What is PCI Genomics?
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 to submit a recommended preprint 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- PCI Genomics is transparent: reviews and recommendations (for unpublished articles) and recommendations (for published articles) are freely available for consultation.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).
Managing board of PCI Genomics
Rosa Fernandez (Barcelona, Institute of Evolutionary Biology (CSIC-UPF), Spain)
Jean-François Flot (Bruxelles, Evolutionary Biology & Ecology, Univ Libre de Bruxelle, Belgium)
Federico Hoffmann (Mississippi State, Mississippi State University, USA)
Danny Ionescu (Neuglobsow, Leibniz Institute of Freshwater Ecology and Inland Fisheries , Germany)
Denis Tagu (Rennes, Inrae, IGEPP, France)
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 The preprint or the preregistration must not be published or under consideration for evaluation elsewhere at the time of its submission to PCI Genomics.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 (whether or not reviewed).
- 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 being evaluated.
PCI Genomics does not guarantee the evaluation or recommendation of all submitted preprints. Only preprints considered interesting by at least one competent recommender (equivalent to an associate editor in a classical journal) will be peer reviewed. The interest of the preprint, as determined by the recommender, can relate to its context, the scientific question addressed, the methodology, or the results. PCI Genomics has a large number of recommenders, ensuring a considerable diversity of interests. The recommendations published by PCI Genomics are designed to draw the attention of the research community to the qualities of the article, including the subjective reasons for the recommender’s interest in it.
Type of articles
The articles recommended may be of different types: reviews, comments, opinion papers, research articles, data papers, technical notes, computer notes, etc. Preregistrations should be submitted to PCI Registered Reports.
Repeatability of science and open science
PCI wants to promote scientific repeatability and reliability to improve the overall robustness and integrity of our scientific conclusions. To this aim, PCI has set up three mandatory rules and makes two suggestions to authors:
Articles recommended by PCI must provide the readers with:
- Raw data, made available directly in the text or through an open data repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI. Data must be reusable, and the metadata and accompanying text must, therefore, carefully describe the data.
- Details on the quantitative analyses (e.g. data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and details concerning simulations (scripts, codes) in the text or through an open data repository, such as Zenodo, Dryad or some other institutional repository (see Directory of Open Access Repositories) with a DOI. The scripts or codes must be carefully described such that another researcher can run 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 their hypotheses, avoiding confusing “postdictions” and predictions, and carefully planning appropriate statistical treatment of the data (e.g. see 10.1073/pnas.1708274114).
- Preregistrations should be submitted to PCI Registered Reports
- 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 judged to be scientifically valid.
Peer Community In is a member of and subscribes to the principles of the Committee on Publication Ethics (COPE). In addition:
- Financial conflicts of interest are forbidden, see the PCI code of conduct.
- Authors should declare any potential non-financial conflict of interest.
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.
Inclusiveness and equity
PCI is attentive to equity and inclusion at all steps of the process of scientific article evaluation. PCI focuses on bringing more people underrepresented in academia among authors submitting to PCI, and reviewers, recommenders and managing board members working for PCI. Underrepresentation is hereby linked to many factors including career stage, gender and geography.
Specific recommendations are made to reviewers, recommenders and managing board members to increase equity and inclusiveness in each of their tasks.
Tools to increase equity and inclusiveness:
- Possibility to submit articles anonymously
- Transparency in the evaluation of articles
- Managing Board members take into account underrepresentation in academia when appointing new recommenders
- Template messages to recommenders and reviewers include recommendations about equity and inclusiveness
- Possibility to review anonymously
PCI is signatory of the Joint Statement of Principles of the Coalition for Diversity and Inclusion in Scholarly Communication (C4DISC)