Nuts and Bolts of the Publication Process : Indian Journal of Rheumatology

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Nuts and Bolts of the Publication Process

Talari, Keerthi; Ravindran, Vinod1,

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Indian Journal of Rheumatology 17(Suppl 2):p S283-S286, December 2022. | DOI: 10.4103/0973-3698.364668
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While our medical care at the clinic or hospital is our meal ticket and the purpose behind our professional degrees, there is a researcher in us which we all would like to nurture. Besides this quest for what is “new” being the motivation for doing research and publishing manuscripts, a more mundane reason for doing so is also to achieve the minimum requirements for promotion in academia, as mandated by the National Medical Council and the erstwhile Medical Council of India. Due to multiple factors such as lack of guidance, training, skills or support, many fail to advance themselves in research. For those few who do research and try to submit a manuscript, shortcomings in the understanding of publication process may make it difficult for them to get an acceptance from a journal. As academic publications not just enhance best practise and knowledge but are also accepted means of professional development and career growth, understanding the publication process and the process of manuscript scrutiny is essential to maximise the chances of acceptance.

The Publication Process

Publishing manuscript in a reputed journal is the culmination of the authors' efforts in conducting scientific research. Before one submits the manuscript, a checklist [Table 1] would ensure a smooth publication process. From deciding the co-authors and getting the authors' order right to selecting the right journal and submitting as per the journal's requirements; getting each step right before submitting the manuscript enhances the chances of its acceptance. As the manuscripts are generally published in the English language, appropriate care in this aspect including grammar is essential. The authors could ask their non-co-author colleagues to read and comment on the manuscript including regarding the language (“local peer review”) or take the help of professional editing agency or use the free grammar check function of software such as Grammarly.

Table 1:
Checklist before submission to a journal

The final version of the manuscript should be read and approved by all the authors.[1] The “right” journal for your manuscript may not be just a journal with better journal metrics such as a high impact factor; other factors including its indexing, accessibility, archiving policies, and most importantly the target readership have to be taken in to account. Selecting the right journal may sometimes appear a Herculean task. However, selecting an inappropriate journal would lead to a manuscript being rejected at the initial stages itself (desk rejections).[2] Complying with the instructions to authors and preparing the manuscript accordingly saves the time in revising later due to technical checks. Some journals also allow suggesting and opposing reviewers. Choosing the right key words will likely make your manuscript more visible in future search listings.

The quality of science remains the most important factor in a manuscript being rejected but there are other factors such as how well the manuscript is written as well.[3] Careful attention to title, abstract, key words, and all components of IMRaD (introduction, methods, results, and discussion), references, tables and figures, supplementary material are integral to a well written scientific manuscript. In this regard, the entire process of manuscript scrutiny is aimed at ensuring scientific paper with sufficient quality which is appropriate, useful and within the scope of that journal. The Enhancing the Quality and Transparency of Health Research (EQUATOR) network guides an author by providing structured guidelines for transparent, uniform and accurate reporting for different study types.[4]

When a manuscript is submitted to the journal, technical checks by an editorial assistant are carried out to ensure the manuscript is in line with the journal's requirements such as manuscript type, word count, plagiarism, or submission format. At this stage, the manuscript may be sent back to the authors to resolve any obvious deviations by suitable revisions. A technically correct manuscript would then be assessed by the Editor in Chief (EiC) for its suitability and appropriateness for the journal. A well written cover letter crisply outlining the subject of research, its relevance and importance to the journal and the addition to the already existing knowledge would help in the process.[5] If the EiC is satisfied in that regard, the manuscript is assigned to an associate/section editor for further handling.

The Associate/Section Editor subject the manuscript to a deeper scrutiny to identify potential flaws in any part of the manuscript. Once again, the relevance and significant advancement of existing knowledge by the work in question and it being within the scope of the journal are established, conflict of interests and similar previous publications are appraised and methodology of the research is assessed. Unless major issues are identified in the manuscript, it is passed to the reviewers for the next stage of peer review.

Simply putting it, peer review is a process of the assessment by an expert, of material submitted for publication.[6] The associate/section editor normally selects two or more peer reviewers based on their expertise and areas of special interest. Most journals maintain a database of reviewers to facilitate reviewer selection by the editor. Editors also often invite reviewers outside the database should the need arise. While the editor may not always select reviewers suggested by the author, those not preferred by the author are generally not invited considering a possibility of potential conflict of interest. Peer review could either be single blind (author is blinded), double blind (author and reviewer both are blinded), or open (no one is blinded).[7]

Before accepting a manuscript for review, a reviewer has to satisfy that they have the expertise to review that paper, and there are no conflicts of interest. The peer review is immensely important task that includes identifying potential scientific misconducts, grammatical errors, correct methodology, appropriate statistics, and relevant literature review. A thorough review of statistical tests used is also a part of ascertaining methodologic rigour of a work. Statistical analysis is an important part of a manuscript because it allows researchers to determine whether or not their results were meaningful on a statistical level. Where uncommon, complex or multiple analyses have been performed with little or no details in the methods section, the reviewer might recommend the need for an expert statistical review of the paper to the editor.[3] A statistical review might well be sought even when the statistical methods have been detailed in order to check the accuracy of such an analysis plan or the accuracy of reporting such analyses.

A reviewer is supposed to keep the manuscript confidential and not discuss or share it with anyone else. The comments submitted should be communicated only to the editor. Reviews should be concise but all inclusive. A good review would include a summary of the study with general comments regarding the strengths and the weaknesses of the study followed by specific comments about the writing style, study design, statistics, results, discussion, and any potential references that have been misinterpreted or missed. Whereas aforementioned appraisal is for the authors, in a separate section, a reviewer would clearly communicate, in confidence decision of acceptance, minor revision, major revision, or rejection to the editor and also share any concerns regarding the authenticity of the work and appropriateness of reporting.[3] Guidelines from the Committee on Publication Ethics (COPE) and International Committee of Medical Journal Editors (ICMJE) could guide reviewers through the scrutiny process.[18]

After reviewing the comments by reviewers, associate/section editor would make a recommendation regarding the manuscript to the EiC. The EiC would then make a final call on the manuscript and communicate the decision to the authors. The decision could be acceptance, minor revision, major revision, or rejection.[3] It is unlikely that a manuscript would be accepted as it is. The editor communicates their comments and decision to authors with the reviewers' and associate/section editors' comments attached. When asked for revision, it is advisable to carefully read all comments. Revision of the manuscript entails replying to all comments pointwsie and revising the manuscript as relevant.[3] We recommend that corresponding authors discuss the comments, replies and revisions with co-authors. The revised manuscript also needs to be approved by all co-authors. Some journals have a structured format for the rebuttal letter where each comment has to be responded to point by point. Normally, two versions of a revised manuscript are required, a clean and a version with changes highlighted or in track changes mode. The journal's requirements have to be read carefully and the revised version submitted. The responses to the reviewers and editors should be polite and professional. In certain instances, if it is felt that a reviewer's comment is wrong or out of the scope of the study, one may explain it and assert in a courteous manner. Authors are given a stipulated time period to revise the manuscript and resubmit it for further peer review. The reviewers for the first cycle of peer review and the subsequent cycles may or may not necessarily be the same. After one or several revise-resubmit cycles, the manuscript may get accepted. It is important to not get discouraged by revision(s) demanded by either the technical team or the editors as this academic exercise only leads to a manuscript getting more polished and attaining due clarity.[3]

Scientific misconduct noted at any stage is taken seriously and may have far reaching repercussions including rejection of the manuscript. Scientific misconduct could find its way into a manuscript intentionally or at times due to lack of awareness, incognizance. Some of the examples of such misconducts are (please see chapter XX), – lack of ethics approval, inadequate informed consent, no data confidentiality, data manipulation, plagiarism, simultaneous submissions, salami publications, overt self-citation, gift authorship, undeclared conflicts of interest etc.[910] When a scientific misconduct is suspected before publication, authors are usually asked to provide clarification. However, when the scientific misconduct is deemed major, the article is immediately rejected and the institute's higher authorities and the ethics committee may also be informed. If a manuscript is already published, the authors are asked to publish the corrections in an erratum, or in instances of major scientific misconduct, manuscript is retracted and the author may be blacklisted.[11] Further, an author may be blacklisted by COPE/ICMJE and all the member journals may be communicated the same. Local bodies such as relevant ethics committee may also take stern action as per the guidelines.

If the author suspects misconduct from the journal's end at any level, he/she should first communicate it to the journal's EiC.[12] Misconduct could be in the form of delayed handling of manuscripts, not following journal's standard operating procedures, reviewer bias, editorial favouritism, conflicts of interest and discourtesy in communications. If the journal's EiC fails to respond or the author is dissatisfied with the EiC's response, ombudsperson for the said journal can be approached. A journal ombudsman, first established by The Lancet exists to record and, where necessary, to investigate episodes of alleged editorial maladministration when a complainant remains dissatisfied with the journal's first response to criticism'. An ombudsman investigates an alleged misdeed from the journal's administration by verifying all the documents and interviewing the editors or the authors when necessary.[13] An ombudsman is impartial and his/her final decision is communicated to the editor and the author. It is important to note that investigation of an author's scientific misconduct alleged by a journal is outside the purview of an ombudsman s job.

Depending on the journal, the acceptance rates for manuscripts (according to the article types) vary. In fact, the rejection rates of reputed journals are usually very high. However, if the response to your manuscript submission has been rejection, it does not mean that it is not a well written manuscript.[3] Manuscripts could be rejected because they are not in the scope of the journal, or they are not well written or the methodology is poor or lack important citations or do not provide any new information or a scientific misconduct has been noted.[314] Usually, the editor communicates the reasons for rejections along with comments of associate/section editors and/or reviewers. If such comments are pondered upon and appropriate modifications in the manuscripts carried out, the chances of its acceptance in a different journal may improve. When authors strongly feel against such rejections and journal offers the recourse to submitting rebuttals, in a carefully structured and polite letter, important merits of the work could be highlighted requesting a re-appraisal.[3] The outcome of such rebuttals may still be rejection.

Upon acceptance of a manuscript, the production team takes over and depending on the journal, basic to extensive language and copy-editing takes place. Formatting including of tables and figures, page layout as per journal's requirements are done. Proofs, when sent to the corresponding author for corrections; generally, have a very tight turnaround time, usually 48 h. This system has evolved tremendously recently, and online corrections are becoming a norm. A journal may place an “accepted but un-edited” version of a manuscript on its website under “ahead of print” or similar category. This version is replaced with a final edited version when available. Articles are moved from ahead of print to online and/or print versions of the journal as per the queue or editorial priorities.


While the task of conducting a study itself is Herculean, understanding the nuts and bolts in the publication process is another gargantuan task. From preparing the manuscript, selecting the right journal, avoiding scientific misconduct, the peer review, the revise/resubmit cycles to the final proof submission to the publisher, there are several steps where author could improve the manuscript and further its chances of acceptance [Figure 1].

Figure 1:
How to get it right during the publication process


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14. Khadilkar SS. Rejection blues: Why do research papers get rejected? J Obstet Gynaecol India. 2018;68:239–41
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