Guide to open

For the online version explained | 3 of this guide please visit f1000.com/open the merits of open | 6

understanding post-publication peer review | 9

what is ? | 12

what is ? | 15

about F1000Research | 18

facts & figures |19 Introduction

What is the history of We hope this will be open access? Where a useful resource for should we share our data? researchers, students, and What are the benefits others with an interest of peer review? Who is in the increasingly open using post-publication of scientific peer review? How can research and publishing. I get involved with Finally, we’d like to open science? express our thanks to To answer these and Peter Kraker, Fabiana other key questions, Kubke, Ross Mounce, Liz F1000Research has put Neeley, Anna Sharman, together this guide to Lenny Teytelman, Kaitlin open science publishing. Thaney and Liz Wager The first four chapters for useful feedback on each focus on one of the individual chapters of underlying principles of this document. F1000Research, and the last addresses other areas of open science.

About the Author

Eva Amsen Outreach Director at F1000Research

Eva holds a PhD in Biochemistry from the University of Toronto, and is interested in all forms of communication between researchers, from hallway conversations to academic papers.

Before joining F1000Research, she worked at the journal Development, where she launched and ran the Node, a community website for developmental biologists.

Guide to open science publishing | 2 Image by KTH Royal Institute of Technology, Stockholm, Sweden. Licensed under CC BY SA 2.0 via https://www.flickr.com/photos/kthbiblioteket/4566250874 Re-used under license conditions. Open access explained

A short although researchers could make their manuscripts available by Open access as we know it was self-archiving. Within the life Although the basic defined in a meeting in Budapest sciences, BioMed Central was in 2001. This meeting produced the first open access publisher to idea of open access the Budapest Open Access launch in 2000. (It was founded is indeed to give Initiative: a statement of principles by Vitek Tracz, who went on to about open access publishing. found F1000Research.) The Public everyone access to the Library of Science announced The resulting document, their intent to publish shortly after, published in 2002, described the contents of a research in 2001. paper, the term “open opportunities that the could provide in opening up access” implies more : Open access today than just making the “…lay the foundation for uniting Since these early open humanity in a common intellectual access publishers, many conversation and quest for content free. others have followed suit, knowledge.” and open access is more popular Despite this occasional lofty than ever. In August 2013, the wording, the document is very European Commission announced clear on the definition of open that access: “open access is reaching the tipping point, with around 50% of scientific “By “open access” to this literature, papers published in 2011 now we mean its free availability on the public internet, permitting any available for free.” users to read, download, copy, distribute, print, search, or link to The ’s research the full texts of these articles, crawl framework Horizon 2020 requires them for indexing, pass them as all research they fund to be made data to software, or use them for available via open access. Similar any other lawful purpose, without requirements are made by large financial, legal, or technical barriers funding agencies around the other than those inseparable from world, such as the Wellcome gaining access to the internet itself. Trust in the UK and the National The only constraint on reproduction Institutes of Health in the USA. and distribution, and the only role for copyright in this domain, should be to give authors control over the Green and Gold open access integrity of their work and the right to be properly acknowledged How can researchers comply with and cited.” these funder regulations? There At this point there were not yet are currently two possible open many open access publishers, access routes: Green and Gold.

Guide to open science publishing | 3 • Green open access is archiving generally retain copyright. (See review process, and to develop of accepted manuscripts in more about new features to support their accessible repositories, for licences in the “further reading” authors and readers, whereas example in their institutional section below). “predatory” journals don’t invest in repository or in PubMed Central. these processes. While this allows researchers to publish in any journal they want 2 Gold open access means But how can you distinguish a and deposit later, the system has “author pays” good journal from a bad one? some limitations: Some journals First of all, you can check if you only allow the archiving of a final No, it just means that it’s accepted , not of the know people who have published publisher-mediated open access. published and formatted paper. in this journal, or members of Some journals open up access Because the publisher does not the editorial board. Has the to all their archived articles rely on subscription fees from journal attended or sponsored after a certain time period, but readers and libraries for those conferences or supported other in other cases authors will have articles, they cover their costs initiatives? Is the journal a member to remember to deposit their in other ways. Some smaller of the Committee on Publication own paper, which can be a time journals can be funded entirely by Ethics (COPE)? Is the journal consuming process. institutes or societies. Larger open included in scholarly databases access publishers often use article • Gold open access is publisher- such as PubMed? So far, that mediated open access. The processing charges (APCs), which all applies equally to both open benefit of this is that the article is allow them to scale their business access and subscription journals. immediately made open access, model once they start receiving For open access journals, there and authors don’t have to take more submissions. The Directory is even an extra level of scrutiny: any extra steps, but there can be of Open Access Journals (DOAJ) The Open Access Scholarly a cost associated with it. Usually lists which model each journal Publishers Association (OASPA) the entire journal will be available uses. regularly re-reviews its members, as an open access journal, but and publishers must comply with some journals operate a hybrid Although APCs are applied on very strict guidelines to remain a model, where researchers can a per-article basis, in reality member, so you can check their pay to publish an open access many authors do not pay these member list. The DOAJ has also article in an otherwise non-open- fees out of pocket. Funders and access journal. recently tightened their criteria institutes who require open access for inclusion, and has removed publication often support authors several journals that do not fit and cover the cost, and many Three misconceptions about these criteria. Their member list publishers will waive APCs for low open access is easy to search, and provides income countries via the HINARI detailed information about each As the above summary illustrates, programme or on a case-by-case publication. open access has a distinct basis for specific situations of definition, but can be applied in economic difficulty. Finally, if a journal has a different ways. That can lead to transparent peer review model, some confusion, and there are a where names of reviewers and/ Open access implies bad quality few misconceptions about open 3 or content of referee reports or access floating around, such as No. Whether an article is free to editorial decision letters are made the following. access or hiding behind a public, you can see for yourself what the peer review process says nothing about the quality of the research itself or about looks like and make an informed 1 Open access just means “free decision about the journal. to read” the peer review carried out on the paper. Not exactly. Although the basic idea of open access is indeed This misconception comes from to give everyone access to the the fact that there is indeed contents of a research paper, the a small group of so-called term “open access” implies more “predatory” publishers who are than just making the content charging researchers to publish free. It also requires making the articles in their journals for the material available for others to re- sole purpose of making money, use, and allowing content mining without considering the scientific (e.g. for meta-analysis). quality and often without even inviting peer reviewers to look Usually, open access articles at the papers. On the surface, are accompanied by a Creative this charge for publication may Commons licence that describes resemble the APC model used by the details of what can be done many open access journals, but with the content of the paper. it is different. Reliable journals Most of these licences require use APCs to cover the cost of giving credit to the authors, who managing the editorial and peer

Guide to open science publishing | 4 REFERENCES & RESOURCES FURTHER READING European Commission: Open Access Claire Redhead/OASPA: Why CC-BY? to Research Publications Reaching (23 October 2012) ‘Tipping Point’ (21 August 2013) http://oaspa.org/why-cc-by/ http://europa.eu/rapid/press-release_ Paul Klimpel (2013) Free Knowledge IP-13-786_en.htm based on Creative Commons Licenses. Budapest Open Access Initiative Consequences, Risks, and side- declaration (February 14, 2002) effects of the license module Non- http://www. Commercial – NC, Wikimedia Germany budapestopenaccessinitiative.org/read The seer of science publishing. Wellcome Trust open access policy Interview of Vitek Tracz by Tania http://www.wellcome.ac.uk/About- Rabesandratana, 4 October 2013, us/Policy/Policy-and-position- Science 342 (6154), 66-67 statements/WTD002766.htm http://www.sciencemag.org/ content/342/6154/66.full NIH public access policy https://publicaccess.nih.gov/ Richard Poynder: The state of open access. http://richardpoynder.co.uk/ Directory of Open Access Journals the-state-of-open-access.html (DOAJ) http://doaj.org/ Stephen Curry: Open Access Richard van Noorden: Open Access - Yes you can. (20 April 2014) Website gets tough , 6 August 2014, http://occamstypewriter.org/ Nature; 512(7512) 17-17 scurry/2014/04/20/open-access-yes- Open Access Scholarly Publishers you-can/ . Association (OASPA) http://oaspa.org/ OASPA’s second statement following the article in Science entitled “Who’s Afraid of Peer Review?” (11 November 2013) http://oaspa.org/oaspas-second- statement-following-the-article-in- science-entitled-whos-afraid-of-peer- review/ Committee on Publication Ethics (COPE) http://publicationethics.org/

Guide to open science publishing | 5 Image by Martin Eckert. Licensed under CC BY NC ND 2.0 via https://www.flickr.com/photos/meckert75/5364825863 Used with permission. The merits of

History of traditional (closed) system is not fool-proof, and a peer review reviewer will still often recognize which lab a paper comes from. Anonymous reviewers Even though scientific publishing In addition, any bias towards has been around since the 17th competitors of the reviewer still can be biased against century, formal peer review of remain, even if that competitor is submitted articles by external anonymised. the authors of the academics is relatively new. The paper, and lean journals Science and JAMA, for Another drawback of traditional example, introduced formal peer peer review is that the referee toward rejection review in the 1940s, and Nature reports are visible only to the or acceptance for didn’t introduce it until 1967. authors and the editor. Nobody else can see what the reviewers unscientific reasons. The peer review system adopted thought of the paper. Especially in the 20th century has now in situations where reviewers Often, the closest become the norm for many disagree, and a single editor “peers” in someone’s journals. It involves an editor makes the final decision, it can (usually a practising researcher, be very informative to see what area of research are but sometimes a journal staff the reviewers thought of an member in the case of journals like article, and whether the editor’s also that researcher’s Nature) sending out a paper to a decision was in line with their direct competitors! few experts in the field, who then opinion. Reviewers are usually provide comments for the paper’s in a position to put the work in authors. Although the reviewers a broader context of the field, can generally see who the authors and often mention this context in are, they themselves remain their reports. They can also point anonymous to the author, and out where the work could be only the editor knows everyone’s expanded into new areas, and may identity. still have some lingering questions. All of this is useful for everyone to Problems with traditional, semi- read – not just the authors. It’s also blind, peer review important to remember that not This “single-blind” system is not all journals use the same criteria without problems. Anonymous for publication. Some journals reviewers can be biased against may turn a great paper down just the authors of the paper, and lean because it doesn’t fit the scope of toward rejection or acceptance the journal. Other journals publish for unscientific reasons. Often, all sound science, including some the closest “peers” in someone’s papers that get extremely high area of research are also that praise in the referee reports. researcher’s direct competitors! One solution is to remove the authors’ names from the manuscript, but this double-blind

Guide to open science publishing | 6 A timeline of open and transparent review

Within the life sciences in particular, several journals have opened their peer review process to address some of the issues discussed above. Sometimes this involves publicly naming reviewers and/or editors. Other journals publish some or all reviewer comments.

1999 After studying various peer review models, BMJ starts revealing reviewer names to authors.

2000 BioMed Central launches, and soon after that starts including reviewer names and pre-publication history for published articles in all medical journals in their BMC series of publications.

2001 Atmospheric Chemistry and Physics introduces a system where manuscripts are placed online as a “discussion paper”, which is archived with all comments and reviews, even before approved and peer-reviewed articles appear in the journal.

2006 Launch of Direct, which includes reviewer comments and names with published articles.

2007 Frontiers launches, and includes reviewer names with articles.

2010 EMBO Journal starts publishing review process file with articles. Editors are named, but referees remain anonymous.

2011 BMJ Open launches, and includes all reviewer names and review reports with published articles.

2012 Several journals launch with an open peer review model: »» GigaScience - publishes pre-publication history with articles and names reviewers (opt-out system) »» PeerJ - Peer review reports published with author approval, reviewer names published with reviewer permission. »» eLife - Decision letter published with author approval. Reviewers anonymous. »» F1000Research - All peer review reports and reviewer names are public, and appear after article is published online.

2014 More journals open their peer review process: »» Science Open launches journal with an open post-publication review model. »» BMJ - moves to a fully open peer review model, where reports and reviewer names are published with each article.

Benefits of open review

Benefits for authors and readers Benefits for reviewers

»» Author can see who reviewed their work »» Shows the reviewer’s informed opinion of the work »» Reviewer comments put paper in context, which is »» Demonstrates experience as a reviewer useful additional information for readers »» Can take credit for the work involved in conducting »» Reduces bias among reviewers the review »» More constructive reviews »» Published reports can serve as peer review examples for young researchers

To make it easier for referees to take credit for their work, some journals, including F1000Research, now provide unique identifiers (DOIs) for referee reports. In addition, F1000Research is co-chairing a working group investigating how to include peer review output in ORCiD profiles.

Challenges

Although open peer review is becoming more common, and addresses several of the issues of anonymous review, a few challenges still remain. A study in the early days of open review suggested that naming referees slightly reduced the likelihood of finding reviewers but did not affect the quality of review. Other studies suggest that open review provides more constructive reports.

Guide to open science publishing | 7 REFERENCES & RESOURCES

Michael Nielsen: Three myths about About the EMBO journal – review scientific peer review (8 January 2009) process files http://emboj.embopress. http://michaelnielsen.org/blog/three- org/about#Review_Process myths-about-scientific-peer-review/ About BMJ Open http://bmjopen.bmj. Timeline: History of the journal Nature com/site/about/ http://www.nature.com/nature/history/ About GigaScience – Publication timeline_1960s.html and peer review process http:// Kathleen Fitzpatrick (2011) The history www.gigasciencejournal.com/ of peer review, in Planned Obsolence: about#publication publishing, technology, and the future PeerJ – How it works https://peerj. of the academy, NYU Press com/about/how-it-works/ Working double-blind. Nature 451, 605- eLife review process http:// 606 (7 February 2008) elifesciences.org/about#process Van Rooyen S, Godlee F, Evans S, F1000Research – How it works http:// Black N, Smith R (1999) Effect of open F1000Research.com/about peer review on quality of reviews and on reviewers’ recommendations: a Science Open – How does it work? randomised trial, BMJ 318, 23-7 http://about.scienceopen.com/how- does-it-work/ Maria K Kowalczuk, Frank Dudbridge, Shreeya Nanda, Stephanie L Harriman, BMJ – Peer review process http:// Elizabeth C Moylan (2013) A www.bmj.com/about-bmj/resources- comparison of the quality of reviewer authors/peer-review-process reports from author-suggested reviewers and editor-suggested reviewers in journals operating on FURTHER READING open or closed peer review models. F1000Posters, 4: 1252 A guide to peer review in ecology and evolution, published by the ORCID & CASRAI Kick-off New British Ecological Society www. Standards Project on ‘Peer Review britishecologicalsociety.org/wp- Services’. (7 April 2014) http://casrai. content/uploads/Publ_Peer-Review- org/435 Booklet.pdf Van Rooyen S, Delamothe T, Evans Peer review: the nuts and bolts, SJW (2010) Effect on peer review published by Sense About Science of telling reviewers that their signed http://www.senseaboutscience.org/ reviews might be posted on the web: resources.php/99/peer-review-the- randomised controlled trial. BMJ 341 nuts-and-bolts Smith R (1999) Opening up BMJ peer How to write a good peer review review: A beginning that should lead to report, published by F1000Research complete transparency. BMJ; 318:4 http://F1000Research.com/peer- Shanahan DR, Olsen BR (2014) reviewing-tips Opening peer-review: the democracy Arjun Raj: How to review a paper of science, Journal of Negative Results (19 April 2014) http://rajlaboratory. in BioMedicine 13:2 blogspot.co.uk/2014/04/how-to- Godlee F (2002) Making Reviewers review-paper.html Visible: Openness, Accountability, and Benos D et al. (2007) The ups and Credit, JAMA 287(21):2762-2765 downs of peer review. Advances in What is ‘open peer review’, as operated Physiology Education, Vol. 31 no. 145- by the medical journals in the BMC 152 series? http://www.biomedcentral.com/ Walbot V (2009) Are we training authors/authorfaq/medical pit bulls to review our manuscripts? Atmospheric Chemistry and Physics Journal of Biology 8:24 – publication policy http://www. atmospheric-chemistry-and-physics. net/general_information/publication_ policy.html Koonin EV, Landweber L, Lipman DJ (2006) A community experiment with fully open and published peer review. Biology Direct 1:1 Frontiers review system http://www. frontiersin.org/about/reviewsystem

Guide to open science publishing | 8 Group work image by Eva Amsen. Used with permission. Understanding post-publication peer review

In the past few years, the phrase 2 Review by volunteer reviewers, “post-publication peer review” has after publication of the un- popped up in various discussions reviewed article When you come about scientific publishing, as either an add-on to, or a This is also a publisher-driven across a mention replacement of, pre-publication method of post-publication peer of post-publication peer review. As is becoming review, and also involves articles increasingly apparent, pre- being published online before peer review, always publication peer review doesn’t peer review, but in this case the pick up all problems that may exist reviewers are not invited by the check which “flavour” with a manuscript. But what is journal. Each publisher may use it is [...] All types post-publication peer review, and different criteria to determine how can it address these issues? who can review, and whether of post-publication Confusingly, the term can refer the reviews change the status of peer review serve a to a number of different models, the published article. At Science which each work in a different way Open, a reviewer must have at purpose, but they – some by introducing a new peer least five of their own published review system within a journal, articles in their ORCID profile. At don’t all serve the others by providing a platform to The Winnower, any registered user discuss any published articles. can leave a review on any of their same purpose. published articles.

Types of post-publication This system closely resembles the peer review: commenting system that several journals have implemented in 1 Review by formally invited addition to a formal (invited) peer reviewers, after publication of the review system, but journals may un-reviewed article ask their volunteer reviewers to address specific aspects of the This type of post-publication peer article, as with invited review. review is used by publications such as F1000Research and the Copernicus journals. Here, peer 3 Comments on blogs or third review is carried out by invited party sites, independent of any reviewers, like it’s done at most formal peer review that may have journals, but the article is already already occurred on the article published online (after an editorial check) before the peer review In recent years, most discussions process starts. Articles that pass surrounding post-publication peer review are clearly marked as peer review have been about new such and are indexed in scholarly platforms that allow researchers databases. to comment on published

Guide to open science publishing | 9 research articles. PubPeer for journals that use voluntary and currently the only way to allows anonymous researchers post-publication peer review know which is being used is to comment on any article (such as Science Open or to look into each specific case with a DOI, or those published The Winnower), low levels of to find out what is meant. For participation might mean that as in arXiv. PubMed example, at F1000Research articles remain unreviewed. we noticed that many people Commons gives authors with at Journals that invite reviewers least one of their own publications for post-publication peer review assume that “post-publication indexed in PubMed the ability to (such as F1000Research and peer review” means that anyone comment on any other articles in Copernicus journals) use a system can provide the formal peer the database but here they cannot quite similar to “traditional” peer reviews on our articles. In fact, all be anonymous. Both services were review, and can make sure that all F1000Research’s peer review is launched to encourage online articles are seen by reviewers. carried out by invited reviewers. discussion about scientific articles » Reviewer expertise Inviting – a practice already taking place » When you come across a mention reviewers also allows journals to on blogs and on social media, of post-publication peer review, ensure their reviewers have the always check which “flavour” it is: and to a much smaller extent in adequate expertise to review each are reviewers invited or is review the comments sections of journal particular paper. Some voluntary articles itself. review systems have also built in voluntary? Is there a check for a checkpoint to control expertise reviewer expertise? Are reviews This sort of discussion can be level: for example, Science Open published on the article itself very valuable and highlights some requires reviewers to have five or on a third-party site? Are of the problems of traditional articles in ORCID, and PubMed reviewers anonymous? Does the anonymous pre-publication Commons requires one article post-publication review replace peer review. Discussions on in PubMed. However, neither traditional peer review or is it an social media and on PubPeer system is able to check that the add-on service? successfully identified issues previously published work of the reviewer is in the field of the with the STAP paper that was All types of post-publication peer article they’re commenting on. published in Nature in early 2014, review serve a purpose, but they and will probably continue to »» Fragmentation of discussion One don’t all serve the same purpose. bring to light other issues with critique of the variety of post- high-profile papers in the future. publication peer review systems is that discussion happens in Sometimes F1000Prime is also multiple places. The same article mentioned in the context of can have comments on the post-publication peer review. This article itself (if that feature is service uses a network of 10,000 available), in PubPeer, on PubMed international Faculty Members to Commons, on ResearchGate, on blogs, on Twitter, on F1000Prime recommend articles from the life and elsewhere. sciences. However, F1000Prime focuses on recommendations only, As these examples show, the as a service to highlight important different versions of post- articles, whereas the other publication peer review all deal methods focus more on criticism with different types of challenges, and debate. so it is important to clearly distinguish between them.

Why does the distinction matter? How to tell which type of post- Post-publication peer review is publication review you’re still new, and is facing several dealing with challenges. However, different types of post-publication peer As described in the previous review are not all affected in chapter, open peer review can the same manner. This is mean named reviewers, or highlighted in the list of challenges public referee reports, or both. included below. In all cases, though, “open peer review” refers to review by invited reviewers. “Post-publication peer Challenges for post-publication review”, on the other hand, can be peer review named or anonymous, and reviews »» Participation Not all published can in some cases be written by articles receive comments via uninvited reviewers who may not systems such as PubPeer and necessarily be literal “peers” in PubMed Commons, although they the field. have been shown to serve as a useful platform for discussion The many different uses of of controversial articles. But the phrase are confusing,

Guide to open science publishing | 10 REFERENCES & RESOURCES FURTHER READING The Guardian view on the end of peer STAP paper discussion on PubPeer review. The Guardian editorial, July 6, https://pubpeer.com/publications/8B7 2014 http://www.theguardian.com/ 55710BADFE6FB0A848A44B70F7D commentisfree/2014/jul/06/guardian- Summary of the “post-publication view-end-peer-review-scientific- peer review” session at the Science journals Online 2014 conference. https://storify. STAP retracted: Two retractions com/jalees_rehman/discussion-about- highlight long-standing issues of post-publication-peer-review-scio trust and sloppiness that must be Kelly Servick: Researcher files lawsuit addressed. Nature 511, 5–6 (03 July over anonymous PubPeer comments 2014) (26 October 2014) Richard Smith: What is post- http://news.sciencemag.org/scientific- publication peer review? (6 April community/2014/10/researcher-files- 2011) http://blogs.bmj.com/ lawsuit-over-anonymous-pubpeer- bmj/2011/04/06/richard-smith-what- comments is-post-publication-peer-review/ Aimee Swartz: Post-publication peer review mainstreamed (22 October, 2013) http://www.the-scientist. com/?articles.view/articleNo/37969/ title/Post-Publication-Peer-Review- Mainstreamed/ Post publication peer-review: Everything changes, and everything stays the same, by Bonnie Swoger on the blog Information Culture, 26 March 2014 F1000Research – How it works http://F1000Research.com/about Copernicus peer review model http://publications.copernicus.org/ services/public_peer_review.html Science Open – How does it work? http://about.scienceopen.com/how- does-it-work/ The Winnower https://thewinnower.com/ What is F1000Prime? http://f1000.com/prime/about/whatis

Guide to open science publishing | 11 Image by John Goode. Licensed under CC BY 2.0 via https://www.flickr.com/photos/johnnieb/17200471/ Re-used under license conditions. What is open data?

Open data in science interpret it, and use it for anything from art projects to teaching to “Open data” is a broad concept data mining to including versions The open data that doesn’t just apply to research of it in their own work. That is data, but also to, for example, the what open data is. movement wants to opening up of government data. Many of the underlying ideas are The open data movement wants apply the principles similar: the goal of open data, to apply the principles of open of open data to not whether it involves research data data to not just big publicly or census data, is to make data funded projects like the human just big publicly available to anyone and reusable genome project, but to all kinds of funded projects like by anyone for further analysis. data however large or small. the human genome In the sciences, data have not always been easy to come by. project, but to all kinds Before the internet, journal articles Why use open data in science? could not feasibly include all the As illustrated by the human of data however large relevant data. If you wanted to use genome example above, opening another group’s data, you had to or small. up research data makes it much ask them for it. easier for other scientists to build One of the first, and one of upon that work and advance the the best-known, data sharing field. Another advantage of open projects in biology is the human data is that availability of the genome project. The sequencing underlying data used to generate of the human genome was a the figures in a paper makes it massive undertaking, by many easier for others to reproduce the researchers across the world. work. This complete transparency The results of their efforts have of data also discourages greatly advanced many areas of researchers from falsifying research and healthcare over the figures in their publication. past decade and a half, but none Too often people get away of that would have been possible with Photoshopped images or if the genomic sequences had not duplicating images from different been widely available. Imagine if studies, and that is much easier every time you wanted to align to catch if the underlying data a DNA sequence or generate is available. Another important PCR primers you had to ask for advantage of open data is that permission, or worse, pay for use it allows datasets to be easily of the information. aggregated for meta-studies.

Instead, anyone can freely download human genomic data,

use it without asking for explicit permission, re-analyse and

Guide to open science publishing | 12 Regulations and principles To encourage data sharing of all for data sharing in biomedical types of data, F1000Research and research (since early 2014) PLOS require their authors to make all data There are a number of underlying their articles openly organisations that recommend, available from the moment of regulate, or advise the use of data publication of the article. sharing in research. A few of them are listed here, and each of their websites includes much more information: Credit for data publication

»» NIH data sharing policies Another incentive for data http://www.nlm.nih.gov/ sharing is to provide credit for NIHbmic/nih_data_sharing_ data. Researchers now generally policies.html get professional credit only for published articles. A few journals »» Biosharing – a resource of now allow researchers to publish various policies, standards and data sets in the form of a research databases for the sharing of article, such as F1000Research research data. (data notes), GigaScience, http://biosharing.org/ Scientific Data and Data. The requirements for such articles »» Wellcome Trust Guidance for (often called “data notes” or researchers: Developing a data “data descriptors”) are that they management and sharing plan include only a brief introduction, http://www.wellcome.ac.uk/ methods, and results – but no About-us/Policy/Spotlight- interpretation. F1000Research issues/Data-sharing/ has had confirmation from many Guidance-for-researchers/ major publishers that this sort index.htm of publication will still allow researchers to later use these Panton Principles for open »» same data sets in another, more data in science in-depth, publication. http://pantonprinciples.org/ Over time, a better way to receive

credit for data would be for Incentives for data sharing funders and institutes to formally Guidelines are a good first recognize data deposition and step, but there also needs to open data sharing as a valuable be an incentive for researchers contribution to research, but until to comply with the guidelines. that happens, this is one way to Funders may ask you to share formally turn unanalysed data into your data, but often lack the a tangible credit. resources to ensure that you really do. To overcome a similar lack of (mandated) open access publication, NIH no longer renews grants if the grantholder did not make their work available by open access standards. A similar enforcement for open data is not (yet) in place.

At the moment, if you want to publish work based on certain formats of data, such as microarray screens or protein structures, journal editors will ask you to deposit your data in a suitable database within a certain period of publishing your article, but they often aren’t able to follow up and make sure that an author has really deposited their data within the required period after publication.

Guide to open science publishing | 13 REFERENCES & RESOURCES FURTHER READING All about the human genome project Wikipedia page on open science data http://www.genome.gov/10001772 http://en.wikipedia.org/wiki/Open_ science_data Panton Principles for open data in science http://pantonprinciples.org/ Open knowledge foundation’s Open definitionhttps://okfn.org/opendata/ Biosharing – a resource of various policies, standards and databases for Guidelines on Open Access to the sharing of research data Scientific Publications and Research http://biosharing.org/ Data in Horizon 2020 (11 December 2013) http://ec.europa.eu/research/ NIH data sharing policies http://www. participants/data/ref/h2020/grants_ nlm.nih.gov/NIHbmic/nih_data_ manual/hi/oa_pilot/h2020-hi-oa-pilot- sharing_policies.html guide_en.pdf F1000Research data sharing information http://F1000Research. com/data-preparation FAQs about PLOS data sharing policy http://www.plos.org/plos-data-policy- faq/ Upcoming Changes to Public Access Policy Reporting Requirements and Related NIH Efforts to Enhance Compliance (November 16, 2012) http://grants.nih.gov/grants/guide/ notice-files/NOT-OD-12-160.html Varsha Khodiyar: Moving to a new research project? Give your old data a new lease of life… (6 May 2014) http://blog.F1000Research. com/2014/05/06/give-your-data-a- new-lease-of-life/ Can I publish an analysis of my published dataset in other journals? http://F1000Research.com/data- policies Format of Scientific Data data descriptors http://www.nature.com/ sdata/for-authors#format Format of GigaScience Data Notes http://www.gigasciencejournal.com/ authors/instructions/datanote

Guide to open science publishing | 14 Lab bench image by cjp24. Licensed under CC BY SA 3.0 via http://commons.wikimedia.org/wiki/File:Paillasse_chimie.jpg Re-used under license conditions. What is open science?

Open science is the concept of This is quite a radical form opening up all aspects of scientific of openness, and few bench research, to allow others to follow scientists use a fully open Major funders are the process and collaborate. There notebook system at the moment. is no formal definition of open The general reluctance of many increasingly insisting science, but it usually incorporates researchers to share ongoing that underlying some of the aspects covered in research data is the fear of being previous chapters, such as open scooped by competing groups data be shared access, open peer review, post- in academia or industry, as well as being unsure whether they publication peer review, and open can still publish the work in their openly, in addition to data. Additionally, it includes journal of choice afterwards. With other ways to make science more publications. the increased use of preprints transparent and accessible during in biology, more journals are Crowdfunded the research process, and we will developing guidelines about discuss them here: open notebook whether they will consider researchers are also science, , and publishing previously shared aspects of research, which may alleviate often incentivised to software and crowdfunded some of the concerns about share their work with research projects. putting lab notes online. their funders. Open notebook science shares some similarities with open data: Open notebook science both make the underlying research data public. However, where data While some groups use online, sharing can occur at the point of password protected, lab publication of the resulting journal notebooks to share notes with article, or after a conference (e.g. collaborators, open notebook by uploading a conference poster science takes this a step further or slides), open notebook science by making day-to-day lab notes happens “live”: data and methods available in real time. By keeping are made public at the moment notes online, rather than in of collection. an offline lab notebook, open notebook scientists are giving everyone direct insight into their work, and enabling easier Citizen science collaboration. For example, you One of the most traditional uses can find open notebooks on of collaborative OpenWetWare (biology and data predates the open science biological engineering), Open movement: citizen science. Here, Notebook Science Network members of the public, who are (chemistry and other disciplines), often not scientists themselves, or The IPython Notebook participate in the collection (interactive computational (and sometimes analysis) of science). scientific data.

Guide to open science publishing | 15 The oldest running citizen science Crowdfunding Open drug discovery project is the Audubon Christmas Bird Count, which started in the Another feature that is sometimes Open drug discovery combines year 1900. In this bird count, and included under “open science” open notebook science, citizen in similar surveys run subsequently is the crowdfunding of research science and open source science by other organisations (see projects. It should be noted, to find new drugs. Different “further reading” below for a few though, that crowdfunding groups use slightly different examples), people are asked to does not require open science: approaches, but all are based on take note of wildlife in their area, researchers can crowdfund closed open science principles. The Open and report which animals they research projects as well. Source Drug Discovery platform, encounter. This sort of work helps based in India, uses community However, like citizen science, ecologists survey populations in participation for initial candidate involvement of a large group large areas, and informs long-term target discovery, and works with of people in the work (now at conservation studies. Since data researchers in academia and the funding level rather than at are collected by citizens, they are hospitals to then synthesize and the data collection stage) often usually made available to test the targets. Other groups are encourages researchers to make the public after analysis. The focused more specifically on one the output openly available so Audubon counts, for example, are disease, such as the Open Source that donors can have access to the on their website. Malaria project, which uses an results of the work. open notebook approach to share In recent years, citizen science all ongoing work. Various other Usually, successfully funded projects have moved to the collaborations are in place to find projects have a clear goal, a small web. Over a million people and test drug targets for a wide budget, and intriguing perks. are registered to participate range of diseases. There are exceptions: one of in Zooniverse’s citizen science the most highly crowd-funded projects, which involve anything science projects is the ARKYD from hunting for planets to space telescope by Planetary Future of open science counting penguins. These web- Resources, which raised 1.5 million based citizen science projects In this guide we’ve looked at US dollars. Crowdfunding often have a very low threshold for several aspects of open science: only works for distinct projects participation, and only require open access, open peer review, and is difficult to scale to running an internet connection and a few post-publication peer review, open a lab long-term. That being said, minutes of time during coffee data, and the topics listed above. the California-based Perlstein Lab breaks. In all cases, they are That leaves a final thought: What did start out as a crowd-funded research projects where human is the future of open science? project, but is currently run as a eyes work better than computers, seed-funded startup company. and where researchers need help Open access has been growing from a large group of individuals steadily over the past decade, and to analyse a large dataset. open peer review is becoming Open source software more popular. Many major Another type of citizen science funding organisations are asking uses computer games to perform Open science also overlaps for not just publications, but scientific calculations: Foldit is a with the open source software also the underlying data to be game that lets players find the movement, which advocates the shared openly, and crowdfunded best protein-folding conformation, use and development of software researchers are also often after which human-driven intuitive that has its source code made incentivised to share their work protein folding solutions are used available to others to re-use and with their funders. Meanwhile, to optimize computational protein build upon. citizen science has been around folding calculations. for over a century, and is Open source software for science only growing with novel web Such projects fall under open includes projects like the BioJS applications that enable everyone science because the researchers library of graphical components, to participate in scientific research are allowing anyone to interact which anyone can use or build and drug discovery. Online post- with their data, but they do on to represent and visualise publication peer review is still restrict and control that analysis biological information. quite new, and open notebook to their own platform. In most science has not spread very far cases, they will make the resulting At the moment, a lot of scientific yet, but both of these are steadily publications available to everyone research and communication growing as well. (both Foldit and Zooniverse still relies on software that is not provide scientific publications open source, and many open So despite researchers’ fear of via their sites), and in exceptional science proponents will, where an competition, and a reward system situations, citizens who equivalent open source alternative that still favours publication participated in these projects may is not available, use software in exclusive journals (where even be listed as co-authors. that is not open, but will make openness is not a main concern), sure the output of their own scientific research is gradually work (including software they moving towards an open produced) is openly available. science system.

Guide to open science publishing | 16 REFERENCES & RESOURCES FURTHER READING Open Notebook Science Network Center for Open Science http://onsnetwork.org/ http://centerforopenscience.org/ Open WetWare: Open Science Federation http://openwetware.org http://opensciencefederation.com/ The IPython Notebook Mozilla Science http://ipython.org/notebook.html http://mozillascience.org/ Audubon Christmas Bird Count Open Science at the Open Knowledge http://birds.audubon.org/christmas- Foundation http://science.okfn.org/ bird-count Open Science Framework Audubon Christmas Bird Count data https://osf.io/4znzp/wiki/home http://netapp.audubon.org/ Science Commons principles for open cbcobservation/ science http://sciencecommons.org/ Zooniverse resources/readingroom/principles-for- https://www.zooniverse.org/ open-science/ Foldit publications Woelfle M, Olliaro P, Todd M (2011) http://fold.it/portal/info/ Open science is a research accelerator about#folditpub Nature Chemistry 3, 745–748 ARKYD: A space telescope for Helen Shen: Interactive notebooks: everyone. (Kickstarter funded 1 July Sharing the code (5 November 2013) https://www.kickstarter.com/ 2014) http://www.nature.com/news/ projects/arkydforeveryone/arkyd-a- interactive-notebooks-sharing-the- space-telescope-for-everyone-0 code-1.16261 How a biotech startup juiced investors The Monarch Program – monitoring with yeast, flies and zebra fish (1 monarch butterflies August 2014) http://www.monarchprogram.org/ http://www.bizjournals.com/ Scistarter – database of active citizen sanfrancisco/blog/biotech/2014/08/ science projects http://scistarter.com/ perlstein-lab-ethan-martin-shkreli- ngly1-biotech.html?page=all SciFund Challenge - helps researchers communicate more clearly about BioJS http://biojs.net/ their work, so that they can be more Corpas M, Jimenez R, Carbon SJ et al. successful in crowdfunding. BioJS: an open source standard for http://scifundchallenge.org/ biological visualisation – its status in Experiment.com 2014 [v1; ref status: indexed, https://experiment.com/ http://f1000r.es/2yy] F1000Research 2014, 3:55 (doi: 10.12688/ Petridish http://www.petridish.org/ F1000Research.3-55.v1) Kraker P., Leony D., Reinhardt W., Open Source Drug Discovery & Beham G. (2011). The Case for an http://www.osdd.net/ Open Science in Technology Enhanced Learning. International Journal of Open Source Malaria Technology Enhanced Learning, 6(3), http://opensourcemalaria.org/ 643–654.

Sabou M, Bontcheva K, Scharl A (2012) Research Opportunities: Lessons from Natural Language Processing. In: 12th International Conference on Knowledge Management and Knowledge Technologies, Special Track Research 2.0 (#STR20) , 5-7 September, Graz, Austria. MacLean D (2013) Cutting edge: Changing the rules of the game eLife 2013;2:e01294 Li FW, Pryer KM (2014) Crowdfunding the Azolla fern genome project: a grassroots approach, GigaScience 3:16 Masum H, Rao A, Good BM, Todd MH, Edwards AM, et al. (2013) Ten Simple Rules for Cultivating Open Science and Collaborative R&D. PLoS Comput Biol 9(9): e1003244. doi:10.1371/ journal.pcbi.1003244

Guide to open science publishing | 17 The F1000Research Publishing Process

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Shaping the Future of Research: a perspective from junior scientists [v2; ref status: indexed, http://f1000r. es/4yc] Gary S. McDowell, Kearney T. W. Gunsalus, Drew C. MacKellar, Sarah A. Mazzilli ... Ayesha Islam, Matthew D. Mattozzi, Kristin A. Krukenberg, lipofsky.com Jessica K. Polka

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