montreal 生信人 2020年8月12日
又到了每月一推的bioRxiv生信好文速览时间了。相信关注我们栏目的朋友都了解，我们的栏目在好文推介的同时，也会顺带对预印本（preprint）的相关知识和文化进行宣传。一直以来，前者都是我们推送的重点。本期节目终于要破例了，因为好文推介栏目被两位“不速之客”挤到了副推。
所谓的“不速之客”就是高水平预印本推荐平台Peer Community In（PCI）的两位主创人员，来自法国国家农业研究院所（INRAE）的Thomas Guillemaud 和 Denis Bourguet教授。两位老师首次做客我们的栏目，向读者朋友们宣传PCI。
左Thomas Guillemaud ，右Denis Bourguet provided by Denis Bourguet
因何而起
在18年9月的好文速览栏目里，我们曾向大家介绍了PCI。将近两年时间过去了，如今的PCI也有了全新的面貌。鉴于大部分网友也许对PCI应该还很陌生，下面先对PCI再次做一简介。
来源：PCI官网（https://peercommunityin.org）
PCI是一个对于高质量预印本文章的评估与推荐（更准确地说是背书endorsement）的免费平台和非盈利组织，其初衷是对预印本服务器上的文章通过（严格）的同行评议进行推荐，以使它们从预印本升华为类似传统杂志所发表的可引用的文章。
众所周知，从某种角度上说，在学术界发表文章是一件奇怪的事，因为作者非但没有稿费，还要向出版商付钱。这笔钱，要么由从实验室的科研经费里出（开放获取，open access，下图左），要么由学校或研究所支付（subscriptions and paywalls），如果你所在的单位没有出钱订阅你访问的杂志，那么相信你对下图右的画面不会陌生。
截自Nature communications（左）和Nature ecology and evolution（右）官网
诚然，学术出版的过程本身要钱，但出版商们从中盈利所得却要多得多。消息指，学术出版商的利润甚至高达近40%【1】。科学家希望把他们的工作发表到好的学术平台，同时又不想在发表文章上花太多钱。有什么办法么？
也许你会想：预印本是免费的，但没有同行评议；传统学术期刊有同行评议，但文章发表烧钱，那么，为何不把二者的优点结合起来呢？你想得没错。这一看似水到渠成实则飞跃的想法，在17年的时候由来自法国国家农业研究所（INRAE；Institut national de la recherche agronomique）的三位科学家通过对PCI的创建而实践，三位教授分别是Thomas Guillemaud, Denis Bourguet 和 Benoit Facon。从那时起，“最低成本发paper”就成了PCI的重要服务宗旨。
如何操作
PCI的具体操作怎样的呢？很简单。你只需先将文章存放到预印本服务器上，便可以向PCI投稿啦。接下来，文章会经历严格的审稿过程，并由有一位“编辑”（在PCI称推荐人recommender）对文章去留最终裁定。一旦被推荐，本着公开透明的原则，文章的审稿意见、作者的回复以及编辑决定也会同时刊出。由于PCI的审稿人和编委大都是领域的知名学者，且PCI采用严格的审稿标准，有理由相信，被PCI推介的文章在业界享有与top journal上发表文章别无二致的待遇。理论上，从对文章的认可度的角度说，文章被PCI推荐相当于完成了在高水平期刊的“发表”。所以，PCI更像是一个类似杂志但完全免费的“出版平台”，preprint只不过是它借助的工具。
当然，PCI推介与在传统期刊发表并不矛盾。目前，已有超过30本杂志【2】欢迎发表在PCI（严格地说，被PCI推荐）的文章的投稿，并会直接采纳和参考PCI的审稿意见（提醒大家：1.文章向传统期刊的投稿和向PCI的投稿不能同步【3】。2.文章在PCI“发表”后向绝大多数杂志投稿没有问题，只不过除这30多家杂志外其他杂志并未声称会采信PCI的审稿意见）。此外，超过30家高等学府、科研机构和学术学会表明了自己对PCI的支持【2】。PCI的影响力在日益扩大。
来自PCI官网（https://peercommunityin.org）
以上是对PCI的一个简单介绍。大家对于这样一个挑战传统学术出版模式的新兴产物，想必还有很多的问题。
本期栏目，我们非常高兴邀请到了前面提到的三位PCI主创人员中的Thomas Guillemaud和Denis Bourguet，两位教授热情地接受了我们的文字采访，并就大家可能感兴趣的几个问题做了细致的解答，下面请见采访原文和中文翻译。
采访译文：
Q1：自17年创办以来，PCI目前有11个PCI社区（相当于不同领域的“杂志”），共推荐近200本预印本文章，这是一个不错的成绩。对于PCI目前所取得的进展你们满意吗？
A1：部分满意吧。看上去发展新的社区（相当于PCI下辖的不同领域的“杂志”，译者注）是一件有吸引力的事，到目前为止我们已经有11个社区了，而今年会有更多的PCI社区与大家见面，还有一些在筹备中。然而从另一个角度讲，对每一个PCI社区而言投稿的文章数仍不是很多，尽管最早创办的几个社区（比如PCI Ecology, PCI Evol Biol）有小幅度的增长，且在新创办的几个社区里也慢慢多了起来。
目前PCI平台下辖的11个社区，来自PCI官网（https://peercommunityin.org/）
Q2：PCI的网站上写道“PCI会通过严格的同行评审以推荐高质量的预印本文章”。那么，关于PCI对投稿文章的筛选标准，有没有更多细节透露给我们呢？
A2：我们的筛选标准和该PCI社区相同领域的最好期刊以及一些综合类杂志如plos系列和peerj是一致的。我们的目的不是为了推荐所有的文章，而只是选择性地推荐我们的编辑们（在PCI称推荐人）认为有价值的。每推荐一篇文章，推荐人会写一段推荐语以阐释推荐的理由，而这些推荐语也会随着文章在PCI上的“发表”与之一同公开。当然，文章的推荐是在同行评审的基础之上的，而这些同行评议过程也会公开以使读者们以对评审有一个自己的评判。
Q2-补充：您刚才提到的几个杂志应该是采用了不同的标准啊。比如，领域内最好的期刊基本都会要求文章的新颖性，而plos one和peerj显然没有这一项。
A2-补充：谢谢。你说得对，我刚才表述有误。在PCI Evolutionary Biology里我们有详尽的答案（由于内容较长请见文末。译者注）。
Q3：在PCI“发表”文章的最大优势在哪里呢？
A3：我们认为有以下几个主要优势：
- 获得一个严谨而又全面的对预印本手稿的同行评议，而且如果文章被PCI推荐，审稿意见也会公布
- 如果被推荐，文章可获得专家——有时候他们是业内非常优秀的学者——的正式推介。
- 被推的荐预印本会被整个学界认为是严密而扎实的研究，就如发表在领域内最好的杂志
- 这一切都是免费的
对于向PCI投稿并最终把文章发表在传统学术期刊的作者，他们向PCI投稿的好处在于两个投稿是互相兼容的。由于PCI严格的评审，那些被PCI所推荐的文章很可能被高水平期刊迅速接受，有时甚至不需要任何修改。目前，有近40本PCI友好学术期刊。所谓对PCI友好的意思是，这些杂志乐意直接参考PCI的审稿和推荐意见以加速审稿和编辑决定。
Q4：你们是否了解那些被PCI推介的文章最终有多少比例又在传统学术期刊上发表？大部分作者倾向于考虑PCI作为他们投稿的最终目的地，还是作为向传统杂志投稿的中间站？
A4: 你说的这个精确的比例呢，我们并不是很清楚。这是因为作者并不需要在文章被传统期刊接受后通知我们：）所以我们无从知晓他们会否在杂志上又发表了文章。大体上说，被我们推荐的文章有五到七成在被推荐后的半年内又发表于业内的高水平期刊上。
对于一些作者来说，很显然PCI只是向传统杂志投稿前的一个跳板，以使他们获取对手稿的反馈。其他一些学者不确定他们的最终目标。有趣的是，有一部分作者明确表示他们会将PCI而非传统杂志作为文章的最终去处。我们希望，随着PCI知名度和认可度的提升（特别是越来越多科研评审和经费资助机构对PCI的支持），这最后一部分作者的比例会越来越高。
Q5：如你所述，投稿到PCI的一个好处在于PCI的审稿意见可以直接被很多传统学术期刊采信。然而，目前有一些平台开始提供对预印本的审稿服务，且这些平台慢慢开始与传统期刊的展开合作。这对PCI会有冲击吗？
A5：确实，目前有越来越多的独立于杂志的对于预印本的同行评议服务，比如说Review Commons， PreLight等等。但是，（i）这些平台仍非常少。（ii）所有这些服务都旨在为传统期刊发表文章做铺垫，这与PCI截然不同。在PCI，预印本不仅会得到全面的评审（而且免费哦），还会像传统杂志一样对文章进行编辑决定，以使预印本最终被validate——成为可被引用的正式文章。
Q6：仅仅出于好奇，（虽说成本低但终归要有开支）你们的资金从哪里来呢？
A6：通过公立研究组织和机构的小笔经费和捐助。我们网站上有一个博客专门写PCI的运营模式 https://peercommunityin.org/2019/05/29/pci-economic-model/。
Q7：PCI的发起人都来自法国。此外，PCI的主要支持及参与机构和学校也都集中在法国和欧洲其他国家。PCI大概也正加强在全世界范围内的推广吧？在推广中你们遇到的最大挑战是什么呢？
A7：你说的对，这大概是出于历史原因吧，比如说创办人和最开始的社区（community，相当于PCI下辖的不同领域的“杂志”，译者注）都来自法国和欧洲其他国家的研究人员。但我们的目标是尽可能地使PCI国际化，这也是我们对新创办的PCI的重要筛选标准之一。整体上讲，PCI的推荐人（相当于审稿人，译者注）来自世界各地，而我们也努力让来自不同国家和地区的科学家参与到PCI大家庭，包括从创办社区到推荐人遴选、以及从投稿到同行评议的每一个环节。因此，在国际上的推广是尤为关键的。推广过程中的另一挑战来自基金委的评审团队对PCI的认可。确实，研究人员需要看到他们发表在PCI上的文章被这些委员会认为是有价值的，这样才能放心大胆（向我们投稿）。
Q8：最后，想对来自中国的研究人员说点儿什么吗？
A8：中国在世界科学领域的地位十分重要，（我们也期待着）中国学者对PCI的积极参与，这对PCI的发展尤其重要。
采访原文：
Q1. First launched in 2017, the family of PCI has expanded to 11 communities and has recommended some 200 preprints. I think that is a great achievement. How satisfied are you with the development of PCI?
A1: We are partly satisfied because the project of setting up new communities seems attractive with now 11 PCIs. More PCIs will be launched this year and others are also under discussion. Within each PCI, however, the number of submissions is still limited although slightly increasing for the oldest PCIs (PCI Ecology, PCI Evol Biol...) and already rising in some new PCIs.
Q2. On the website it says identifying high-quality unpublished articles by a specific recommendation obtained after rigorous peer-review. Can you tell us more about the selection standard for preprints submitted to PCI?
A2: The selection criteria are the same as those used in the best journals in the field covered by PCIs and in generalist journals (e.g. PLoS, PeerJ...). The aim of the PCI is not to recommend all articles, but only those that the editors (we call them “Recommenders”) consider interesting to highlight. The recommendation texts that the recommenders write and that we publish on the PCI websites are intended to explain the reasons why they do recommend an article (on the basis of peer-reviews that are also made available to readers, allowing them to judge the quality of the evaluation process).
There is a follow-up question at the end of the blog.
Q3. What are the biggest advantages you think to have preprints recommended by PCI?
A3: We see several major advantages:
-obtaining a critical and thorough evaluation of your preprint with reviews that are published if the preprint is accepted and therefore recommended,
-obtaining a recommendation text signed by a - sometimes very renowned - recommender and, ultimately,
-obtaining a validated preprint that can be considered by the community as serious and solid as articles published in the best journals in the field.
And all this is free of charge for authors and readers.
For those who ultimately want to publish in a journal and not just be recommended by PCI, the advantage of submitting to PCI is that they can then submit their article to a journal. The evaluation by PCI results in a high quality preprint that is likely to be accepted quickly (and sometimes as it stands) in an excellent journal. Nearly 40 scientific journals are PCI-friendly journals, meaning that they are willing to consider PCI reviews and recommendations to support/accelerate their editorial decision.
Q4. Do you know the proportion of PCI recommended papers that are later published in traditional journals? Would you think most authors consider PCI as the destination of their manuscript or they plan to get their study published in traditional journals but want some feedbacks at PCI?
A4: We do not know the exact proportion because the authors do not necessarily keep us informed and, for recently recommended articles, we cannot know whether they will ultimately be published in traditional journals. For preprints recommended for more than 6 months, the proportion seems to be between 50 and 70% of them being published in (very good) journals.
For some authors, PCI is clearly seen as a step prior to a submission to a traditional journal and to get a first feedback on their preprint. Others don't know in advance what they will do after their preprint recommendation. Interestingly, a fraction of the authors clearly want to turn to PCI to validate their article and avoid publishing in journals. We hope that, as awareness and recognition of PCI increases (especially among the evaluation/recruitment committees and funding agencies), the proportion of the latter will increase over time.
Q5. As I understand, an advantage of submitting to PCI is that the review comments can be transferred to many traditional journals. However, there are a few platforms conferring peer review for preprints, some of which have recently started to collaborate with traditional journals. Do you think this will have any impact on PCI?
A5: There is indeed an increase in initiatives of journal-independent peer-review services (e.g. Review Commons, PreLight...), but (i) this number remains limited and (ii) these services, outside of PCI, are clearly intended to be a pre-submission/publication step in a traditional journal. PCI not only evaluates preprints (and free of charge!), but also makes editorial decisions in the same way as journals, allowing a preprint to be validated - which then becomes a reference in the same way as articles published in journals.
Q6. Just curious, how is PCI funded?
A6: Through small support and donations from many public research organisations and institutions - see https://peercommunityin.org/pci-network/.
We have written a blog post about the PCI business model, available here: https://peercommunityin.org/2019/05/29/pci-economic-model/
Q7. I see PCI’s founders are all from France. Also, PCI’s most supporting or participating institutions are from France in addition to some European countries. Does it mean that it is important to promote PCI to the world? And could you tell us some of the challenges in promoting PCI?
Q7: Yes, it is. For historical reasons (the founders and the first communities were founded by French and European researchers), but the aim of PCI is indeed to be as international as possible - this is one of the selection criteria for the opening of new PCIs. The recommenders are generally of more diverse origins and we wish to continue to diversify as much as possible the geographical origin of the founders, recommenders, authors, reviewers… It is therefore crucial to promote PCI especially in international networks. The other challenge in promoting PCI is its recognition by evaluation/recruitment committees and by funding agencies. Indeed, researchers need to be confident that their preprints recommended by a PCI will be considered as a valuable article by these committees and agencies.
Q8. Last, is there anything you would like to say to researchers in China?
A8: Given the importance of the Chinese research community, an massive involvement of the Chinese researchers would be particularly important.
对于审稿标准的补充说明
Q2-followup：However, it seems to me that they could apply different criteria. For example, while top journals in the field may ask for novelties, some generalists journals like plos one or peerj are certainly not that picky. Would you please mind clarifying this point?
A2-followup：Thanks. You're right, the answer is not correct. You can find a detailed answer in the about of eg PCI Evol Biol:
"PCI Evol Biol recommends only preprints of high scientific quality that are methodologically and ethically sound. To this end, PCI Evol Biol: - 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 preregistration submissions and 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 reviewers and referees have no conflict of interest with the content or authors of the study being evaluated. PCI Evol Biol 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 Evol Biol has a large number of recommenders, ensuring a considerable diversity of interests. The recommendations published by PCI Evol Biol 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. "
想给你的preprint一个新去处吗？不妨试试PCI吧。有关PCI的更多的咨询，请浏览它的官网：https://peercommunityin.org。最后，对Thomas Guillemaud和Denis Bourguet 两位老师接受我们的专访表示衷心感谢。
引文
1. 2018. Time to break academic publishing's stranglehold on research. NewScientist.
2. https://peercommunityin.org/pci-network/
3. https://peercommunityin.org/faq/
作者原创
