# How to Track and Document Major Revisions ## Quick Answer - Build a spreadsheet with columns for each reviewer comment, your response, status, and verification to ensure every requested change is addressed before resubmission. - Use version control on your manuscript files so you can identify exactly what changed between the original submission and the revised version. - A tracking system only works if you verify each response against the final manuscript, and it cannot replace careful judgment about which reviewer requests are appropriate to accept. ## Why Tracking Reviewer Comments Matters Peer review exists to improve the quality and integrity of published research. When a journal sends you reviewer comments, those comments represent a formal request for changes to your manuscript. The Committee on Publication Ethics Core Practices describe peer review as a process that journals should operate fairly and rigorously, and authors have a corresponding responsibility to respond to reviewer feedback in a transparent manner. Failing to track comments can lead to missed requests, incomplete revisions, and a resubmission that does not address what the reviewers asked for. The practical problem is that a single round of peer review can produce dozens of comments. Some comments are major, requiring new analyses or substantial rewriting. Others are minor, such as clarifying a sentence or adding a citation. Without a system, you risk losing track of the minor comments while you focus on the major ones. The result is a resubmission that still contains obvious problems the reviewers already identified, which can delay publication and damage your credibility with the editor. A tracking system also helps you write the response letter. Most journals expect a point-by-point response that shows each reviewer comment and your reply. The Committee on Publication Ethics notes that journals should have policies for handling peer review, and your response letter is the primary record of how you addressed the review. A spreadsheet or similar tool gives you the raw material for that letter and lets you confirm that every comment has a corresponding action. ## Core Principles of Revision Tracking ### Treat the Reviewer Comments as a Work List The first principle is to treat the reviewer comments as a work list, not as a vague set of suggestions. Each comment is a task that needs a decision. You can accept the request and change the manuscript, you can decline the request and explain why, or you can partially accept it and make a modified change. The tracking system should record which decision you made for each comment. ### Separate the Comment from the Response A common mistake is to write responses directly into the margins of the manuscript or to keep notes in an email thread. That approach mixes the comment, your thinking, and the final response in a way that is hard to verify. Instead, keep the comment text in one column and your response in another column. This separation lets you check that every comment has a response and that every response is complete. ### Verify the Change in the Manuscript The most important principle is verification. A response letter can say that you changed the manuscript, but the editor will check the actual file. Before you submit, you need to confirm that each accepted comment has a corresponding change in the revised manuscript. The verification step is what separates a tracking system that works from one that only creates the appearance of work. ## The Spreadsheet Tracking System ### Setting Up the Columns A spreadsheet is the most practical tool for most researchers because it is widely available and does not require special software. Create a new spreadsheet with the following columns: | Column | Purpose | | --- | --- | | Comment ID | A unique number for each comment, such as R1C1 for Reviewer 1 Comment 1 | | Reviewer | Which reviewer made the comment | | Comment text | The full text of the comment, copied exactly | | Location | Where in the manuscript the comment applies, such as page and line number | | Decision | Accept, partially accept, or decline | | Response | Your response to the comment | | Manuscript change | A description of the change you made | | Status | Pending, in progress, done, or verified | | Verification date | The date you confirmed the change is in the manuscript | The comment ID column is important because it gives you a short reference for each comment. You can use these IDs in your response letter and in your manuscript notes. For example, you might write R1C3 in the margin of the manuscript to show where you addressed reviewer 1 comment 3. ### Entering the Comments Start by copying every reviewer comment into the spreadsheet. Do not skip comments that seem trivial. A comment about a typo is still a comment that the editor expects you to address. If you skip it, the editor may notice and question your attention to detail. When you paste the comment text, keep it in the original wording. Do not paraphrase the comment in the spreadsheet. The original text is the record of what the reviewer asked for, and you need that record when you write your response letter. ### Assigning Decisions For each comment, make a decision. The decision is your professional judgment about whether to accept the comment, partially accept it, or decline it. The Committee on Publication Ethics Core Practices note that journals should have policies for handling peer review, and those policies typically expect authors to respond to each comment. The decision is not about whether the reviewer is right or wrong. It is about what you will do in response. Accept means you will make the change the reviewer requested. Partially accept means you will make a related change that addresses the underlying concern but not exactly what the reviewer asked for. Decline means you will not change the manuscript and you will explain why in your response. ### Writing the Response Write the response for each comment in the response column. The response should be direct and specific. State what you did or why you did not do it. If you declined a comment, explain your reasoning with evidence from your data or from the literature. The response letter is a formal document, and the Committee on Publication Ethics Core Practices describe the importance of integrity in research and publication. Your responses should be honest. Do not claim you made a change that you did not make. Do not claim that a change addresses a concern when it does not. ### Updating Status Use the status column to track where each comment is in the process. A simple set of statuses is pending, in progress, done, and verified. Pending means you have not started. In progress means you are working on it. Done means you have made the change and written the response. Verified means you have checked the manuscript and confirmed the change is present. The status column is what makes the spreadsheet a tracking system instead of a list. You can sort by status to see what remains. You can filter to show only pending comments. This gives you a clear picture of your progress. ## Version Control for the Manuscript ### Why Version Control Matters The spreadsheet tracks the comments, but you also need to track the manuscript itself. When you make changes, you need to know which version of the manuscript contains which changes. Version control is the practice of saving a new version of the manuscript each time you make a significant change. The simplest version control is to save the manuscript with a version number and a date in the filename. For example, you might save the file as manuscript_v1_2025_01_15.docx, then manuscript_v2_2025_01_20.docx. This gives you a history of the file and lets you go back to an earlier version if you need to. ### Using Track Changes Most word processors have a track changes feature that records every edit you make. This feature is useful during the revision process because it shows the editor and the reviewers exactly what you changed. Many journals require or strongly prefer that you submit a version with track changes along with a clean version. When you use track changes, you can see the history of edits in the document. This is a form of version control that is built into the document itself. The track changes record is useful for verification because you can search for the changes you made in response to each comment. ### Naming Conventions A consistent naming convention is important. Use a format that includes the version number and the date. Do not use names like final_v2 or final_really_final. These names are not informative and can cause confusion. A clear name like manuscript_v3_2025_02_01.docx tells you exactly what the file is and when you saved it. ### Storing the Versions Keep all versions of the manuscript in one folder. Do not delete old versions. The old versions are your backup and your record of the revision process. If you need to check what the manuscript looked like at a certain point, you can open the old version. ## The Response Letter The response letter is the formal document you send to the editor with your revised manuscript. The letter should address every reviewer comment. The spreadsheet gives you the content for the letter, but the letter has its own format. ### Structure of the Response Letter The response letter typically starts with a brief summary of the changes you made. Then it addresses each reviewer comment in order. For each comment, you restate the comment and then give your response. The response should be clear and direct. The Committee on Publication Ethics Core Practices describe the importance of integrity in the peer review process. The response letter is part of that integrity. It should be honest and complete. Do not omit comments that you declined. The editor needs to see that you considered every comment. ### Using the Spreadsheet to Build the Letter You can build the response letter directly from the spreadsheet. Copy the comment text and the response text into the letter document. Format the letter so that each comment is clearly separated from the next. Use the comment ID to help the editor find the comment in the manuscript. ### The Verification Step Before you send the letter, verify that every comment has a response and that every response has a corresponding change in the manuscript. This is the final check. Go through the spreadsheet and check the status column. Every comment should have a status of verified. ## Practical Implementation Steps ### Step 1: Create the Spreadsheet Open a new spreadsheet and create the columns described above. If you prefer, you can use a table in a word processor or a project management tool. The important thing is that you have a structured place to record each comment. ### Step 2: Paste All Comments Copy every comment from the review file and paste it into the spreadsheet. Include the reviewer number and the comment number. Do not skip any comments. ### Step 3: Assign Decisions For each comment, decide whether you will accept, partially accept, or decline. Write the decision in the decision column. This step is the first pass through the comments. ### Step 4: Write Responses For each comment, write your response. The response should be specific and direct. State what you did or why you did not change. ### Step 5: Make the Manuscript Changes For each comment that you accepted or partially accepted, make the change in the manuscript. Use track changes so that the editor can see what you changed. ### Step 6: Verify Each Change After you make a change, go back to the spreadsheet and update the status to done. Then, before you submit, go through the manuscript and verify that each change is present. Update the status to verified. ### Step 7: Build the Response Letter Use the spreadsheet to build the response letter. Copy the comment and response for each item. Format the letter according to the journal requirements. ### Step 8: Final Check Before you submit, do a final check. Confirm that every comment has a response and that every response has a corresponding change. Confirm that the manuscript file you are submitting is the correct version. ## Common Failure Patterns ### The Incomplete Response Letter The most common failure is a response letter that does not address every comment. This happens when the researcher relies on memory instead of a tracking system. The editor will notice the missing comments and may return the manuscript without review. ### The Unverified Change Another common failure is a response that claims a change was made, but the change is not in the manuscript. This can happen when the researcher writes the response before making the change and then forgets to make the change. The editor will check the manuscript and find the discrepancy. ### The Vague Response A response that says "we have addressed this concern" without explaining what was done is not useful. The editor and the reviewer need to know what you actually did. A vague response suggests that you did not take the comment seriously. ### The Declined Comment Without Justification If you decline a comment, you need to explain why. A response that says "we disagree" without reasoning is not acceptable. The editor needs to see that you considered the comment and had a reason for not accepting it. ### The Version Confusion Saving multiple versions of the manuscript with unclear names can lead to submitting the wrong file. This is a serious error that can delay publication. ## Records and Measurements The tracking system is a record of your revision process. It is useful for your own reference and for the editor. The spreadsheet shows the history of each comment, the decision you made, and the response you wrote. The verification step is a measurement of your completeness. When every comment has a status of verified, you have a measurable confirmation that you have addressed all the comments. This is a useful check before you submit. The version control system is a record of the manuscript history. It shows the changes you made over time and allows you to go back to an earlier version if needed. ## Limitations of the Tracking System The tracking system is a tool, and it has limitations. It does not tell you whether your responses are good. It only tells you that you have a response for each comment. The quality of the responses depends on your judgment and your understanding of the research. The system also does not tell you whether a reviewer comment is appropriate. Some reviewer comments may be based on a misunderstanding of your work. You need to use your judgment to decide whether to accept or decline a comment. The tracking system does not make that decision for you. The system does not replace the need for careful reading of the reviewer comments. You need to understand what the reviewer is asking for before you can respond. The tracking system helps you organize the comments, but it does not help you understand them. ## Professional Escalation Criteria There are situations where you should seek help beyond your own judgment. If you are unsure whether a reviewer comment is appropriate, you can discuss it with a colleague or your supervisor. If you are concerned about a comment that seems to ask for something unethical, you should contact the editor. The Committee on Publication Ethics Core Practices describe the responsibilities of authors, reviewers, and editors. If you believe a reviewer has made an inappropriate request, you can raise the issue with the editor. The editor is responsible for the peer review process and can address concerns about reviewer conduct. If you are concerned about a conflict of interest or a question about authorship, you should address it before you submit. The Committee on Publication Ethics Core Practices describe the expectations for authorship and conflicts of interest. The tracking system does not address these issues, but you need to be aware of them during the revision process. ## A Decision Framework for Accepting, Partially Accepting, or Declining Comments The spreadsheet system records your decision for each comment, but it does not help you make that decision. Researchers often struggle because reviewer comments arrive with varying levels of validity, feasibility, and alignment with the study's scope. A structured decision framework helps you move from reacting to each comment individually toward a consistent, defensible position across the entire review. ### Step 1: Classify the Comment Type Read each comment and place it into one of four categories before deciding how to respond. This classification forces you to understand what the reviewer is actually asking for instead of responding to the surface wording. | Comment Type | Description | Typical Decision | | --- | --- | --- | | Factual correction | The reviewer identifies an error in your data, citation, calculation, or interpretation | Accept and verify the correction against your source data | | Clarification request | The reviewer asks you to explain something more clearly | Accept and revise the relevant text | | Methodological concern | The reviewer questions your study design, analysis, or interpretation | Evaluate carefully, often partially accept or decline with evidence | | Scope expansion | The reviewer asks for additional analyses, data, or content beyond the original study | Decline or partially accept based on feasibility and relevance | The National Library of Medicine research methods resources emphasize that sound methodology is the foundation of trustworthy research. When a reviewer raises a methodological concern, you should treat it seriously and examine whether the concern reveals a genuine limitation or a misunderstanding of your approach. ### Step 2: Apply the Three-Part Feasibility Test For every comment that is not a simple factual correction, run the comment through three questions. Write the answers in a notes column or in the response column before you finalize your decision. **Is the request within the scope of the original study?** A reviewer may ask for a new research question, an additional patient cohort, or a different outcome measure. If the request would change what the study set out to answer, you can decline it while explaining that the request represents a separate study. The NIH Grants and Funding guidance on research conduct reinforces that studies should answer the questions they were designed to answer. **Can you complete the request with the data or materials you already have?** Some requests require data you did not collect or materials you no longer have. If the request is impossible with your existing resources, you should decline it and state the specific limitation. Do not claim you performed an analysis that you did not perform. **Does the request align with reporting standards for your study type?** The EQUATOR Network provides reporting guidelines for many study designs, including randomized trials, observational studies, and systematic reviews. If a reviewer asks for information that a relevant reporting guideline already requires, you should accept the comment and add the missing information. If the request goes beyond what the guideline requires, you have more latitude to decline or partially accept. ### Step 3: Choose the Decision with Justification After classification and the feasibility test, assign the decision. For each decision, write a one-sentence justification in the response column before you draft the full response. **Accept** when the comment identifies a genuine error, a missing piece of required reporting, or a reasonable clarification that improves the manuscript without changing the study's conclusions. **Partially accept** when the reviewer's underlying concern is valid but the specific request is not the best way to address it. For example, a reviewer may ask for a subgroup analysis that your sample size cannot support. You can partially accept by adding a limitation paragraph that discusses the potential for subgroup differences instead of performing an underpowered analysis. **Decline** when the request is outside the study scope, impossible with your data, or based on a misunderstanding that you can correct with a clear explanation. The Committee on Publication Ethics Core Practices describe the expectation that authors respond to peer review with integrity. Declining a comment is legitimate when you provide a reasoned justification, but it is not legitimate to decline a comment simply because the change is inconvenient. ### Step 4: Record the Justification and Revisit Before Submission Write the justification in the spreadsheet when you make the decision, not when you draft the response letter. This prevents the common failure pattern where a researcher writes a vague response because they no longer remember why they declined a comment. Before submission, review every declined and partially accepted comment to confirm that your justification still holds after you have made the other manuscript changes. ### Handling Conflicting Comments from Multiple Reviewers Reviewers sometimes make requests that contradict each other. One reviewer may ask you to shorten the discussion while another asks you to expand it. The decision framework helps you resolve these conflicts by applying the same classification and feasibility test to both comments. If both requests are reasonable, you can partially accept both by finding a middle ground that addresses the underlying concerns. If the requests are truly incompatible, you should accept the one that aligns with the reporting guidelines for your study type and decline the other with an explanation that references the conflict. ### When to Seek a Second Opinion The decision framework does not replace professional judgment. If you are uncertain whether a comment is appropriate, discuss it with a coauthor or a colleague who understands your field. The Committee on Publication Ethics Core Practices note that journals should have policies for handling disputes in peer review. If you believe a reviewer comment crosses an ethical line, such as requesting the inclusion of an unqualified author or asking you to misrepresent data, you should contact the editor directly instead of trying to resolve it in the response letter. ### Integrating the Framework into the Spreadsheet Add two columns to your spreadsheet to support this framework. The first is a comment type column where you record the classification from Step 1. The second is a justification column where you record the one-sentence reasoning from Step 3. These columns give you a searchable record of your decision process and make it easier to write the response letter because the reasoning is already documented. The comment type column also helps you identify patterns across the review. If you see that most comments are clarification requests, you may have a writing clarity problem that you should address throughout the manuscript instead of only at the specific locations the reviewers identified. If you see many methodological concerns, you may need to reconsider whether your analysis is adequately described or whether a reporting guideline from the EQUATOR Network applies to your study. ### Using the Framework to Prevent Common Failure Patterns The decision framework directly addresses the vague response failure pattern. When you have a documented justification for each decision, you cannot write a response that says only "we disagree." You have already recorded why you disagree, and that reasoning becomes the body of your response. The framework also addresses the declined comment without justification pattern. By requiring a one-sentence justification at the time of the decision, you build the habit of explaining your reasoning while the comment is fresh. This is more reliable than trying to reconstruct your reasoning weeks later when you draft the response letter. The framework does not replace the verification step. After you make all decisions and draft all responses, you still need to confirm that every accepted comment has a corresponding change in the manuscript. The decision framework improves the quality of your decisions and your responses, but it does not change the requirement that the manuscript must actually contain the changes you claim to have made. ## Frequently Asked Questions ### How do I track reviewer comments without a spreadsheet? You can use a word processor table or a project management tool. The key is to have a structured format with columns for the comment, response, status, and verification. The format matters less than the structure. ### What should I do if I disagree with a reviewer comment? You can decline the comment, but you must explain why. State your reasoning clearly and respectfully. The editor will decide whether your response is acceptable. ### How do I know if I have addressed every comment? Use the status column in your spreadsheet. Every comment should have a status of verified before you submit. The verification step is the check that the change is in the manuscript. ### Should I use track changes in the manuscript? Most journals require or prefer track changes. It shows the editor and the reviewer exactly what you changed. Check the journal instructions for the specific requirement. ### How do I write a response letter? The response letter should address every comment in order. Restate the comment and then provide your response. Be specific and direct. Do not use vague language. ### What if I miss a comment? If you miss a comment, the editor will likely return the manuscript to you. The tracking system is designed to prevent this. Check the spreadsheet before you submit to confirm that every comment has a response. ### How do I handle comments from multiple reviewers? Use the reviewer column in the spreadsheet to separate comments from different reviewers. Address each reviewer's comments in a separate section of the response letter. ### What is the difference between a response and a manuscript change? A response is what you write to the editor and the reviewer. A manuscript change is the actual edit you make in the manuscript. Both are necessary. The response explains what you did, and the manuscript change is the evidence that you did it. ## Related Articles - [The Role of the Research Ethics Committee: What Researchers Need to Know](/blog/guides/the-role-of-the-research-ethics-committee-what-researchers-need-to-know) - [Bioinformatics Careers: What You Need to Know Before You Start](/blog/careers/bioinformatics-careers-what-you-need-to-know-before-you-start) - [Cross-Sectional Study Limitations: What You Need to Know Before You Start](/blog/guides/cross-sectional-study-limitations-what-you-need-to-know-before-you-start) - [biology major jobs](/blog/news/biology-major-jobs) - [Human Biology Major](/blog/careers/human-biology-major) ## References and Further Reading - [Research Methods Resources](https://www.ncbi.nlm.nih.gov/books). National Library of Medicine. - [EQUATOR Network](https://www.equator-network.org/). EQUATOR Network. - [Core Practices](https://publicationethics.org/core-practices). Committee on Publication Ethics. - [NIH Grants and Funding](https://grants.nih.gov/). National Institutes of Health. - [ORCID for Researchers](https://info.orcid.org/researchers). ORCID. - [Data Management and Sharing Policy](https://sharing.nih.gov/data-management-and-sharing-policy). National Institutes of Health. - [NCBI Literature Resources](https://www.ncbi.nlm.nih.gov/). National Center for Biotechnology Information. - [PubMed](https://pubmed.ncbi.nlm.nih.gov/). National Library of Medicine. > This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.