montreal 生信人 2020年8月12日
又到了每月一推的bioRxiv生信好文速覽時間了。相信關注我們欄目的朋友都瞭解，我們的欄目在好文推介的同時，也會順帶對預印本（preprint）的相關知識和文化進行宣傳。一直以來，前者都是我們推送的重點。本期節目終於要破例了，因爲好文推介欄目被兩位“不速之客”擠到了副推。
所謂的“不速之客”就是高水平預印本推薦平臺Peer Community In（PCI）的兩位主創人員，來自法國國家農業研究院所（INRAE）的Thomas Guillemaud 和 Denis Bourguet教授。兩位老師首次做客我們的欄目，向讀者朋友們宣傳PCI。
左Thomas Guillemaud ，右Denis Bourguet provided by Denis Bourguet
因何而起
在18年9月的好文速覽欄目裏，我們曾向大家介紹了PCI。將近兩年時間過去了，如今的PCI也有了全新的面貌。鑑於大部分網友也許對PCI應該還很陌生，下面先對PCI再次做一簡介。
來源：PCI官網（https://peercommunityin.org）
PCI是一個對於高質量預印本文章的評估與推薦（更準確地說是背書endorsement）的免費平臺和非盈利組織，其初衷是對預印本服務器上的文章通過（嚴格）的同行評議進行推薦，以使它們從預印本昇華爲類似傳統雜誌所發表的可引用的文章。
衆所周知，從某種角度上說，在學術界發表文章是一件奇怪的事，因爲作者非但沒有稿費，還要向出版商付錢。這筆錢，要麼由從實驗室的科研經費裏出（開放獲取，open access，下圖左），要麼由學校或研究所支付（subscriptions and paywalls），如果你所在的單位沒有出錢訂閱你訪問的雜誌，那麼相信你對下圖右的畫面不會陌生。
截自Nature communications（左）和Nature ecology and evolution（右）官網
誠然，學術出版的過程本身要錢，但出版商們從中盈利所得卻要多得多。消息指，學術出版商的利潤甚至高達近40%【1】。科學家希望把他們的工作發表到好的學術平臺，同時又不想在發表文章上花太多錢。有什麼辦法麼？
也許你會想：預印本是免費的，但沒有同行評議；傳統學術期刊有同行評議，但文章發表燒錢，那麼，爲何不把二者的優點結合起來呢？你想得沒錯。這一看似水到渠成實則飛躍的想法，在17年的時候由來自法國國家農業研究所（INRAE；Institut national de la recherche agronomique）的三位科學家通過對PCI的創建而實踐，三位教授分別是Thomas Guillemaud, Denis Bourguet 和 Benoit Facon。從那時起，“最低成本發paper”就成了PCI的重要服務宗旨。
如何操作
PCI的具體操作怎樣的呢？很簡單。你只需先將文章存放到預印本服務器上，便可以向PCI投稿啦。接下來，文章會經歷嚴格的審稿過程，並由有一位“編輯”（在PCI稱推薦人recommender）對文章去留最終裁定。一旦被推薦，本着公開透明的原則，文章的審稿意見、作者的回覆以及編輯決定也會同時刊出。由於PCI的審稿人和編委大都是領域的知名學者，且PCI採用嚴格的審稿標準，有理由相信，被PCI推介的文章在業界享有與top journal上發表文章別無二致的待遇。理論上，從對文章的認可度的角度說，文章被PCI推薦相當於完成了在高水平期刊的“發表”。所以，PCI更像是一個類似雜誌但完全免費的“出版平臺”，preprint只不過是它藉助的工具。
當然，PCI推介與在傳統期刊發表並不矛盾。目前，已有超過30本雜誌【2】歡迎發表在PCI（嚴格地說，被PCI推薦）的文章的投稿，並會直接採納和參考PCI的審稿意見（提醒大家：1.文章向傳統期刊的投稿和向PCI的投稿不能同步【3】。2.文章在PCI“發表”後向絕大多數雜誌投稿沒有問題，只不過除這30多家雜誌外其他雜誌並未聲稱會採信PCI的審稿意見）。此外，超過30家高等學府、科研機構和學術學會表明了自己對PCI的支持【2】。PCI的影響力在日益擴大。
來自PCI官網（https://peercommunityin.org）
以上是對PCI的一個簡單介紹。大家對於這樣一個挑戰傳統學術出版模式的新興產物，想必還有很多的問題。
本期欄目，我們非常高興邀請到了前面提到的三位PCI主創人員中的Thomas Guillemaud和Denis Bourguet，兩位教授熱情地接受了我們的文字採訪，並就大家可能感興趣的幾個問題做了細緻的解答，下面請見採訪原文和中文翻譯。
採訪譯文：
Q1：自17年創辦以來，PCI目前有11個PCI社區（相當於不同領域的“雜誌”），共推薦近200本預印本文章，這是一個不錯的成績。對於PCI目前所取得的進展你們滿意嗎？
A1：部分滿意吧。看上去發展新的社區（相當於PCI下轄的不同領域的“雜誌”，譯者注）是一件有吸引力的事，到目前爲止我們已經有11個社區了，而今年會有更多的PCI社區與大家見面，還有一些在籌備中。然而從另一個角度講，對每一個PCI社區而言投稿的文章數仍不是很多，儘管最早創辦的幾個社區（比如PCI Ecology, PCI Evol Biol）有小幅度的增長，且在新創辦的幾個社區裏也慢慢多了起來。
目前PCI平臺下轄的11個社區，來自PCI官網（https://peercommunityin.org/）
Q2：PCI的網站上寫道“PCI會通過嚴格的同行評審以推薦高質量的預印本文章”。那麼，關於PCI對投稿文章的篩選標準，有沒有更多細節透露給我們呢？
A2：我們的篩選標準和該PCI社區相同領域的最好期刊以及一些綜合類雜誌如plos系列和peerj是一致的。我們的目的不是爲了推薦所有的文章，而只是選擇性地推薦我們的編輯們（在PCI稱推薦人）認爲有價值的。每推薦一篇文章，推薦人會寫一段推薦語以闡釋推薦的理由，而這些推薦語也會隨着文章在PCI上的“發表”與之一同公開。當然，文章的推薦是在同行評審的基礎之上的，而這些同行評議過程也會公開以使讀者們以對評審有一個自己的評判。
Q2-補充：您剛纔提到的幾個雜誌應該是採用了不同的標準啊。比如，領域內最好的期刊基本都會要求文章的新穎性，而plos one和peerj顯然沒有這一項。
A2-補充：謝謝。你說得對，我剛纔表述有誤。在PCI Evolutionary Biology裏我們有詳盡的答案（由於內容較長請見文末。譯者注）。
Q3：在PCI“發表”文章的最大優勢在哪裏呢？
A3：我們認爲有以下幾個主要優勢：
- 獲得一個嚴謹而又全面的對預印本手稿的同行評議，而且如果文章被PCI推薦，審稿意見也會公佈
- 如果被推薦，文章可獲得專家——有時候他們是業內非常優秀的學者——的正式推介。
- 被推的薦預印本會被整個學界認爲是嚴密而紮實的研究，就如發表在領域內最好的雜誌
- 這一切都是免費的
對於向PCI投稿並最終把文章發表在傳統學術期刊的作者，他們向PCI投稿的好處在於兩個投稿是互相兼容的。由於PCI嚴格的評審，那些被PCI所推薦的文章很可能被高水平期刊迅速接受，有時甚至不需要任何修改。目前，有近40本PCI友好學術期刊。所謂對PCI友好的意思是，這些雜誌樂意直接參考PCI的審稿和推薦意見以加速審稿和編輯決定。
Q4：你們是否瞭解那些被PCI推介的文章最終有多少比例又在傳統學術期刊上發表？大部分作者傾向於考慮PCI作爲他們投稿的最終目的地，還是作爲向傳統雜誌投稿的中間站？
A4: 你說的這個精確的比例呢，我們並不是很清楚。這是因爲作者並不需要在文章被傳統期刊接受後通知我們：）所以我們無從知曉他們會否在雜誌上又發表了文章。大體上說，被我們推薦的文章有五到七成在被推薦後的半年內又發表於業內的高水平期刊上。
對於一些作者來說，很顯然PCI只是向傳統雜誌投稿前的一個跳板，以使他們獲取對手稿的反饋。其他一些學者不確定他們的最終目標。有趣的是，有一部分作者明確表示他們會將PCI而非傳統雜誌作爲文章的最終去處。我們希望，隨着PCI知名度和認可度的提升（特別是越來越多科研評審和經費資助機構對PCI的支持），這最後一部分作者的比例會越來越高。
Q5：如你所述，投稿到PCI的一個好處在於PCI的審稿意見可以直接被很多傳統學術期刊採信。然而，目前有一些平臺開始提供對預印本的審稿服務，且這些平臺慢慢開始與傳統期刊的展開合作。這對PCI會有衝擊嗎？
A5：確實，目前有越來越多的獨立於雜誌的對於預印本的同行評議服務，比如說Review Commons， PreLight等等。但是，（i）這些平臺仍非常少。（ii）所有這些服務都旨在爲傳統期刊發表文章做鋪墊，這與PCI截然不同。在PCI，預印本不僅會得到全面的評審（而且免費哦），還會像傳統雜誌一樣對文章進行編輯決定，以使預印本最終被validate——成爲可被引用的正式文章。
Q6：僅僅出於好奇，（雖說成本低但終歸要有開支）你們的資金從哪裏來呢？
A6：通過公立研究組織和機構的小筆經費和捐助。我們網站上有一個博客專門寫PCI的運營模式 https://peercommunityin.org/2019/05/29/pci-economic-model/。
Q7：PCI的發起人都來自法國。此外，PCI的主要支持及參與機構和學校也都集中在法國和歐洲其他國家。PCI大概也正加強在全世界範圍內的推廣吧？在推廣中你們遇到的最大挑戰是什麼呢？
A7：你說的對，這大概是出於歷史原因吧，比如說創辦人和最開始的社區（community，相當於PCI下轄的不同領域的“雜誌”，譯者注）都來自法國和歐洲其他國家的研究人員。但我們的目標是儘可能地使PCI國際化，這也是我們對新創辦的PCI的重要篩選標準之一。整體上講，PCI的推薦人（相當於審稿人，譯者注）來自世界各地，而我們也努力讓來自不同國家和地區的科學家參與到PCI大家庭，包括從創辦社區到推薦人遴選、以及從投稿到同行評議的每一個環節。因此，在國際上的推廣是尤爲關鍵的。推廣過程中的另一挑戰來自基金委的評審團隊對PCI的認可。確實，研究人員需要看到他們發表在PCI上的文章被這些委員會認爲是有價值的，這樣才能放心大膽（向我們投稿）。
Q8：最後，想對來自中國的研究人員說點兒什麼嗎？
A8：中國在世界科學領域的地位十分重要，（我們也期待着）中國學者對PCI的積極參與，這對PCI的發展尤其重要。
採訪原文：
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.
對於審稿標準的補充說明
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. "
想給你的preprint一個新去處嗎？不妨試試PCI吧。有關PCI的更多的諮詢，請瀏覽它的官網：https://peercommunityin.org。最後，對Thomas Guillemaud和Denis Bourguet 兩位老師接受我們的專訪表示衷心感謝。
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/
作者原創，原載於生信人公衆號