# The 'Clarify in Response' Strategy ## Quick Answer - Start provisional revisions immediately by grouping reviewer comments into those needing clarification and those you can address with reasonable assumptions. - Flag every assumption-based change clearly in your response letter using tracked changes or highlighted text so reviewers can verify your interpretation. - Adjust all provisional edits once clarification arrives, and document the revision timeline in your response letter to show transparent handling of the peer review process. ## Understanding the Clarify in Response Strategy Peer review feedback often arrives with ambiguous comments that leave researchers uncertain about the exact changes expected. Tight deadlines compound this problem, creating pressure to either wait indefinitely for clarification or proceed with revisions that might miss the mark. The clarify in response strategy offers a middle path: begin revising immediately using your best interpretation, mark those provisional changes explicitly, and refine them when the editor or reviewer provides additional guidance. This approach aligns with the practical realities of manuscript revision. Journals expect timely responses, and editors appreciate authors who engage constructively with reviewer feedback instead of stalling on ambiguous points. The strategy does not mean guessing blindly. It means making transparent, well-reasoned assumptions and communicating those assumptions clearly enough that reviewers can correct them without difficulty. The Committee on Publication Ethics Core Practices emphasize that peer review should be fair and transparent, with journals having clear processes for handling manuscripts and appeals. When you flag provisional revisions properly, you give reviewers the information they need to evaluate your work fairly, even when some comments were initially unclear. ## Core Principles of Provisional Revision ### Distinguish Clarification Requests from Actionable Feedback Before starting any revision work, sort every reviewer comment into one of two categories. The first category contains comments you can address with reasonable confidence based on the manuscript content, the journal's scope, and standard practices in your field. The second category contains comments where the requested change is genuinely ambiguous, contradictory with other feedback, or dependent on information only the editor or reviewer possesses. This sorting step takes thirty to sixty minutes for a typical set of reviewer comments but saves substantial time later. Create a simple table with columns for the comment number, the reviewer's request, your interpretation, and whether clarification is needed. This table becomes the backbone of your response letter and helps you track which revisions are provisional versus final. ### Make Your Best-Faith Assumptions Explicit When you encounter a comment that needs clarification but can be reasonably interpreted, proceed with your best assumption and document it. For example, if a reviewer asks for additional statistical analysis without specifying the exact test, choose the most appropriate test for your data structure and note in your response letter that you selected this test based on the study design and would adjust if the reviewer intended a different approach. The key is making your reasoning visible. Reviewers are more likely to accept a well-reasoned assumption they can see than a silent guess they cannot evaluate. Your response letter should state the assumption, explain why you chose it, and invite correction. This turns a potential point of friction into a demonstration of your methodological competence. ### Track Every Provisional Change Use your word processor's track changes feature or maintain a detailed revision log for every assumption-based edit. Record the original text, the revised text, the reviewer comment that prompted the change, and your rationale. This log serves two purposes. It helps you locate and adjust provisional changes quickly when clarification arrives, and it provides evidence of your revision process if questions arise later. For manuscripts with extensive provisional revisions, consider color-coding changes in the manuscript itself. Use one color for changes that directly address clear reviewer comments and another color for provisional changes awaiting clarification. This visual distinction helps reviewers navigate your revised manuscript and understand which changes require their confirmation. ## Practical Workflow for Starting Revisions ### Step 1: Read All Comments Before Making Any Changes Read the complete set of reviewer comments and the editor's decision letter before touching the manuscript. This prevents the common mistake of addressing comments in isolation without recognizing connections between them. Reviewers sometimes raise related points across different sections, and the editor's letter often provides context about the overall concerns driving the decision. Take notes on recurring themes. If two reviewers raise similar concerns about your methods section, addressing the underlying issue once may satisfy both. If reviewers contradict each other, flag this for the editor in your response letter instead of choosing one reviewer's preference arbitrarily. ### Step 2: Create Your Comment Response Table Build a working document with every reviewer comment listed verbatim or closely paraphrased. Add columns for your response plan, the manuscript location affected, whether clarification is needed, and the status of the revision. This table becomes your master tracking tool throughout the revision process. For comments requiring clarification, add a column noting what specific information you need. This forces you to articulate exactly what is unclear, which often reveals that you can proceed with a reasonable assumption after all. The discipline of writing out your clarification question frequently clarifies your own thinking. ### Step 3: Prioritize Revisions by Dependency Some revisions are independent and can proceed immediately. Others depend on decisions made elsewhere in the manuscript. For example, if you need to add a sensitivity analysis, you might need to decide on the primary analysis approach first. Map these dependencies before starting to write. Begin with revisions that unblock other work. Statistical analyses, figure regeneration, and data reanalysis typically fall into this category because their results affect multiple sections of the manuscript. Text-only revisions can proceed in parallel while analyses run. ### Step 4: Draft the Response Letter Early Write a preliminary version of your response letter before completing the revisions. This letter should list every comment, your planned response, and any clarification requests. Drafting the letter early forces you to think through your responses systematically and reveals gaps in your revision plan. The response letter is your primary communication tool with the editor and reviewers. A well-structured letter that addresses every comment, flags provisional changes, and requests clarification where needed demonstrates professionalism and reduces the likelihood of extended back-and-forth. ## At a Glance | Scenario | Recommended Action | Documentation Needed | Escalation Point | | --- | --- | --- | --- | | Comment is clear and actionable | Complete the revision normally | Standard response letter entry | None | | Comment is ambiguous but interpretable | Make best-faith assumption and flag as provisional | Tracked change plus assumption note in response letter | Adjust when clarification arrives | | Comment requires information only reviewer possesses | Request clarification and proceed with other revisions | Clarification request in response letter with specific questions | Follow up with editor if no response within expected timeframe | | Comments from different reviewers conflict | Address both interpretations or request editor guidance | Explanation of conflict and your resolution approach in response letter | Escalate to editor for adjudication | | Comment requests data or analysis not feasible with current resources | Explain limitations and propose alternative | Detailed feasibility analysis and alternative proposal in response letter | Discuss with editor about scope adjustment | ## Drafting Clarification Requests That Get Answers ### Ask Specific Questions Vague clarification requests produce vague answers. Instead of asking a reviewer to clarify their comment, present your interpretation and ask them to confirm or correct it. For example, instead of writing "Could you clarify what you meant by additional analysis?", write "We interpreted your request for additional analysis as a need for sensitivity testing using the X method. Please confirm this interpretation or specify the analysis you intended." This approach makes it easy for reviewers to respond. They can simply confirm your interpretation or provide a brief correction. It also demonstrates that you have engaged seriously with their feedback, which tends to generate more cooperative responses. ### Bundle Related Clarification Requests Reviewers are busy people. Sending multiple separate clarification requests creates friction and delays. Bundle all clarification requests into a single section of your response letter, organized by reviewer and topic. This allows reviewers to address all their clarification needs in one pass. When bundling, group related questions together. If you need clarification on both the statistical approach and the interpretation of results, keep those questions in the same section so the reviewer can see the connection between them. ### Set a Reasonable Response Window Journals typically expect authors to respond to reviewer comments within a defined timeframe, often two to four weeks depending on the journal and the extent of revisions required. When you request clarification, note that you are proceeding with other revisions while awaiting the response. This signals that you are using your time productively and prevents the impression that you are stalling. If the clarification does not arrive within a reasonable window, follow up with the editor. The editor has an interest in moving the manuscript forward and can often facilitate a response from the reviewer. Your follow-up should be polite and factual, noting the date of your original request and the progress you have made on other revisions. ## Managing Provisional Revisions in the Manuscript ### Use Track Changes Strategically Track changes serve different purposes depending on the journal's preferences. Some journals require clean manuscripts for review, while others accept tracked changes. Check the journal's author guidelines before deciding how to present your revisions. For provisional changes specifically, consider adding a comment bubble or footnote in the manuscript noting that the change is provisional and based on an assumption awaiting clarification. This makes it impossible for reviewers to miss the provisional nature of the change, even if they do not read the response letter carefully. ### Maintain a Separate Provisional Change Log Beyond track changes, maintain a separate document listing every provisional change with its location, the original text, the revised text, the triggering comment, and your assumption. This log is your working document for adjusting changes when clarification arrives. When clarification arrives, work through this log systematically. For each provisional change, determine whether the clarification confirms your assumption, requires adjustment, or necessitates reverting to the original text. Update the manuscript accordingly and note the resolution in your response letter. ### Prepare for Both Outcomes Clarification can confirm your assumption or require a different approach. Prepare for both possibilities by considering alternative interpretations before clarification arrives. For each provisional change, think through what you would do if the reviewer meant something different from your assumption. This preparation speeds up the adjustment process when clarification arrives. Instead of starting from scratch, you can implement the alternative approach you have already considered. It also helps you write better clarification requests because you understand the range of possible interpretations. ## Common Failure Patterns in Provisional Revision ### Pattern 1: Silent Guessing The most common failure is making assumption-based changes without flagging them. Researchers sometimes worry that admitting uncertainty will reflect poorly on them, so they present provisional changes as final. This backfires when reviewers detect the mismatch between their intent and the revision, leading to frustration and additional revision rounds. The clarify in response strategy requires transparency. Flagging provisional changes does not signal weakness. It signals careful engagement with reviewer feedback and a commitment to getting the revision right. ### Pattern 2: Waiting Indefinitely for Clarification The opposite failure is refusing to proceed until every ambiguity is resolved. This stalls the revision process and can lead to missed deadlines. Most reviewer comments can be addressed with reasonable assumptions, and the few that cannot should not block progress on the rest of the manuscript. Proceed with all revisions you can complete confidently. Request clarification for the rest and continue working. The response letter can note that certain revisions are provisional pending clarification, which is acceptable in most peer review processes. ### Pattern 3: Overloading the Response Letter Some researchers respond to ambiguity by writing extensive explanations for every assumption, burying the actual revisions under layers of justification. This makes the response letter difficult to navigate and can obscure the changes you made. Keep the response letter focused. For each comment, provide a brief response that states what you changed, where, and any assumption you made. Reserve detailed explanations for comments that genuinely require them. The manuscript itself should demonstrate the quality of your revisions. ### Pattern 4: Failing to Track Provisional Changes Without a systematic tracking system, provisional changes get lost in the revision process. When clarification arrives, you cannot find all the affected passages, leading to inconsistent revisions where some sections reflect the clarified intent and others still reflect your original assumption. The provisional change log is not optional. It is the operational core of the clarify in response strategy. Invest the time to maintain it properly from the start of the revision process. ## Records and Measurements for Revision Tracking ### Revision Status Table | Comment ID | Reviewer | Summary of Comment | Clarification Needed | Status | Provisional Flag | Resolution | | --- | --- | --- | --- | --- | --- | --- | | R1-01 | Reviewer 1 | Add discussion of study limitations | No | Complete | No | Final | | R1-02 | Reviewer 1 | Clarify inclusion criteria | Yes | In progress | Yes | Awaiting clarification | | R2-01 | Reviewer 2 | Add sensitivity analysis | Yes | In progress | Yes | Awaiting clarification | | R2-02 | Reviewer 2 | Revise abstract conclusions | No | Complete | No | Final | | E-01 | Editor | Shorten introduction | No | Complete | No | Final | ### Time Tracking for Revision Milestones Track the time spent on each revision phase to identify bottlenecks and improve future revision processes. Record the date you received the decision letter, the date you submitted your clarification requests, the date clarification arrived, and the date you submitted the revised manuscript. This data helps you set realistic expectations for future revisions. If clarification typically takes two weeks to arrive, factor that into your planning. If certain types of revisions consistently take longer than expected, allocate more time for them in future projects. ## Quality Controls for Provisional Revisions ### Internal Consistency Check Before submitting your revised manuscript, verify that all provisional changes are internally consistent. If you made an assumption about the statistical approach, ensure that the methods, results, figures, and discussion all reflect that same assumption. Inconsistencies between sections signal carelessness and undermine reviewer confidence. Read the revised manuscript as a whole, not section by section. This holistic read catches inconsistencies that section-by-section review misses. Pay particular attention to transitions between sections where assumptions from one section may not carry through to the next. ### Peer Review of Your Revisions If possible, have a colleague review your provisional revisions before submission. A fresh reader can identify assumptions that are not clearly flagged and passages where your interpretation of reviewer comments may have gone astray. This is especially valuable for provisional changes where your judgment is already stretched. Choose a colleague familiar with your field and the journal's standards. Ask them to focus specifically on the provisional changes and whether the flags are clear enough for a reviewer to understand. Their feedback can prevent misunderstandings before the manuscript reaches the editor. ### Verification Against the Response Letter Cross-check the final manuscript against your response letter to ensure every comment is addressed and every response accurately reflects the manuscript content. This verification step catches discrepancies between what you claim in the response letter and what you actually did in the manuscript. Work through the response letter comment by comment, locating each change in the manuscript and confirming it matches the description in the letter. This is tedious but essential work. Discrepancies between the letter and the manuscript are a common source of reviewer frustration and additional revision requests. ## Limitations of the Clarify in Response Strategy ### Not All Comments Are Suitable for Provisional Revision Some reviewer comments are so fundamental that proceeding with assumptions is inappropriate. For example, if a reviewer questions the core study design or the validity of the primary outcome measure, making provisional changes based on assumptions could lead to substantial wasted work if the clarification reveals a different intent. In these cases, request clarification before proceeding with the affected revisions. Continue with other revisions that are independent of the fundamental question, but do not guess on issues that could require redoing major portions of the work. ### Clarification May Not Arrive Reviewers do not always respond to clarification requests promptly, and some may not respond at all. The editor can help, but even the editor may not be able to extract a response from an unresponsive reviewer. Prepare for this possibility by making your best assumption and proceeding, while clearly documenting that the change is provisional. If clarification never arrives, your documented assumption becomes the basis for the revision. The response letter should note that clarification was requested but not received, and that you proceeded with your best interpretation. This transparency protects you if the reviewer raises the issue again in a subsequent round. ### Journal Policies Vary Different journals have different policies regarding revision timelines, tracked changes, and communication with reviewers. Some journals have strict deadlines that do not accommodate extended clarification processes. Others are more flexible. Check the journal's author guidelines and the specific instructions in your decision letter before implementing the clarify in response strategy. The Committee on Publication Ethics Core Practices emphasize that journals should have clear policies for handling manuscripts and appeals. Familiarize yourself with the journal's policies before starting your revision to avoid conflicts with their expectations. ## Safety and Ethical Context ### Maintain Research Integrity Throughout the Revision Process The clarify in response strategy must never compromise research integrity. Provisional revisions are based on assumptions about reviewer intent, not on changing data or results to fit expectations. The Committee on Publication Ethics Core Practices address the importance of honest and transparent research conduct, including proper handling of data and accurate reporting of findings. When making provisional changes, ensure that your assumptions do not lead to misrepresentation of your findings. If a reviewer's comment could be interpreted in a way that would require changing your conclusions, flag this explicitly and request clarification before making the change. ### Data Management Considerations Provisional revisions may involve reanalysis of data or additional analyses. The NIH Data Management and Sharing Policy provides expectations for planning and managing research data, including sharing data in a timely manner. When you conduct additional analyses during revision, document the analysis process and maintain records of what was done and why. If your provisional revisions involve new analyses, consider whether the results should be shared or made available to reviewers. Transparency about your analysis process supports the integrity of the revision and helps reviewers evaluate your work fairly. ### Author Identity and Record Maintenance The revision process is part of your scholarly record. The ORCID for Researchers guidance emphasizes the importance of maintaining an accurate record of your research activities. When you complete revisions and the manuscript is published, ensure that your ORCID record reflects the publication accurately. During the revision process, keep records of your correspondence with the editor and reviewers, including clarification requests and responses. These records document the revision history and can be valuable if questions arise about the process later. ## Professional Escalation Criteria ### When to Contact the Editor Contact the editor when clarification requests go unanswered for an extended period, when reviewer comments are fundamentally contradictory, or when you believe a reviewer's request exceeds the scope of reasonable revision. The editor has authority to adjudicate disputes and facilitate communication with reviewers. Frame your contact with the editor as a request for guidance instead of a complaint. Describe the situation factually, note what you have done to address it, and ask for the editor's recommendation. Editors appreciate authors who handle difficult situations professionally. ### When to Request an Extension If the clarification process is delaying your revisions and you cannot meet the journal's deadline, request an extension from the editor. Explain the situation, note what you have completed, and provide a realistic timeline for completion. Most editors grant reasonable extension requests when authors communicate proactively. Request the extension before the deadline passes, not after. Late requests are harder to grant and create a negative impression. The clarify in response strategy should reduce the need for extensions by allowing you to proceed with revisions while awaiting clarification, but some situations still warrant additional time. ### When to Consider Withdrawal In rare cases, the gap between reviewer expectations and your ability to address them may be so large that withdrawal is the appropriate option. This might occur if a reviewer requests fundamental changes that would transform the manuscript into a different study, or if the clarification process reveals that the manuscript is not a good fit for the journal. Before withdrawing, discuss the situation with the editor. The editor may offer alternatives such as transfer to a different journal or a revised scope for the manuscript. Withdrawal should be a last resort, not a first response to difficult feedback. ## Frequently Asked Questions ### How do I decide which reviewer comments need clarification versus which I can address with assumptions? Read every comment in full and consider whether you can identify a reasonable interpretation based on the manuscript content and standard practices in your field. If you can articulate a specific interpretation and explain why it is reasonable, proceed with that assumption and flag it as provisional. If you cannot identify a reasonable interpretation, or if the comment could lead to substantially different revisions depending on the intended meaning, request clarification. ### What should I include in a clarification request to a reviewer? Present your interpretation of the comment and ask the reviewer to confirm or correct it. Include the specific manuscript location and the exact wording of the comment so the reviewer can reference it easily. Bundle all clarification requests into one section of your response letter instead of sending separate communications. ### How long should I wait for clarification before proceeding with provisional revisions? Proceed with provisional revisions immediately instead of waiting for clarification. The clarify in response strategy is designed to keep the revision process moving while clarification is pending. If clarification has not arrived by the time you have completed all other revisions, follow up with the editor and note the pending clarification in your response letter. ### How do I flag provisional changes in the manuscript itself? Use your word processor's comment feature to add a note at the location of each provisional change, stating that the change is based on an assumption awaiting clarification. If the journal does not accept comments in manuscripts, add a footnote or use a distinct formatting style such as colored text or highlighting to mark provisional changes. ### What happens if clarification never arrives? Proceed with your best assumption and document clearly in your response letter that clarification was requested but not received. Explain your reasoning for the assumption and invite the reviewer to request changes if the assumption does not match their intent. This transparency protects you if the issue arises in a subsequent revision round. ### Can I use the clarify in response strategy for major revisions that change the study conclusions? Use caution with provisional revisions that could change your conclusions. If a reviewer's comment could lead to different conclusions depending on the intended interpretation, request clarification before making the change. Proceeding with an assumption on a conclusion-altering revision risks substantial wasted work and potential integrity concerns. ### How do I handle conflicting comments from different reviewers? Address both interpretations if possible, or explain in your response letter why you chose one interpretation over the other. If the conflict is fundamental and cannot be resolved through reasonable judgment, request guidance from the editor. The editor can adjudicate conflicts between reviewers and provide direction for your revision. ### Should I tell the editor that some revisions are provisional? Yes, transparency with the editor is essential. Note in your response letter which revisions are provisional and why. This helps the editor understand your revision process and facilitates communication with reviewers. Editors are generally supportive of authors who engage thoughtfully with reviewer feedback and communicate clearly about their revision decisions. ## Related Articles - [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) - [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) - [Feasibility of a Research Study: How to Assess Before You Start](/blog/guides/feasibility-of-a-research-study-how-to-assess-before-you-start) - [Variant Calling Workflow: Design Decisions Before You Start](/blog/guides/variant-calling-workflow-design-decisions-before-you-start) ## 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.