New DataCite / ORCID Integration Tool

A new service allows researchers to add research datasets – and other content with DataCite DOIs, including all figshare content – to their ORCID profile by integrating with the DataCite Metadata Store. The tool is an adaption (or fork) of the CrossRef Metadata Search developed by Karl Ward, and was developed by Gudmundur Thorisson and myself as part of work in the EU-funded ODIN project. More details can be found here.


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Announcing Markdown for Science Workshop on June 8th

On Saturday June 8th – exactly a month from today – the PLOS San Francisco offices will host a workshop/hackathon about using markdown for science. A lot of people are experimenting with markdown for authoring scientific articles – see blog posts herehere or my post here, and the scientific manuscript here.

Markdown is a simple markup language for text, and is primarily used for HTML content on the web, but can also be converted to PDF, LaTeX and others. One challenge with markdown is that there are a number of slightly different “flavors” out there, from the original markdown to multimarkdown, github-flavored markdown and pandoc. Some of the advanced formatting of scientific documents – tables, citations, math – is still a challenge for markdown.

Will markdown become our next authoring format for scientific content? Will there be yet another flavor, scholarly markdown? How will markdown writing tools be different from LaTeX tools or Microsoft Word? If you care about any of these questions and are in or near San Francisco, join us on for all full day on June 8th. Free registration is open at http://mdsci13.eventbrite.com. We are collecting workshop ideas at https://github.com/karthikram/markdown_science/wiki/workshop, the Twitter hashtag is #mdsci13.

This event is organized by Stian Haklev and myself, with generous support by a 1K Challenge prize from Force11, and hosting provided by PLOS.

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Baby steps toward better metrics

Article-Level Metrics provide new ways to look at the impact of scholarly research. Two important concepts are a) to track metrics for individual scholarly articles instead of using numbers aggregated by journal, and b) to go beyond citations and also include usage stats and altmetrics.

Article-Level Metrics is also doing something else: instead of tracking impact by year, it looks at usage, altmetrics and citations in real-time. There might have been technical reasons to do so 20 years ago, but there really is no longer any reason why scholarly impact should be tracked on a yearly basis in 2013. Unfortunately there is one big stumbling block:

The publication date of a scholarly article is often difficult or impossible to obtain. Publication year may be the only available information.

A good example is CrossRef. They provide a lot of interesting metadata about an article and make this information available in a very nice search interface. But they only require the publisher to provide the publication year, information about the publication month and day is optional. There are many other examples of journals and services that just can’t tell you when exactly an article was published. This might have made sense when periodicals were printed on paper, but doesn’t work for digital content.

 

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You should be able to install my software in less than one hour – or why DevOps is important

Cameron Neylon yesterday wrote a great blog post about appropriate business models for shared scholarly communications infrastructure. This is an area I have also been thinking about a lot recently, and in this post I want to add a technical perspective (and an announcement) to the discussion.


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Mendeley and Elsevier

Earlier this week the rumors that started in January became official: Elsevier is buying Mendeley (see also here). A lot has been written about this announcement, in particular about the fear that Mendeley as a product and organization will turn into something not as open and collaborative as before.

I first met Victor and Jan from Mendeley in 2008 and did an interview with Victor in September 2008. We worked together in the organization of two Science Online London conferences (2009 and 2010, together with Nature.com and others), and my current job started with an entry for an API programming contest co-organized by PLOS and Mendeley, with the first lines of code written in the Mendeley offices during the Science Online London 2011 hackathon. I wish Mendeley all the best with their new parent.

What this acquisition signals to me is that commercial publishers are now moving into the software tools for scientists business at full speed. They have always done this, but with ReadCube by Digital Science (a Nature Publishing Group sister company) in 2011, the acquisition of Papers by Springer last year and now Mendeley, reference management now often means using a tool owned by a publisher – this market used to be dominated academic software such as Zotero and commercial software vendors such as Thomson Reuters (Endnote) or ProQuest (RefWorks).

For me this trend signals that publishers have realized that we are moving into an Open Access publishing model, which in contrast to subscription publishing is not about owning the content, but about providing valuable services around content that is free to read and reuse.

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Comment: the case for open preprints in biology

Last week Philippe Desjardins-Prouly et al. published the article The case for open preprints in biology – naturally as a preprint on figshare. The article sees preprint servers as a great opportunity for open science, and discusses the status of preprints in the biological sciences. In this blog post I want to add some comments to the text.


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Some Thoughts on Beyond the Paper

Today the journal Nature has released a special on the Future of Publishing. It includes a lot of interesting reading, but I want to focus on the comment Beyond the Paper by Jason Priem. In the comment Jason describes his vision of the future of scholarly communication, a future where many of today’s roles for articles and journals will be replaced by the decoupled journal and online tools taking the lead in dissemination and filtering of scholarly content.

Jason makes a strong case for this vision, and takes his time to also discuss the concerns and challenges. He doesn’t have the space to discuss in more detail how we get to that future, and in particular what the role of researchers, publishers, libraries and funders be in that transition.

Jason’s vision will probably be overwhelming for many researchers, and might not directly address what is probably the biggest issue for most researchers: funding for grants and jobs is limited, and the processes we use to select for good science and good scientists are inefficient and often arbitrary. Most students entering graduate school will not be able to have a career in academia, and most academics will say that they spend far too much time with evaluations – of their own work and the work of others. It is unclear to me how we can get from the current system – where one misstep such as denied grant or submission to the wrong journal can mean the end of a career – to the system that Jason envisions. The current climate doesn’t really foster experimentation by researchers and I am interested to understand how researchers can take part in this process of change.

The vision of the decoupled journal is very threatening for some of the stakeholders of the current scholarly communication ecosystem, in particular publishers and libraries. Every journal publisher and library knows that it has to reinvent itself to survive the digital transformation, but a vision that is build around a new ecosystem of service providers needs to be clear how publishers and libraries can be part of the transformation process.

Lastly, I disagree with the notion that today’s publication silos will be replaced by a set of decentralized, interoperable services that are built on a core infrastructure of open data and evolving standards — like the Web itself. I would argue that both scholarly communication and the web in general have a tendency for centralization, and that scientific infrastructure needs to be interoperable first and decentralized second. Without a focus on interoperability the future of scholarly communication will not be open and in the hands of many, but will be a race to become one of the dominant players in this new ecosystem, and we might end up with not 1000s of libraries and publishers but just a handful of technology companies holding the keys to our scientific infrastructure.

Priem, J. (2013). Scholarship: Beyond the paper Nature, 495 (7442), 437-440 DOI: 10.1038/495437a

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Using d3.js to visualize Article-Level Metrics over time

PLOS Article-Level Metrics (ALM) are a great set of data (available via API and as monthly data dump) for some nice data visualizations. I have recently become a big fan of the d3.js javascript library, and have now used d3 to look at some ALM data over time.


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New version of Article-Level Metrics app released

On Tuesday we released the latest version of the PLOS Article-Level Metrics application. As always, the source code is available at Github. The changes in this version focus on improving API perfomance, making it easier to install the application, and RSS feeds for the most popular articles by source and publication date (e.g. the most tweeted papers published in the last 7 days). See the Github Wiki page for more details, in the Wiki you also find the development roadmap and the issue tracker for feature suggestions.

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The Price of Innovation – my Thoughts for Beyond the PDF

The Beyond the PDF Conference is currently taking place in Amsterdam. Unfortunately I am unable to attend in person this time (I took part in the first Beyond the PDF in January 2011), but I was watching the livestream of the Business Case panel disucssion yesterday afternoon.


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