to clarify this process and structure. 5) Table 2: Why is the column “CRF” blank for some elements? Explain in legend to table 2. The reason the CRF column is blank for some data elements is that these elements originate from a research visit instead of a CRF. This explanation was added as a footer to Table 2. 6) Element ‘Current State’: Please explain what that means. To avoid initial confusion about the meaning of this data element, it was removed from Table 2. When it is mentioned later in the text in section 4.1.1, we explain that ‘Current State’ refers to the geographic location of the participant. 7) l 233: GROR: It is not explained what that is. We added an explanation of what GROR refers to in section4.1.2. The exact meaning of the GROR acronym is not made apparent by the All of Us program or OMOP terminology. Instead, we explained the general purpose of the GROR CRF. 8) l 245: Brackets not consistent. We fixed this with the addition of a close bracket for bracket agreement. 9) Table 6: Add the event counts. Why do the “Percent of Element Values” not add up to 100%? Please explain what the percent refers to. Please additionally use such a reference population that the percentages add up to 100%. Table 6 has been redone to include the count of total responses and responses by value chosen to describe the percentage. All values were included to see 100% of the population’s responses. A sentence was added before the table to explain the contents. 10) 5.1 EHR and research data integration: “An example of this can be seen with cigarette smoking quantification (OMOP concept_id: 40766929) which may be established by research questionnaire (in 97.2% of instances) but later updated via EHR import (in 2.8% of instances).” Discuss the possibility of bias because of the low follow-up percentages which might result in selective, biased information. Sentences were added to section 5.1 to discuss this possibility. We have added sentences to this section describing the consideration of bias in the data due to the differences in population follow-up caused by the inclusion of EHR data instead of research process repetition. 11) l. 388f: grammar error This sentence was edited to ensure proper grammar and clarify meaning. 12) 5.3 Types of CDEs: Please illustrate the two axes and the number of elements contained in the four sets by a table or Venn diagram. Table 9 was added to the section to better show this crossover and process. This should help clarify the premise described regarding the types of CDEs and the axes. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0283601.r002
13 Mar 2023 Decision Letter - Jake Michael Pry, Editor Learning important common data elements from shared study data: the All of Us program analysis PONE-D-21-40725R1 Dear Dr. Mayer, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: (No Response) ****** 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: (No Response) ****** 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 Response) ****** 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: All comments addressed. Overall the paper is well written. Increased CDE usage in large studies like the All of Us program would better facilitate the usability of the data. 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.0283601.r003
Formally Accepted
17 Mar 2023 Acceptance Letter - Jake Michael Pry, Editor PONE-D-21-40725R1 Learning important common data elements from shared study data: the All of Us program analysis Dear Dr. Mayer: I'm 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 let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Jake Michael Pry Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0283601.r004

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