Author: drgunn

Changes to the Elsevier manuscript sharing policy: how they affect Mendeley & you

drgunn

On April 30th, Elsevier updated its policies regarding how Elsevier papers may be used to more closely align with the STM Association principles and to address usage on social networks, which have become popular since the last time the policy was updated (yeah, it was that old!) For Mendeley and other sites on which research is shared, the main thing is that there are fewer restrictions on what sorts of use are permitted, but we also get some technical help with a new article tagging proposal.

What it means for a Mendeley user

The day-to-day experience of a researcher using Mendeley won’t change. We plan to use the new machine-readable information in the PDFs to improve our catalog search, recommendation features, and article-level information available via the Mendeley API. We would also like to encourage researchers to add the new author manuscripts to their researcher profiles.

While we continue to dream of and work towards a world where all research is available to anyone without restriction, this is a welcome step forward. At Mendeley, we worked closely with Elsevier to ensure these changes help the whole scholarly communications ecosystem – researchers, publishers, librarians, and developers of new technology – and found Elsevier a willing and forthcoming partner in our work to meet the changing needs of of researchers. For any new startups that have bold new ideas about how to make research better, get in touch with Alicia or Alexandra – they don’t bite!

What we like about the policy

  • We like that the policy is much simpler to understand. The old policy was complicated and had all sorts of exceptions. Simpler policies allow us to provide a better user experience.
  • We like that the policy is not too prescriptive re: sharing platforms. The online world changes rapidly and it’s good that Elsevier is signaling willingness to work with existing sites and whatever YikYak-for-research might be yet to come.
  • We like that author manuscripts have a CC license applied. This helps remove the uncertainty about reuse permissions.
  • We like that the policy isn’t just words – a proposed new standard for article tagging, to be developed in collaboration with sharing platforms and other publishers, will make it easier for us to build advanced search and discovery features, as well as to provide better article usage stats to Scopus, Altmetric.com, Plum Analytics, etc. Importantly for stats, the machine-readable tags will now include information such as article license & document version.

The above changes aren’t just good for us, they’re good for everyone – Mendeley user or not. We understand that researchers need a range of tools and services to support their work, so we worked hard to ensure these changes help the whole scholarly communications ecosystem – researchers, publishers, librarians, and developers of new technology. Of course, we’re on the progressive end of things at Mendeley, so there are some parts of the policy we don’t feel goes far enough.

What we don’t like about the policy

  • The author manuscript embargo. We believe that libraries and researchers will still value the permanently archived, DOI-linked, more readable and fully-citable version of record, regardless of the prevalence of author manuscripts. We’re not alone in our dislike of this, either. Harnad and Kevin Smith single this out as the main issue. Here’s the thing – it’s entirely reasonable for Elsevier to worry that IR copies might end up substituting for publisher copies. If librarians and researchers do actually value the permanently archived, DOI-linked, and variously enhanced version of record, you need to make your voices heard on this so that we can get policies based on evidence and demand, not worry and risk projections.
  • The NC-ND bit of the Creative Commons license on author manuscripts. The NC license will create confusion about use of the work in academic settings and the ND license will cause uncertainty in applications such as text-mining. For what it’s worth, we have been told the license isn’t intended to restrict use in classrooms or text mining.
  • The distinction between commercial and non-commercial sites. We don’t like that for-profit enterprise is singled out as if we’re somehow more risky to partner with. Mendeley reached out to Academia, ScienceScape, MyScienceWork, Pubchase, Sparrho and others for guidance as we worked with Elsevier, and their feedback has helped shape the policy. We would therefore like to suggest that the disdain we sometimes encounter within academia for for-profit enterprise is misplaced.

    • Overall, we think the positives outweigh the negatives. Though there’s bound to be some cases where one particular part of the policy has an outsized and unforeseen effect – this is inevitable when trying to restrict use of digital content – they are not presenting this policy as cast-iron and immutable for the next decade, so please let them know if some part of the policy is really ill-suited to your particular application.

    There’s one other thing we’d like to mention. It’ll do no good if this overture from Elsevier is ignored or repudiated, so we’d also like to suggest that criticism of the policy be done with a fresh set of eyes. We’re not suggesting that the past be forgotten and we’re certainly no stranger to grand-standing and revolutionary rhetoric, but we also think good behavior should be rewarded if there is to be more of it. Embargo aside, this does lift the burden somewhat on those trying to innovate in the scholarly communications space, so that’s why it is, on balance, a positive step forward in our eyes.

    Mendeley supports the FORCE11 Data Citation Principles

    drgunn

    Mendeley was at the very first “Beyond the PDF” meeting in San Diego, which grew into FORCE11. We have been engaged with this community for almost as long as we have existed as a company, and though we aren’t on the group which drafted these principles and as yet have no formal stake in data management, we know personally and frequently interact with many of the people who are and do, thus we think it’s important that we announce our support for their work.

    The Data Citation Principles cover a wide range of issues related to data, including specific issues relevant to us, such as credit, attribution, research impact, unique identification, and access. After all, what good is a citation that fails to resolve to the cited object, for either the citing or cited entity, and thus what use are they to a citation manager?

    With our work as a leader in the altmetric community, we support researchers getting credit for all their work, not just that which is presented as a narrative publication. Looking at the broader research ecosystem, we can see that we must connect the whole provenance trail from the generation of the raw data to the publication of the figure to complete the cycle from reading and post-publication peer review to the generation of new hypotheses, protocols, and experiments. To this end, we’re also working on reproducible workflows with the Reproducibility Initiative, the importance of which was highlighted by a recent Nature editorial from the Director of the NIH and featured in today’s Elsevier Connect article from Genomics Data.

    Congratulations to the FORCE11 team and the Data Citation Synthesis Working Group for taking this important step forward.

    Read and add Pubmed papers to Mendeley on your Android device with Pubchase

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    Mendeley - PubChase Sync

    If you’re a life science researcher, you’re in luck. There’s now a way for you to search PubMed and add to your Mendeley library from your Android device. Pubchase is a new Android app from Zappylabs, a mobile development company that specializes in life science. Here’s what the app offers:

    • Search PubMed and add papers to your Mendeley library from your Android device (works on iOS too).
    • Read your Mendeley papers* on your Android device
    • Get life-science specific recommendations from PubChase, based on your Mendeley library, with no need to build a separate library in PubChase.

    PubChase also has a neat section with essays written by other researchers about papers which may be of interest to you. Please note, however, this is just a way to get PubMed papers from Android into Mendeley and Mendeley papers into PubChase. PubChase isn’t a Mendeley app. Here’s what Lenny from PubChase has to say:

    The forte of ZappyLab is mobile and web technology. We have no plans to build citation management plugins. So, from the beginning, we wanted to make it easy for our users to import their libraries from Mendeley, Papers, Endnote, and other software. However, adding newly recommended papers to your PubChase library means that you then have to export your PubChase library to the other software when writing a paper. The Mendeley sync greatly simplifies this process. Though our Endnote and Papers users keep asking for a similar integration, those tools do not have open APIs, so it is not an option for us. Therefore, we will be focusing our developmental efforts on deeper integration with Mendeley.

    The conclusion of that paragraph is precisely why we make the Mendeley API available and we’re happy to feature them on our Developer Portal. We hope to see great things from PubChase and from all the other talented developers using our platform to serve their constituents.

    To get started with PubChase and the Mendeley Sync, follow the instructions at Pubchase.

    *I know many of you are disappointed we don’t have an official Android app for Mendeley. We’re working on it for the new year and think PubChase and Mendeley will be a nice pair for life science researchers who use Android.

    Crowdsourcing and the value of curation – Mendeley pairs with F1000 Prime to recommend great research.

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    Image via psd

    What makes Mendeley more than just a reference manager is the community of researchers who use our tool to share research, recommend papers to others, and collaboratively work together. In practical terms, what this means is that the work of finding and organizing a collection of papers about a specific topic can be shared by a group of people via Mendeley Groups. Hundreds of thousands of you have created groups and saved your colleagues hundreds of thousands of hours, which I like to think has made research progress at least a little faster. But the benefits of groups go beyond crowdsourced literature discovery – you can annotate and comment on the collection of papers as well. There’s recently been quite a lot of activity around the idea of commenting on research, given the high-profile launch of Pubmed Commons and the growing attention given to tools such as PeerLibrary and PubPeer. We believe that post-publication commenting on research can become an important part of scholarly communication, but the past few years of our experience and the experience of PLOS shows that much of the literature doesn’t elicit comments, for whatever reason. Here’s where we feel a combination of traditional editorial insight into what is attention getting can be blended with the crowdsourced approach to yield high quality comments on high quality research. Our first experiment with this is the launch of F1000 Prime recommendations on Mendeley. Check out these great papers chosen by experts in Bioinformatics and Computational Biology in the first of what I hope will be a series of F1000 Prime groups. You can read F1000’s take here.

    This content normally requires a subscription, but is made available free in the group. Just follow the group to get updates!

    The Reproducibility Initiative, supported by Mendeley data, gets $1.3M to replicate key findings in cancer biology.

    drgunn

    The Reproducibility Initiative, a project we’ve written about before, has reached a major milestone. They have been awarded $1.3M in funding from the Center for Open Science and the Laura and John Arnold Foundation to replicate 50 key findings in cancer biology. Mendeley has supported the initiative by helping to design the selection process for papers, using Mendeley readership in addition to traditional citation measures.

    We try to keep ahead of the issues in research, pushing for open access and better tools for researchers, and over the past few years, from the Stapel affair in psychology to the reports from Bayer and Amgen reports of their failures to replicate most of the high-impact biomedical research they have studied in-house, reproducibility has emerged as a key issue. This comes as no surprise to us, and in fact, John Ioannidis’ paper “Why Most Published Research Findings Are False” has been one of the all-time most highly read papers on Mendeley.

    Read More »

    Mendeley's top time-saver tips for early career researchers.

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    So you’ve slaved away all year long, passing up pool party and barbecue invitations to feed the needs of the research beast, and you’ve finally got something to show for it. The next question is how do you get it published, where, and what do you do after that so it doesn’t end up with two readers, one of which is your mom? We won’t presume to tell you where, but we do have a few tips for things to consider, which you may have missed because you were slaving away at the bench or in the library like a good student and not reading up on all the cool stuff that’s happened this summer in the exciting world of academic publishing. So here’s our summary of the new (and we presume you’ve already heard the old from your PI).Read More »

    New Release: Literature Search from within Mendeley Deskop

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    [Editor’s Note–We thought you’d like to know: this 2013 post is a bit dated. Find Mendeley’s updated search features here, and info about Mendeley’s other features in the Mendeley Guides.]

    Often the most impressive thing about a new software release is infrastructural and not immediately apparent, but not this time! In our latest release, we have added one of our all time most requested features – literature search from Mendeley Desktop. Also included in this release are a few improvements to how Mendeley Groups work, making it easier to collaborate with others using Mendeley.

    We’ve always had the vision of Mendeley Desktop and Mendeley Web working as parts of a whole, but there have been some gaps, perhaps most notably how research discovery works. For example, to search your existing collection of research, you’d use Mendeley Desktop, but to search for new research in Mendeley’s catalog, you would go to the website. With the latest release, you’ll see a new section in the folder tree in the left pane. Where there was previously a division between My Library and Groups, there’s now a new section for discovery tools, hosting a literature search tool and Mendeley Suggest, our research recommendation service which learns about your academic interests and recommends new research specifically for you. There will be more discovery tools coming to this space, but for now let’s focus on how to use catalog search from Desktop.

    Read More »

    Wish PeerJ Charlie a Happy Birthday!

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    Our friends at PeerJ published their first articles on the birthday of Charles Darwin (Feb 12th) and today PeerJ has their first anniversary, so let’s wish Charlie a happy birthday. Exactly one year ago, we helped announce their launch with an interview of the co-founders Jason Hoyt and Peter Binfield.

    Since that time, the demand for access to research has continued to grow, Mendeley and Frontiers have been acquired, the US and UK have mandated open access, and the volume of articles that are published in an openly accessible format has increased dramatically. PeerJ has contributed to this change by allowing authors to publish open access for $99 per author, just a fraction of the fees that similar open access publishers charge (in fact, cheaper than the page charges at many non-open access journals!), and also by opening PeerJ PrePrints and helping illuminate the hidden effort expended by editors and reviewers through their Academic Contribution metric.

    PeerJ is raising the bar for what an academic publication should be (a bar already set fairly high by Elsevier’s Article of the Future), and we wish our colleagues at PeerJ many more successful years!

    Mendeley labs project turns heads at Webscience 2013

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    headstart

    Head Start, a Mendeley Labs project, has been nominated for best poster by conference participants at Web Science 2013. Head Start is intended to facilitate and improve the process of literature search. The visualization aims at providing an overview of an academic field, based on Mendeley data.

    You know the problem… when you’re first exploring a research area, it is very hard to get an overview of the field. First, you might enter some keywords into an academic search engine such as Google Scholar. Then, you might read through the top results and read their references, provided your institution has access or if they’re available from an open access journal. With time and patience, you build a mental model of the field. There are several drawbacks to this approach: it is very laborious and time-consuming, and it’s very hard to read papers in their order of importance or even to know if you’ve found all the most important papers.

    Peter Kraker from the Know-Center at Graz University of Technology has taken on the challenge to overcome these problems. During a research stay at Mendeley for the EU project TEAM, he has developed Head Start in cooperation with the Data Science group led by Kris Jack. The application presents you with the main areas in an academic field, and lets you zoom into relevant publications within each area. This allows a researcher to do most of the exploration in a single user interface.

    The overview is generated (almost) automatically using Mendeley’s data about readership of academic papers within a discipline. Readership co-occurrence is used as a measure of subject similarity. The more often two books are checked out of the library together, the more likely they’re on the same subject, and so with academic papers – the more often two papers occur in someone’s Mendeley library, the more likely they are to be on similar subjects. The documents are then grouped by subject area and displayed using D3.js, a JavaScript library for making interactive visualizations on the web, made popular by the New York Times graphics department.

    Peter will present Head Start at a webinar of the Web Science Trust Laboratories. The virtual presentation will take place on Wednesday, June 12 at 16:00 London time. Attendance is free; it just needs a simple registration following this link. More information is also available from this paper.

    Please check out Peter’s demo and poster and let us know what you think!

    Do you know an example of open access research helping the public good? Nominate the team for a $30k ASAP award!

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    The Public Library of Science, the Wellcome Trust, and Google recently announced the Accelerating Science Award Program. If you know someone who has applied or reused scientific research in an innovative way to advance science, medicine, or technology, you can nominate them for an ASAP award. The goal of ASAP is to reward people for publishing and re-using open access research and also to gather compelling use cases for open access.

    This program has major support from publishers, funders, and the tech community and they have put up some serious prize money – $30,000 for each of three winners. The nomination period opened May 1 and runs through June 15. Potential nominees may include individuals or teams of scientists, researchers, educators, entrepreneurs, policy makers, patient advocates, public health workers, students, or anyone else, as long as they have reused open access research in a innovative way. The winners will be announced during Open Access Week in October 2013 in Washington, DC at an event hosted by SPARC and the World Bank. Mendeley is assisting by publicizing the event and gathering nominations, and Creative Commons, along with several other library organizations, publishers, and research organizations are also sponsoring the event.

    More information is available at http://asap.plos.org/