1. Introduction to PCI and PCI Genomics
PCI Genomics is a community of recommenders, playing the role of editors, who recommend unpublished articles based on peer reviews, thereby converting them into complete, reliable and citable articles, without the need for publication in ‘traditional’ journals. Evaluation and recommendation by PCI Genomics are free of charge. When recommenders decide to recommend an article, they write a recommendation text that is published along with all the editorial correspondence (reviews, recommender's decisions, authors’ replies) by PCI Genomics. The article itself is not published by PCI Genomics; it remains on the preprint server on which it was posted by the authors. PCI Genomics recommenders can also recommend postprints, but this is much less frequent.
PCI Genomics is a community of the parent project Peer Community In, an original idea of Denis Bourguet, Benoit Facon and Thomas Guillemaud.
PCI Genomics is not designed to be a free peer reviewing service for authors aiming to improve their articles before submission to a journal, although, of course, it remains possible for authors to submit their recommended article to a traditional journal.
- PCI Genomics is stimulating: it recommends remarkable articles.
- PCI Genomics is free: there are no fees associated with the evaluation process, and no charge for access to the comments and recommendations. The website is freely accessible.
- PCI Genomics is transparent: reviews and recommendations (for unpublished articles) and recommendations (for published articles) are freely available for consultation. Recommendations are signed by the recommenders. Reviews may also be signed if the reviewers agree to do so.
- PCI Genomics is not exclusive: an article may be recommended by different Peer Communities in X (a feature of particular interest for articles relating to multidisciplinary studies) and may even be published in a traditional journal (although this is not the goal of PCI Genomics).
2. Submission requirements, review policy and workflow
The scope of this PCI encompasses all aspects of genomics (structural genomics, functional genomics, epigenomics, evolutionary genomics, population genomics, proteomics, bioinformatics) dealing with every type of organism (viruses, bacteria, fungi, plants, animals,...) as well as metagenomes.
PCI Genomics recommends preprints addressing genomics questions about all types of organisms. We cover all fields of biology, provided that the context of the study and the key question addressed relate to genomics. The preprint or the preregistration must not be published or under consideration for evaluation elsewhere at the time of its submission to PCI Genomics.
PCI Genomics recommends only preprints of high scientific quality that are methodologically and ethically sound. To this end, PCI Genomics:
- Requires data, computer codes and mathematical and statistical analysis scripts to be made available to reviewers and recommenders at the time of submission and to readers after recommendation.
- Welcomes reproductions of studies.
- Welcomes preprint submissions based on preregistrations (with or without prior review)
- Welcomes preprints reporting negative results, provided that the questions addressed and the methodology are sound.
- Does not accept submissions of preprints presenting financial conflicts of interest. Other conflicts of interest must be minimal and declared.
- Ensures that, as far as possible, the recommenders and referees have no conflict of interest with the content or authors of the study evaluated.
2.2 Types of articles
The articles recommended may have diverse formats: reviews, comments, opinion papers, research articles, data papers, technical notes, computer notes, etc. No editing, formatting or proofs of the recommended papers are required, but we provide the authors with a template to help them to format their article, if they so wish. We also ask the authors of recommended articles to add a sentence to the acknowledgements stating that their article has been recommended by PCI Genomics.
PCI Genomics welcomes anonymous submissions (see details).
Preregistrations should be submitted to PCI RR.
2.3 Repeatability of science and open science
PCI wishes to promote scientific repeatability and reliability, to improve the overall robustness and integrity of the scientific conclusions drawn. To this end, PCI has established three mandatory rules and makes two suggestions to authors:
Articles recommended by PCI must provide the readers with:
-Raw data, made available either in the text or through an open data repository, such as Zenodo, Dryad or another institutional repository (see Directory of Open Access Repositories) with a DOI. Data must be reusable, so the metadata and accompanying text must describe the data carefully and accurately.
-Details concerning the quantitative analyses (e.g. data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and simulations (scripts, codes), either in the text or through a correctly versioned deposit in an open repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI or another permanent identifier (such as a SWHID of Software heritage). Note that Git URLs are not permanent. Information on how to issue a DOI for a GitHub repository is given at https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content. Scripts or codes must be carefully described such that another researcher can reuse them.
-Details on experimental procedures must be given in the text.
Suggestions to authors:
-PCI encourages authors to submit preprints based on preregistrations. Authors may post their research questions and analysis plan to an independent registry before observing the research outcomes, and, thus, before writing and submitting their article. This provides a way of clarifying hypotheses, avoid confusing “postdictions” and predictions, and carefully planning appropriate statistical processing of the data (e.g. 10.1073/pnas.1708274114).
-Preregistrations should be submitted to PCI RR
-PCI welcomes submissions proposing replication studies. All submissions are assessed according to the same criteria, provided that the article is considered interesting by the recommender handling it and the research question is considered scientifically valid.
2.4 Ethics approval
In fields in which research requires approval from an ethics committee or institutional review board, the authors should generally ensure that the proposed research has received all necessary approvals before submission.
2.5 Transparency for data and materials
In general, authors are required to make all study data, digital materials, and computer code publicly available (at submission), to the maximum extent permissible by the relevant legal or ethical restrictions.
2.6 Transparent review
PCI Genomics publishes all reviews of recommended manuscripts, with reviewers retaining the right to choose whether to sign their reviews or remain anonymous. All reviews and recommender decision letters are published on the PCI Genomics platform on recommendation. Reviews of rejected submissions are sent to the authors, but are not published. Reviewers and recommenders are expected to adhere to the PCI code of conduct, avoiding abusive or discriminatory language in their comments. Reviews considered to violate the code of conduct may be edited by recommenders or the Managing Board, returned to the reviewer for editing, or discarded.
2.7 Handling of manuscript by recommenders
A recommender finding a submitted preprint particularly interesting can decide to initiate the process of evaluation for the article concerned. In this case, the authors are notified by e-mail. The recommender invites reviewers, so as to obtain at least two high-quality reviews. Note that the recommender and reviewers must declare that they have no conflict of interest of any kind with the content or the authors of the preprint – see the code of conduct.
If no recommender – including all recommenders in the corresponding field of expertise – has initiated the evaluation of the preprint after 20 days, the authors are notified by e-mail. If this happens, we suggest that the authors cancel their submission.
2.8 Appeals process
The authors of rejected manuscripts can appeal the PCI Genomics decision within 30 days of receiving the decision, by contacting us at firstname.lastname@example.org. Appeals will be considered by the specialist recommender(s) handing the manuscript and the PCI Genomics Managing Board. Decisions following appeal are final.
2.9 Word limits and formatting requirements
PCI Genomics imposes no word limits or specific formatting requirements on submissions. Manuscripts should be as concise as possible, but as long as necessary to ensure that the description of the rationale and methods is clear and comprehensive, and that all methods are reproducible. Authors should ensure that they follow established formatting conventions for articles in their discipline. Authors who intend to publish their article in a journal should also take note of any sectional or overall word limits or other formatting requirements that apply to specific journals.
3. Top tips for recommenders
PCI recommenders manage the evaluation of articles in the same way as associate editors do at journals, with a few differences (see below). PCI only accepts (“recommends”) preprints of high scientific quality that are methodologically and ethically sound.
3.1 Main differences between recommenders and journal editors
You handle a manuscript evaluation only if you’re willing to do so: you should not feed obliged to take charge of an evaluation. You have to be positively motivated to do so because you are scientifically interested in the preprint. You also have to be available to take charge of the evaluation throughout the whole process, from submission to recommendation.
As there is no Editor-in-Chief, you are solely responsible for editorial decisions. If you have co-recommenders, you share this responsibility with them.
The evaluation process (including reviews, your decisions, and author responses) is published by PCI only if you decide, at the end of the evaluation process, to recommend the preprint.
If you decide to accept a text for recommendation, you will write a recommendation text. This text describes the qualities of the preprint, including the subjective reasons for your interest in it.
There is no acceptance/rejection rate to be respected. All articles of high scientific quality that are methodologically and ethically sound should be accepted. Articles that are do not achieve these standards should not be accepted.
3.2 General advice
Follow the PCI Code of conduct.
Be kind, respectful and constructive in your decisions.
Be open to new approaches.
When inviting reviewers to evaluate a preprint, bear in mind that a broad mix of scientists of different genders, career stages and geographic origins, is desirable.
Try to keep to the deadlines at each step in the process, it shows respect towards the authors.
3.3 What you should NOT DO
Do not agree to handle the evaluation of a preprint if you have not taken the time to read it, if you are not familiar with the subject, and if you have no time to handle it in a timely manner from submission until recommendation.
You should not have any conflict of interest with the authors or with the content of the article (see the PCI Code of conduct). If you do, you must decline the invitation.
You should not invite reviewers who have a conflict of interest with the authors or with the content of the article (see the PCI Code of conduct).
You do not need to determine whether the article falls within the scope of the PCI. Once a submission has been validated by the managing board, its scope is considered suitable for the PCI.
Do not discredit negative results.
Avoid unconstructive, ambiguous, and unsupported comments.
You do not need to check the format of the references.
You do not need to check the availability of data and scripts – this is checked by the managing board.
You do not need to check for plagiarism – this is checked by the managing board.
You do not need to copy and paste the comments of the reviewers in your decision (as the reviews are automatically attached).
You do not need to submit an “Acceptation” decision when you are ready to recommend the article. You should directly post your recommendation.
3.4 What you should DO
Reply rapidly to the invitation to handle an article, on the website, by accepting or declining. Once you agree to handle a manuscript, you are expected to do so until final rejection or recommendation.
Start inviting reviewers as soon as you agree to handle the manuscript or as soon as you receive the revised version of an article that you intend to evaluate again. Send invitations to 5-10 potential reviewers within 48 hours, and then send new invitations until you find at least two reviewers willing to review the preprint. This process of finding reviewers should, ideally, take no more than one week.
Try to personalize your invitation letters as much as possible, to maximize response rates.
Search for additional reviewers if the reviews received are too light and insufficient to enable you to come to a decision.
Make a decision based on the reviews. This is your duty and responsibility, not that of the reviewers.
Post your editorial decision or write your recommendation text within 10 days of receiving the reviews or the revised version of the preprint.
Your editorial decision should summarize the most relevant comments of the reviews and your own points of criticism.
State whether you disagree with some of the points raised by the reviewers.
Feel free to reject an article at any step of the evaluation process (even after several rounds of review) if there are scientifically sound reasons justifying this rejection.
Pay attention to any kind of error in the text of the article (typography, grammar etc.). A recommended article must be as close to perfect as possible in terms of its form, because it is a completed final article. If the language is poor, mention it to the authors and suggest that they check for typographical errors and/or have the text proofread by a native English speaker.
If you decide to recommend the preprint, you must write a recommendation text. This text is a short article, similar to a News & Views piece. It has its own title, contains between 300 and 1500 words, describes the context, explains why you find it interesting and why you decided to recommend it. This text also contains references (at a minimum the reference to the article being recommended).
Inform the managing board if there is likely to be any delay or if you are unexpectedly unable to carry out your recommender duties.
Inform the managing board if you suspect scientific misconduct.
4. The evaluation and recommendation process
- Authors can suggest recommenders when they submit their preprints. If you are among the suggested recommenders, you will receive an alert by e-mail.
- If you have time to handle the preprint, if you have no conflict of interest of any kind with the content or with the authors of the preprint and if, and only if, you consider it sufficiently interesting, you can start the evaluation process. You will then be responsible for managing the evaluation process until you reach a final decision (i.e. recommend or reject the article).
- If you start the evaluation process of a preprint, you will play a role very similar to that of a journal editor: finding at least two reviewers, collecting reviews, taking editorial decisions based on reviews. The evaluation process often requires several review/decision/author response cycles. After each round of review, you can decide whether to reject or recommend the article. Alternatively, you can decide to ask the authors to revise their article, thus generating another round of reviews. As a recommender, you will sign all decisions sent to the authors. Reviewers may choose to remain anonymous or to sign their reviews. Reviewers are expected to write their reviews within three weeks and, once the reviews have been completed, you will be expected to make your decision within 10 days.
- If you eventually decide to reject the article, the reviews and decision will be sent to the authors but will not be published or publicly released by PCI Genomics. They will be safely stored in our database, to which only the Managing Board has access.
- Alternatively, if you decide to recommend the article, you will need to write a “recommendation”, which will have its own DOI and be published by PCI Genomics under the license CC-BY-ND. The recommendation is a short article, similar to a News & Views piece. It has its own title, contains between about 300 and 1500 words, describes the context and explains why the recommender finds it interesting and why they decided to recommend it. This text also contains references (at least the reference of the article recommended). All the editorial correspondence (reviews, your decisions, authors’ replies) will also be published by PCI Genomics.
- Once PCI Genomics publishes your recommendation text, the article can be considered a high-value article. Recommended articles can be used by scientists and cited in the scientific literature. The authors no longer need to publish the article in a ‘traditional’ journal, although they remain free to do so, if they wish.
5. Postprint Recommendation
PCI also recommends “postprints”, which we define as research papers that have already been published in peer-reviewed journals. PCI also considers books to be postprints because, despite not being evaluated by reviewers or editors before being published, they are often treated as such by academics.
As postprints (other than books, see above) have already undergone peer review before publication, an additional PCI peer review is not required for their recommendation. Each postprint recommendation is written by at least two PCI recommenders. Authors cannot submit their own articles or books to a thematic PCI for postprint recommendation. Instead, a postprint recommendation must be initiated by a recommender who has read the postprint and considers it worthy of recommendation. The recommender must then find at least one other co-recommender for completion of the recommendation process.
When a postprint recommendation is published by a thematic PCI, the word “postprint” is printed below the image illustrating the postprint, to differentiate it from preprint recommendations.
The recommendation text is published with a DOI, but is not accompanied by a peer review or editorial decision.