Publishing News in 2016 – an Overview

Publishing News in 2016 – An Overview

Dear Reader,

The landscape in the publishing industry is constantly changing and evolving. It can get quite

challenging to stay updated on the latest happenings, products, and innovations around the world.

We have tried to compile some of these in this free downloadable e-book and hope that you find

them informative.

We have also added some popular links at the end as additional resources that you can refer to.

These pieces will also lead you to the original sources, which will definitely provide you detailed

information.

Happy Reading!

Regards,

Enago Academy Team

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Contents

Recognizing Peer Review through Publons ...... 4 Using Publons ...... 4 Growing Partnerships ...... 4 Sentinels of Science ...... 4 Yewno for Education: A New Approach to Knowledge Discovery ...... 5 Using Yewno ...... 5 Yewno for Education ...... 5 A Promising Tool ...... 5 Reaxys: Chemistry Search Engine by Elsevier ...... 6 Who uses Reaxys? ...... 6 New Updates to Reaxys ...... 7 ChemSearch Challenge ...... 7 Research Ideas and Outcomes (RIO) Journal: Making the Research Cycle Public ...... 8 Making the Research Cycle Transparent ...... 8 Collaborative Writing and Review ...... 9 Good for Scientists, Good for Science ...... 10 How is Sci-Hub Affecting Academic Publishing? ...... 10 Publishing Process and Journal Access ...... 10 Effects of Sci-Hub ...... 11 Moving Forward ...... 11 The Journal of Brief Ideas is Making Your Ideas Citable...... 12 Archiving Intellectual Capital ...... 12 Benefits for Researchers ...... 13 Quality Control ...... 13 Sparrho: An Innovative Way to Remain Updated ...... 13 Channels and Pinboards ...... 14 The Discovery Engine ...... 14 Revolutionising Science ...... 14

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Important Global Events ...... 15 Open Access Week ...... 15 Peer Review Week ...... 15 Brexit: It’s Impact on Research in the UK ...... 15 The Nature scandal ...... 15 Some Important Links ...... 15 Latest News ...... 15 Featured Interviews ...... 15 Manuscript Preparation Resources ...... 15 Author Workshops Conducted by Enago ...... 15

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Recognizing Peer Review through Publons

The peer review process is a crucial part of scholarly communication, but without good referees, the system would not work. However, researchers barely get credit for this important job. To ensure that reviewers receive the appreciation they deserve, scientific publishers and peer review institutions have started an initiative to recognize peer review. You must have read our recent article on Publons, an online platform that helps researchers track, verify, and showcase their peer review activity across several journals. Publons also rewards top referees several times per year. Using Publons Publons, which was launched in 2012, already has more than 80,000 registered members. Researchers who sign up to Publons can use their verified peer reviews and editorial records for funding and promotion applications. Also, using the service does not affect reviewer anonymity. By default, the content of the reports is not publicly displayed and only the year of the review and the name of the journal appear on a reviewer’s profile. The content of the report can be made open access after a paper has been published only if both the reviewer and the journal agree. Growing Partnerships Four years after its inception, Publons already has partnerships with several leading scientific publishers, such as BMJ, SAGE, Cambridge University Press, Springer Nature, IOP Publishing, and Wiley. It also works with ORCID such that scientists can easily connect their reviewer activities to their ORCID record. Following a six-month pilot program conducted in 2015, Wiley recently announced that more than 750 of its journals will be integrated with Publons. The 2015 trial showed an improvement in reviewer acceptance rates for the pilot journals—and faster review times among the reviewers that opted in—indicating that referee recognition can be an excellent way to speed up the peer review process and let reviewers know that their work is being valued. Sentinels of Science A survey carried out in 2015 among nearly 3000 reviewers showed that researchers spend a huge amount of time evaluating other scientists’ work (they spent twenty-two million researcher hours reviewing papers for the top 12 publishers in 2013 alone). Most of the participants of the survey said that feedback from the journals they review for and acknowledgment are the best rewards for these efforts. In line with this, the first Peer Review Week was introduced last year to celebrate the fundamental role that peer review plays in ensuring scientific quality. The inaugural event was a success, and in September this year, more than 20 institutions gathered to organize the second annual Peer Review Week, which involved a number of activities, such as webinars, interviews, social media campaigns, and others. The highlight of this year’s event was the introduction of the annual Sentinels of Science Awards program, where Publons teamed up with

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top publishers and industry leaders to honor the “highest achievers in peer review across the world’s journals.”

Yewno for Education: A New Approach to Knowledge Discovery

Yewno is a new search engine that claims to mimic the workings of the human brain. In contrast to traditional tools, such as Google, Yahoo, or Bing, which are based on keyword search, Yewno is able to extract meaning from a great number of scholarly publications in the form of concepts. It enables searching for ideas rather than specific expressions. The platform uses a combination of full-text analysis, computational semantics, neural networks, and machine learning algorithms to visualize information, uncovering relationships between different sources. Using Yewno The platform explores connections between various pieces of information and displays them graphically. Two panels are shown: a graph or concept map on the left-hand side and a context bar on the right-hand side. Users can search for concepts they are interested in and then connect relevant ideas by clicking on them. After each search, a new graph showing orange and blue nodes appears. The orange nodes represent the main concepts and are centrally placed within the concept map, whereas the blue nodes show ideas that are related to the central concepts. Double clicking on the blue nodes adds specific ideas to the user’s map and discloses further connections. In addition, users can directly access content sources from the relevant nodes.

Yewno for Education The first product in the series of Yewno research tools—Yewno for Education—was launched in June this year and is currently being tested in the Beta phase. This new service for scholars and students is being tested by academic libraries at several prestigious institutions including Stanford University, Harvard, the University of California-Berkeley, and the Massachusetts Institute of Technology (MIT). The product uses a growing database that already contains millions of scholarly publications including journal articles, books, theses, and other documents from publishers, universities, and government institutions from all over the world. At present, most resources are in English, but new resources are being constantly added. High-quality content published by Springer Nature, Oxford University Press, and others is already “discoverable” in this new way. A Promising Tool Some librarians believe that Yewno could play an important role in supporting the development of critical-thinking skills. This might be particularly suitable for students at the beginning of a

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research project to analyze the landscape surrounding a particular topic. One of the main benefits of the new discovery engine is that it allows researchers to explore information across several disciplines in a simple way. However, users might get lost in all the cross-references, and although the content covered by Yewno already includes many academic publications, there are still some gaps in the system. This emphasizes the fact that technology can support but not replace proper research. Detailed investigations in libraries and archives remain a crucial part of academic work. Currently, Yewno for Education covers content in different areas, such as medicine and biology, physical sciences, humanities, engineering, social sciences, and others. In the future, the company expects to address other segments including financial services and news.

Reaxys: Chemistry Search Engine by Elsevier

Reaxys is a web-based tool that was launched in 2009 and is licensed by Elsevier. It allows chemists to retrieve chemistry information and data from published literature, such as journals and patents. The information it provides includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and chemical patents. Reaxys was formerly known as the CrossFire database. This tool serves as a chemistry database allowing researchers to access historical and current, relevant, organic, inorganic, and organometallic chemistry information, from reliable sources using an easy-to-use interface. The content in this database covers more than 200 years of chemistry and is basically an online chemical encyclopedia that contains relevant information for more than 7 million organic chemical compounds, inorganic compounds, and chemical and life sciences patents from the United States and the rest of the world. Currently, when new data is added it is drawn from selected journals and chemistry patents, wherein each reaction or substance data has to meet three conditions. It must have a chemical structure, must be supported by an experimental fact, and have a credible citation.

Who uses Reaxys? The goal in designing Reaxys was to enable chemistry research to reach new heights and is also meant to aid a number of organizations worldwide, including the pharmaceutical industry, chemical companies, and academic institutions. Pharmaceutical companies use Reaxys to boost drug development success and efficiency. It allows chemists to filter through potential compounds and obtain a promising set of hits. Reaxys benefits chemical companies because it aids in the development of chemical products by helping chemists optimize synthesis reactions and identify the required chemical properties in intermediate and end products. It also contributes to academia, because faculty and students at educational institutions use the tool to access and

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investigate chemistry literature and data, thus helping academic institutions to produce first-rate future chemists.

New Updates to Reaxys Since its first launch, there have been regular releases and enhancements to Reaxys bringing us to the latest product release that has been specifically tailored based on user requirements, innovative use of technology, and rigorous customer testing. This release promises to be a new gold standard for chemistry research tools. In addition, the new version now has an enhanced and streamlined user interface that includes the addition of critical patents and literature, a powerful new layer of indexing and data excerption, and is easier to integrate with existing informatics environments. The new search, analysis, and workflow tools are designed to meet the needs of the users. Overall, the goal of this new release is to ensure that even beginners can promptly get answers to questions, thus providing chemists with the shortest path to chemistry literature, data, and success. Here are several of the changes that were made in this release.

 Ease of use: The interface is now simplified making it easy for even novice users to quickly become experts. At the same time, experienced users will find it very capable of doing everything they expect it to do. For example, now, when performing a literature search, input into only one search field is required to start getting results.  Expanded content: The patent content now includes Asian language patents from Japan, South Korea, China, and Taiwan. In 2016, over 650,000 new compounds were added from Asian patents.  Better indexing: This release has also improved indexing capabilities, which covers more of the literature and searchable compounds. This includes being able to retrieve compound properties and reaction data from the full texts of over 16,000 journals and the entire patent content in Reaxys.  Improved integration: Reaxys now has an enhanced application program interface (API) that helps chemoinformaticians, medicinal chemists, and computational chemists query the database using their chosen system to then export the data to modeling tools.

ChemSearch Challenge In 2015, Elsevier launched the ChemSearch Challenge. Scientific output is doubling every nine years and this is being distributed through a growing number of digital channels making it more challenging for chemists to find relevant data quickly. The goal of the ChemSearch Challenge is to provide an assessment of the relative merit of different approaches of searching chemistry databases. In 2015, the challenge attracted nearly 1,700 participants from 442 companies and academic and government institutions around the world. The participants were given chemistry challenges and were allowed to use any chemistry search tool to solve the challenge questions. The first round of the challenge revealed that Reaxys users were able to find the correct answer more than twice as fast as users of any other chemistry research database. In 2016, Elsevier announced the second challenge, however, this time it provided all the challenge players with access to Reaxys through the ChemSearch Challenge platform. By completing one challenge, the users get a free 30-day trial of Reaxys. The 2016 challenge, is a series of 8 weekly online challenges for future and professional chemists to compete based on their chemistry search skills. The participants compete based on

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the speed and accuracy of their answers which helps them earn badges. The winners are announced each week, and Elsevier donates $200 to one of five charities in the winners’ name. The results of these challenges provide Elsevier with information about how the chemistry community can identify and understand bottlenecks in search tools and produce better products for chemists.

Research Ideas and Outcomes (RIO) Journal: Making the Research Cycle Public

Behind each reach study, there are research proposals that are either rejected or accepted, conference papers, posters, PhD theses, project reports, new workflows, and endless drafts that are never seen by anyone outside the research team. Thus, as scientists, there is a lot more that has to be accomplished, in addition to having articles being published in international peer- reviewed journals. Previously, a lot of research-related information such as grant proposals, conference proceedings, raw data, project reports, supplementary information could not be easily published or made accessible to a wide audience. However, now many scientists are trying to encourage the development of new publishing models that encourage the publication information related to the complete research cycle. The Research Ideas and Outcomes Journal (RIO) publishes all types of information, including project proposals, data, methods, workflows, project reports and research articles on a single collaborative platform, with the most transparent, open and public peer-review processes.

Making the Research Cycle Transparent RIO intends to make the whole scientific research cycle transparent, public, and open. RIO offers a whole platform for scientists to publish their entire research output, from their first research proposal and ideas, to their final results write up. By doing this, RIO aims to shed light on how science is actually done, the ideas that get rejected or remain incomplete, as well as share the long, mainly uncredited, process of scientific research. This initiative has two major benefits for the researcher. First—and perhaps most importantly from a career perspective—it allows researchers to get credit for their ideas and work from the very beginning. When a proposal can be published, whether successful or not, it can also be cited and added to his/her profile. Second, RIO allows researchers to connect all the research outputs from a single research project or group. This means that every conference paper, PhD thesis, new workflow or method, grant application can be published and the actual output produced in the lab can be seen by funding bodies, future employers, and possible collaborators.

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Collaborative Writing and Review This transparency also extends to their peer review process, which is entirely open and collaborative. Initial peer review occurs before submission and is a part of their open, collaborative writing tool: ARPHA. ARPHA stands for Authoring, Reviewing, Publishing, Hosting and Archiving and it aims to make scientific writing and publishing as painless and collaborative as possible. Within ARPHA, authors invite external reviewers to comment on the work to be published in an open, collaborative fashion. After submission and publication, the reviews themselves are published individually, with the reviewer’s name, and are citable. This innovation makes every step of the writing, revision and publication process visible and therefore holds reviewers accountable to their critiques, recommendations and language. In addition to mandatory pre-submission review, authors can also opt for further peer review, managed by the journal editors, which allows the publication to be revised further and to be marked as a valid publication. Alternatively, authors can opt out of this and publish the work as a reviewable publication, allowing the community to review and comment on the work.

RIO’s innovative and open review process encourages collaboration, and this is an extension of its novel writing tool on which all RIO publications are written. RIO itself has no formatting requirements as they wish to place the focus on writing of ideas rather than format and structure. The ARPHA tool has automated buttons for inserting citations, figures and tables. Moreover, references can be imported from a number of reference managers, and ARPHA offers instant and automated “technical validation” that identifies inconsistencies for the writer. ARPHA exists entirely online and encourages collaborative writing and aims to remove the need for having multiple versions of a single document by helping authors work on one common platform.

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Good for Scientists, Good for Science The wider aim of RIO is to change science itself, making it more efficient, open and effective. RIO aims to make ideas that do not get funded or new methods that never get published available to other researchers to comment on, reuse or suggest improvements. RIO wants everyone in the academic community, from funding bodies to PhD students, to be able to communicate openly about their ideas and take them forward into new, successful projects. RIO’s initiative for a better scientific research landscape could help encourage the development of similar platforms in the future by other publishers or funding agencies.

How is Sci-Hub Affecting Academic Publishing?

In 2011, Alexandra Elbakyan, a graduate student in Kazakhstan, started a website known as Sci- Hub. Since its inception, the site has gained an increasing amount of attention. In fact, from September 2015 to February 2016 over 28 million scientific papers were downloaded from Sci- Hub by many researchers worldwide. The downloaded articles were from major renowned journals like Nature and Science and also from smaller journals in specialized fields of science. Sci-Hub basically provides free access to over 50 million articles, and researchers can simply search by using the title of a paper or the DOI to gain immediate, free access thus making it an easy to use search engine for finding academic papers. Overall, the idea of free access to journal articles may seem like a great advantage for researchers all over the world, but in order to truly understand how Sci-Hub is turning the academic publishing world upside down we have to understand how publishing and access to journals is traditionally done.

Publishing Process and Journal Access There are essentially two avenues of publishing and accessing journals. In the first, researchers write and submit their manuscripts to a journal that then publishes the paper without a fee, but in order for other researchers to access the paper they must pay a fee. The second avenue is when a researcher writes and submits their manuscript and also pays a publishing fee thus, making their article open access so that other researchers do not have to pay to read the article. For the most part, researchers at major universities do not really notice a difference either way when it comes to access because most libraries at these universities pay to subscribe to the journals in order to

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provide access for their academic researchers. On the other hand, researchers from smaller less funded universities often lack such access because it just not affordable.

Effects of Sci-Hub Sci-Hub is creating havoc for both these avenues of publishing, as the type of open access created by Sci-Hub is basically considered piracy and therefore, is illegal. From the perspective of the first avenue, large academic journal publishers are against Sci-Hub because these publishers rely on their subscription services to generate revenue. If researchers can gain access to journals for free then why should academic organizations pay to get access to journal articles? This has led publishers to claim that Sci-Hub is seriously damaging the academic publishing world. From the perspective of the second avenue, researchers can pay around $2000 in publishing fees for an open access article and with Sci-Hub offering open access for all articles, researchers might be less inclined to pay these fees and might rather opt for publishing via the first avenue. This kind of thinking should be a part of research ethics considering its legality. Although researchers have accepted these two avenues for many years, there has always been an underlying frustration among researchers that paying such ridiculous costs and having a paywall for information they submitted and reviewed for free is simply too much to pay. Sci-Hub is now facing a lawsuit for piracy. However, Elbakyan is motivated to push through this lawsuit. She is not aiming to be an activist, but is actually trying to get the academic publishing industry to change. Her goal is to make academic research freely available to anyone and this revolves around the notion of open access. In general, open access articles end up getting more citations than paid articles, which makes sense because researchers must be able to read the article in order to cite it, and since open access articles are available to all researchers they are going to be cited more frequently. Researchers desire access to articles and some publishers provide this access for a fee. However, Sci-Hub removes the need for all these types of fees.

Moving Forward Interestingly, fees for journal access have grown increasingly high and it is becoming more and more common for researchers to be unable to access even their own published work, as even the wealthier universities are unable to pay these rising fees. Because of this, we see changes arising as researchers are beginning to fight back against the problems caused by closed-access publishers. This is the main reason many researchers are turning to Sci-Hub, and in spite of the growing legal pressure that it faces, Elbakyan continues to push forward. Sci-Hub seems to be here to stay, and although the actions behind Sci-Hub are clearly meant to provide everyone with free access to academic research, the approach taken is wrong and unethical.

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The Journal of Brief Ideas is Making Your Ideas Citable

In this age of information overload, there are several ideas that can be considered innovative or can lead to a new scientific development. Given the extent of information that is being accessed, there are several potential ideas that can be considered; however, there is no medium to record this. The Journal of Brief Ideas, the beta format of which was launched in 2015, publishes short ideas within 200 words. Their objective to record ideas in such a form is drawn from the old tradition of European journals, where scientists primarily published short letters outlining their ideas and on-going research, rather than in extensive papers that are written after years of work. This journal was co-founded by David Harris, a former astrophysicist, who was also previously the founding editor-in-chief of Symmetry magazine and the founding magazine section editor of the Proceedings of the National Academy of Sciences and Arfon Smith who is a scientist at GitHub and co-creator of the Zooniverse. Their aim is to provide a space for scientists to archive and maybe start discussions about the unformed, early, and small ideas that they are considering while conducting large-scale research. Harris argues, “Good scientists have far more ideas than they know what to do with,” and this journal provides a platform for scientists to do something, albeit something small, with these ideas.

Archiving Intellectual Capital Harris and Smith call these early ideas “intellectual capital” and hope that The Journal of Brief Ideas will allow that intellectual capital to be placed in a searchable, citable, and archivable format. Other researchers can then explore the ideas that have been uploaded by searching category tags, comment on them, and start new conversations. The ideas can be submitted in less than 200 words, as long as the users have an ORCID profile. Ideas are written directly within the journal’s online platform and can be instantly submitted and approved. The users do not need to add references, although they can be included with an embedded link function. The ideas, therefore, are quickly and easily uploaded onto the site by just about anyone, and with very little effort. The journal does not have a peer review process, as the editors argue that peer review reports would likely be longer than the ideas themselves. Thus, they encourage readers instead to “review” ideas through the user rating button or to respond with critique and suggestions in the comments section that is attached to each submitted idea. Their aim is to encourage researchers to submit their ideas and brief thoughts with the least effort possible and to remove any barriers to submission. They aim to stimulate conversation and potential collaboration, not act as gatekeepers of appropriate ideas. To facilitate this, researchers can also create Collections to help them track interesting ideas, save them for the future or follow conversations that occur in the comments section of each idea.

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Benefits for Researchers First, the primary and most immediate benefit of publishing in the journal is, of course, credit for your ideas. Every idea that is submitted is archived has to be given an ORCID reference, which means that it is immediately added to your ORCID profile and can, therefore, be cited and added to your CV. So, by publishing in the journal you could demonstrate a list of ideas that you have thought of to various hiring committees and collaborators with whom you would like to work in the future. Second, submitting an idea to The Journal of Brief Ideas helps form a list of ideas that you may have considered. In particular, when a long project is coming to an end or when it comes time to explore new research possibilities, the ideas that you have submitted to the journal could act as a convenient way to start new research collaborations. Finally and perhaps most importantly, submitting an idea to the journal opens it to critique and conversation much earlier in the research process than is usually possible. Moreover, it opens the idea to a much wider range of readers at a very early stage, which means that more perspectives and voices can be heard and potential collaborators can be immediately found, no matter where they are in the world. This means that the potential (or lack thereof) of an idea can be demonstrated early, those that have no potential can be immediately discarded, and researchers who may be able to help can be identified. Thus, The Journal of Brief Ideas can function as a form of collaborative, open notebook for the individual researcher, where “intellectual capital” is shared, cited, and developed.

Quality Control There are, of course, challenges in this extremely open model. When anyone can submit anything, there is always the possibility that ridiculous, offensive, or pseudo-scientific ideas will overwhelm sincere ideas that are being discussed. Thus, the journal tracks the overall content that is being published and ideas that do not meet the necessary logical flow or seem silly or offensive are taken off to ensure that the target audience continues to use the platform.

Sparrho: An Innovative Way to Remain Updated

When Vivian Chan was studying for her PhD in Biochemistry, she encountered a problem that most scientists have confronted: how can you keep yourself updated with the enormous amount of new research that is being published every day? In fact, for scientists, it is getting increasingly difficult to remain updated with the latest developments in their own field of expertise. Generally, nowadays it has become the norm to read journal articles, RSS feeds, and email updates every morning, thus missing updates on a single day can make it very overwhelming for an individual researcher.

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To overcome this issue, Chan built her own unique solution, Sparrho, which is a science recommendation engine that looks like a familiar social networking or news aggregation site. Sparrho combines the power of machine and human intelligence to find recommendations and aims to make the process of finding new, relevant research within your field of interest easy as possible. Sparrho’s database includes updates on journal articles, grant announcements, patents, to conference proceedings and so on, which helps researchers see everything they require in one place.

Channels and Pinboards Sparrho’s clean look and user interface has been inspired by popular social networking platforms. While using Sparrho, a user can search for keywords or journal titles, the results of which can be saved as personal channels. In this manner, users can have access to a number of personal channels and Sparrho updates these channels hourly such that the newest content is present at the top. Sparrho also allows users to save and share useful articles using pinboards, which can be private and used to collect articles for personal use, or can be shared with colleagues or interest groups such that users can collaborate, run virtual journal clubs, or simply share interesting studies.

The Discovery Engine Sparrho used a discovery engine that uses natural language processing to develop a semantic understanding of each user and their requirements such that channels and news feeds are truly relevant and offer useful results. This engine can search and categorize over 45,000 journals every hour. Sparrho personalises channels and feeds even further by tracking the interaction of users, as well as identifying what they share, read, and save. This allows the discovery engine to identify overlapping interests and show results that may be useful based on these interactions. Sparrho also offers users to rate individual results as relevant or not relevant, so with increase in usage, it is able to give better and relevant suggestions to its users. Revolutionising Science Sparrho aims to create a revolution by democratising science and disrupting traditional disciplinary boundaries. Unlike Scizzle and PubChase, which are platforms similar to Sparrho but focus on life science, Sparrho includes suggestions from multiple disciplines and data forms. Thus, Sparrho allows researchers to easily find novel and important research as well as offer a brand new, user-friendly, and exciting way to do better science.

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Important Global Events Open Access Week https://www.enago.com/academy/open-access-week-2016-open-in-action/ Peer Review Week https://www.enago.com/academy/what-is-peer-review-week/ https://www.enago.com/academy/peer- review-week-2016-recognition-review/ Brexit: It’s Impact on Research in the UK https://www.enago.com/academy/brexit-impact-on-research-in-the-uk/ The Nature scandal https://www.enago.com/academy/author-accused-of-misconduct-for-stem-cell-papers/

Some Important Links Latest News https://www.enago.com/academy/category/industry-news/publishing-hot-topics/ Featured Interviews https://www.enago.com/academy/category/featured-interviews/ Manuscript Preparation Resources https://www.enago.com/academy/category/academic-writing/ Author Workshops Conducted by Enago https://www.enago.com/academy/author-workshops/

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