New Authors 101

Questions to Ask Yourself As You Write for Publication

  1. What do you want to know, and why do you want to know the answer?

    Your research question and your hypothesis are the foundation for writing the INTRODUCTION to your paper, which should include background about the topic, your hypothesis, and the aims of your research.

    This might sound daunting for new authors. Sometimes the goal is to report interesting or new cases, and that’s fine too. There’s still a question in there - what is important about these cases (or this case) and what will the report contribute to the existing literature?

    Always ask yourself, “Why does this matter?” IS IT WORTH DOING? WHY? No matter how “small” or “easy” a paper might seem, they all take a lot of work and time. So it’s essential to ask this question at the outset,

    A good paper is built on good science:

    • Start with a question that you want to answer.
    • Or start with a story you want to tell.

    “A good research question should have a strong rationale or justification for pursuit: it should fill a gap in existing knowledge, be relevant and important, and for many research studies lead to a hypothesis that can be tested. A hypothesis forms the cornerstone of a research study; it is what you postulate to be true.” – Christopher M, and Young K. Writing for Publication in Veterinary Medicine: A Practical Guide for Researchers and Clinicians. Wiley-Blackwell Authoring Services. 2015.

    A comprehensive literature review is crucial. One of the main reasons for this is to answer the question, “Why does this matter?” Your paper needs to fill a gap or add to existing knowledge in a useful way. You can’t answer that question without knowing what has already been published.

    Use your academic mentors to assist because they have access to journal articles at no charge. Read all of the papers and organize them into a concept map to help you identify common threads and questions in need of answers.


    Use Pubmed or Google Scholar for an initial literature search.

    A great time-saver is to limit the initial search to the most recent few years (depending how big the literature is). Look for a couple of really good reviews or book chapters and start with those. The authors have already done the hard work of finding the most relevant references and summarizing them. They will give you a good sense of where the gaps in knowledge are. You can also “steal” important references from their list, and supplement with your own literature search for any gaps.

    It’s important to read the full text of anything you reference. There are a few good ways to find full text:

    • Open access journals, of course!
    • Google the name of the article and add “full text.”
    • Ask anyone under the age of 25. Some sources are questionable but many references are available for free.
    • Ask a friend with academic library access.
    • Worst case, pay for online access, only for critical references (if they don’t allow downloads, you can store screenshots for future reference).


    We recommend a free reference manager like Zotero, which works with both Google Docs and Microsoft Word, or Mendeley. Use this to store your files and conveniently generate reference lists.

    Different investigators have different ways of managing information they have gathered. Some form of summary can be really helpful, especially for those of us who forget what they have read! A couple of approaches:

    • Annotate the papers you find by adding highlights and notes to the articles inside your reference manager. Also mark your favorites.
    • Create folders for specific papers or projects.
    • Use a spreadsheet to summarize the papers - this allows you to create categories and apply filters.
    • Summarize the papers in a document (Zotero can help you do this too).
    • List important points to include in your Introduction and Discussion as you read the references. Subheadings are really helpful because this can become chaotic.

    Some important points for how to quote literature:

    • Don’t cherry-pick only papers or statements that agree with your existing bias. Try to put bias aside. Good science is objective.
    • Don’t “daisy chain” - often a statement is quoted over and over again, and the original source is non-existent or doesn’t say what has been reported. Important statements should come from original source literature.
    • Provide at least one reference for each factual statement. The more specific the fact, the more specific the reference. For example:
      • “Panleukopenia is an important disease of cats” can quote a review or book chapter. (least specific reference)
      • “Kittens in shelters should be vaccinated from 4 weeks of age” should quote a recent vaccination guideline. (more specific reference)
      • “90% of feral cats vaccinated at TNR developed protective antibodies to FPV” - quote original source reference (Fischer 2007) (very specific reference)
  2. What type of study will you use and what reporting guidelines will you follow?


    Adhere to the PICO format for your study design. PICO stands for Patient/Population (who were the subjects of your study?) Intervention (what did you do?), Comparison (what were you watching for?), and Outcomes (what did you observe or find as a result?).

    Your study design is the foundation for writing the METHODS section of your paper, which should include details about the subjects (animals, people) included in your study, the sample size you used, as well as how you ensured that the study treated pets and patients ethically and humanely Did you have an IACUC (Institutional Animal Care and Use Committee) or IRB (Institutional Review Board) review of your study design before you started?  If you and your co-authors want to perform practice-based research and are not a member of an institution with a review board, consider the RCVS Ethics Review Panel.

    If you are not associated with a college or university, we HIGHLY recommend that you collaborate with a more experienced academic researcher rather than try to design a study alone. Have them review your study design and suggest refinements BEFORE you begin. Faunalytics offers virtual office hours to help with research design.

    Your research question informs which type of study design to use. Depending on your question, you might use a survey, prospective, retrospective, descriptive, clinical trial, cohort, or other approach to answer your question. Each of these types of studies has different guidelines that you must document that you followed when you write your paper.

    A study protocol is highly recommended, even for case reports or case series. It can be very detailed, or very simple, but at the least should be clear on objectives/questions/hypotheses, sample size, inclusion and exclusion criteria, main methodology and statistical analysis. Not all of these are needed for every study. Think of the protocol as a roadmap. Protocols are very important to avoid post-hoc bias in decision-making (“I don’t have enough cases so I am going to match my inclusion criteria to available cases”) and avoid unexpected problems and dilemmas.

    Reporting Guidelines

    While reporting guidelines can see like just one more hurdle to cross, they can make the job of drafting your manuscript MUCH easier by presenting a step by step guide to what should be in the manuscript. Just following the checklist will help you write nearly your entire introduction, methods and results.

    For example:

    • PetSORT for clinical trials in dogs and cats
    • CARE for clinical case reports
    • CHERRIES for online surveys
    • CONSORT for randomized clinical trials
    • PRISMA for systematic reviews and meta-analyses
    • SRQR for qualitative research
    • STROBE for observational studies (cohort, case control, cross-sectional studies)

    Refer to the EQUATOR Network as “Your one-stop-shop for writing and publishing high-impact health research.”

    Refer to the JSMCAH Instructions for Authors to see what article types the journal accepts and what information to include as well as the Style Guide for formatting.

    For more information, see:

    Browner W S, NewmanT B, Cummings S R, Grady D G, Huang A J, Kanaya A M, Pletcher M J Designing Clinical Research. (2022). Argentina: Wolters Kluwer Health. ISBN:9781975174408.

  3. Who are the authors for your study and in what order should they be listed on the paper?

    Anyone listed as an author is assumed to be responsible and accountable for the work. Because such listings can have a significant impact on a researcher’s career (either positively or negatively), it is important that you decide who the authors are and in what order they will be listed on your manuscript BEFORE you begin your study. Revisit this agreement before you begin writing and again before you submit your paper for consideration of publication. All co-authors should approve of the final manuscript BEFORE you submit it.

    By convention:

    • First Author: (the author listed first) is the person who was primarily responsible for the study and drafting the paper.
    • Last Author: (the author listed last) is usually the mentor of the first author.
    • Co-Authors: (all others listed as authors) can be listed in whatever order makes sense.
    • Corresponding Author: will be indicated on the publication as the person to whom inquiries can be directed and their contact information will be shared with readers.
    • Non-Author Contributors: are those who contributed to the preparation and should be acknowledged, but who are not authors. These include proofreaders, editors, administrative support, artificial-intelligence editing, etc. Their participation should be described in the ACKNOWLEDGEMENTS section.

    “According to the International Committee of Medical Journal Editors (ICMJE), an author is someone who has made substantive intellectual contributions” to the study conception and design or data acquisition, analysis, and interpretation, and who takes responsibility for at least part of the work.” – Christopher M, and Young K. Writing for Publication in Veterinary Medicine: A Practical Guide for Researchers and Clinicians. Wiley-Blackwell Authoring Services. 2015.

    For more information, see:

    ICMJE | Recommendations | Defining the Role of Authors and Contributors. Accessed July 31, 2023.

    All authors should have an ORCID identification number so that their publications get linked correctly to their names. If you don’t have one, you can create one for free by visiting the ORCID website.

    Tips from the Trenches: Once you have designated someone as a co-author, it’s disastrous to remove them if they don’t do the work they are meant to, or don’t return materials on time. Though not “best practice”, it’s best not to remove authors after designating them. You can make lifelong enemies this way. So think carefully before you offer authorships!

  4. In what order should you draft the paper?

    A scientific paper usually follows the AIMRD outline of:

    • Abstract
    • Introduction
    • Methods and Materials
    • Results
    • Discussion

    However, do NOT write the paper from top to bottom! The best papers begin by drafting the METHODS first, followed by the RESULTS. Tell the key takeaways of your story from the images/tables/figures that you produce as you analyze your data. Write the INTRODUCTION next, followed by the DISCUSSION. The ABSTRACT is last.

    Follow this process: New authors are often intimidated by their data analysis and results. It’s helpful to draft an introduction early to justify the study and lay out the objectives/hypotheses. Then work only on the methods and results until those are done. Then go back to the introduction and discussion.

    Every paper will begin with: a title, list of authors, list of keywords.

    Every paper will end with: a list of acknowledgements, disclosure of any financial support or conflicts of interest, complete list of citations, and appendices of images, tables, and figures.

    • Methods and Materials Section: these are factual and usually the easiest to write. They should be written in logical order and give enough detail that another researcher could reproduce your study. Include the study design, which research guidelines you followed, what analytical and statistical methods you used, and include statements about ethical use of animals and people in this section (include the IACUC and/or IRB approval number).
    • Results Section: should parallel the logical sequence in the methods section, briefly state the major findings, and present the data in clear, concise tables/graphs/figures. Cite all tables and figures in the correct order as they are referenced in the text.
    • Introduction Section: should be approximately two or three paragraphs that succinctly summarize why this subject is important; what is currently known; the rationale for this study; and describes your research question, hypothesis, and specific objectives. It should end with a sentence that states how this study will help fill any gaps you identified in the previously published literature about this subject. A helpful way of looking at this is:
      • What is known?
      • What is not known?
      • What did we do to fill a gap in knowledge?
    • Discussion Section: this is where you interpret your results and explain them in the context of your research question, hypothesis, and objectives, and draw conclusions about their meaning and applicability to similar situations or populations. All studies have strengths and limitations that should be identified. Suggest future research that should be conducted based on the findings of your study but avoid generic phrases such as "more research is required".

    “The discussion section is often the most difficult to write, in part because the format and content are highly study-dependent. The first paragraph should encapsulate the most important and new findings of the study or case and should indicate whether your hypothesis was correct and your objectives were achieved. The last paragraph (often broken out as a separate Conclusion section) should state the main conclusions and implications drawn from your findings. The paragraphs in the middle can parallel the order of the results or lead from the most to the least important finding in the study, using a new paragraph for each discussion point. Always begin paragraphs with the most important sentence and follow with supporting sentences.” – Christopher M, and Young K. Writing for Publication in Veterinary Medicine: A Practical Guide for Researchers and Clinicians. Wiley-Blackwell Authoring Services. 2015.

    Update your REFERENCES as you go (if you're using a reference manager this should be easy). Be sure to read and cite original (primary) sources, not just summaries excerpted from the introductions and discussions published by others because you cannot be certain that others quoted prior publications accurately. Use an online citation manager that integrates with your word processing system so your life will be much easier as you rearrange paragraphs and sentences during the editing process.

    “For authors, this means using only primary sources to ensure that meaning has not been lost or distorted during subsequent citation by others. It also means refraining from the all-too-common practice of citing what an author said or speculated (e.g., in an Introduction or Discussion) because that lends the impression that such statements were supported by something the author actually did (e.g., as shown by data in the Results). In the age of electronic databases, this type of verification is no longer the daunting task it once was, and journals could require assurances that all references are original and/or have been verified by authors at the time of submission.” – Patronek, 2016

    Drafts are usually reviewed, revised, edited, and proofread multiple times by all listed authors before the manuscript is final and ready for submission to the journal.

    The ABSTRACT and TITLE are the most read parts of a paper. They should be carefully written so that they capture the attention of potential readers and online search engines. Therefore, the title should be succinct but also indicate the nature of the study and/or its findings.

    The abstract will have strict word limits set by the journal and should clearly summarize your study. If the journal requires an unstructured abstract for the type of study you did, this will usually consist of a single paragraph. If the journal requires a structured abstract for the type of study you did, then it will follow the same headings as you used in your paper.

    “At a minimum, abstracts should include one or two sentences of background that set the context and rationale for the study; the purpose or objectives of the study; a brief description of methods; a summary of the main results, including data and probabilities (specific statistical tests need not be listed); and one or two sentences that summarize the main conclusions and implications…Abstracts for case reports should begin with salient information about the animal(s), methods used in the investigation, the findings, and the novel information gained.” – Christopher M, and Young K. Writing for Publication in Veterinary Medicine: A Practical Guide for Researchers and Clinicians. Wiley-Blackwell Authoring Services. 2015.

    Select four to six KEYWORDS that are different from the words used in your title. Keywords are used to search for relevant papers by other authors. You can paste your abstract into MeSH on Demand to search for appropriate medical keywords to use.

  5. How do I respond to peer reviewers?

    The first thing to understand is that ANYTHING that is not an outright rejection is a WIN. Don’t be disheartened even if major changes are recommended - think about all the time you have already put in, and why you thought the work was important in the first place. It’s worth going the extra mile.

    The second point is that the tough reviewer, whom you initially might be upset with, is usually the one whose suggestions create dramatic improvements in your paper.

    Respond completely, politely and with evidence.

    Maintain a respectful tone and assume good intent

    While it can be difficult to receive constructive feedback on your manuscript, this process is essential for peer review. In general reviewers are volunteering their time because they believe in the peer review process and want to support academic research and progress. Sometimes as an author you may disagree with reviewers or may have a differing opinion, but you are still obligated to take their input seriously. In most cases the reviewer(s) have the ability to decide whether or not your manuscript can be published in the journal to which you have submitted. How you respond to reviewer feedback (even if you sincerely believe the reviewer is incorrect) can impact the outcome for the submission.

    Generally the author’s response to the reviewers should include a statement thanking the reviewers for the time they have taken with the review and then explaining where they can find the revisions. I will generally start by creating a document that lists each reviewer comment. At the top of this document, I will include a general statement of thanks to the reviewers. If the reviewer comments are not numbered for you it can be very helpful to number them so that it is clear to which comment you are referring. For example, I might number reviewer 1’s comments from 1 to 23 and then refer to those as R1-1, R1-2, etc and do the same for the comments from reviewer 2. Make sure to address each and every comment. See an example of a reviewer response with explanatory text

    Take the feedback to heart and consider how to make changes to align with the reviewer’s requests

    Generally it is not helpful to become defensive or argumentative. Instead, address each comment point by point and indicate how you have edited the manuscript as suggested. If something needs to be clarified then you can clarify that in the response, but in general if the reviewer doesn’t understand something then it is likely that another reader would not either and you should consider if the manuscript can be clarified. Sometimes reviewers ask for things that you can not do. In such cases a polite explanation is still indicated.

    Decide which battles to fight

    Don’t argue about necessary or unimportant changes. It’s much easier to contest some suggestions if you have agreed to most or all of the others. In particular, you are justified in not making changes that will take a lot of time but are not directly related to the objectives of the study.

    Make it clear how you have edited the manuscript

    In addition to responding to each reviewer comment in order as demonstrated above, edits to the manuscript should be made with track changes so that the reviewer can see how you have incorporated their feedback; it is helpful to include the line numbers where they can find the change.

    Finally, in addition to your point-by-point document and document with track changes, please upload a "clean" version as well with all changes accepted.

  6. Additional Resources for Learning How to Write for Publication

    11 steps to structuring a science paper editors will take seriously. Accessed August 1, 2023.

    Browner W S, NewmanT B, Cummings S R, Grady D G, Huang A J, Kanaya A M, Pletcher M J Designing Clinical Research. (2022). Argentina: Wolters Kluwer Health. ISBN:9781975174408.

    Christopher M, Young K. Writing for Publication in Veterinary Medicine: A Practical Guide for Researchers and Clinicians. Wiley-Blackwell Author Services. 2011 – free pdf

    Englar, Ryane E. “Finding Yourself in the Arena of Scientific Writing: The Journey From Idea to Publication in Shelter and Community Medicine”. Journal of Shelter Medicine and Community Animal Health, vol. 2, no. 1, Dec. 2023, doi:10.56771/jsmcah.v2.60.

    Englar RE. Writing Skills for Veterinarians. Sheffield, UK. 5M Publishing. 2019.ISBN 10: 178918035X

    ICMJE | Recommendations | Defining the Role of Authors and Contributors. Accessed July 31, 2023.

    Kennedy, MS. Journal Publishing: A Review of the Basics. Seminars in Oncology Nursing. 2018;34(4)361-371.

    Patronek GJ, Bradley J, Cleary D. Who is minding the bibliography? Daisy chaining, dropped leads, and other bad behavior using examples from the dog bite literature. Journal of Veterinary Behavior. 2016;14:17-19. doi:10.1016/j.jveb.2016.06.004

    Seals DR. Publishing particulars: part 1. the big picture. Am J Physiol Regul Integr Comp Physiol. Published online February 7, 2023. doi:10.1152/ajpregu.00265.2022

    Seals DR. Publishing particulars: part 2. tips for effective manuscript development. Am J Physiol Regul Integr Comp Physiol. Published online February 7, 2023. doi:10.1152/ajpregu.00267.2022

    Seals DR. Publishing particulars: part 3. general writing tips, editing, and responding to peer review. Am J Physiol Regul Integr Comp Physiol. Published online February 7, 2023. doi:10.1152/ajpregu.00270.2022

    Study designs — Centre for Evidence-Based Medicine (CEBM), University of Oxford. Accessed July 31, 2023. https://www.

    Wiley Authoring Resources:

    Williams H.C. (2004). How to reply to peer review comments when submitting papers for publication. Journal of the American Academy of Dermatology, 51, 79-83.