Mendeley labs project turns heads at Webscience 2013

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!

Mendeley handles 100 million calls for Open Science, per month

Imagine the rich ecosystem of third-party Facebook and Twitter apps, now emerging in the domain of science. More than 240 applications for research collaboration, measurement, visualization, semantic markup, and discovery – all of which have been developed in the past year – receive a constant flow of data from Mendeley. Today, Mendeley announced that the number of queries to its database (termed “API calls”) from those external applications had surpassed 100 million per month.

Akin to a “Wikipedia for academic data”, the information fueling this ecosystem has been crowdsourced by the scientific community itself. Using Mendeley’s suite of document management and collaboration tools, in just three years its global community of 1.9 million researchers has created a shared database containing 65 million unique documents and covering – according to recent studies – 97.2% to 99.5% of all research articles published. Commercial databases by Thomson Reuters and Elseviers contain 49 million and 47 million unique documents respectively, but access to their databases is licensed to universities for tens of thousands of dollars per year.

In contrast, Mendeley’s database is freely accessible under a Creative Commons license, and it is the only one that allows third-party developers to build their own tools with the research data anywhere on the web, on mobile devices, or on the desktop. Moreover, because Mendeley’s data is crowdsourced, it has a unique social layer: Each document comes with anonymized real-time information about the academic status, field of research, current interests, location of, and keywords generated by its readers. Mendeley’s API also adds information about related research documents and public groups on Mendeley that the document is being discussed in.

The most popular apps built on Mendeley’s platform fulfill academia’s need for faster and more granular metrics of scientific impact: ReaderMeter.org and Total-Impact.org display a researcher’s or a labs’ real-time impact on the academic community, while Mendeley itself recently announced the first sales of its real-time research impact dashboard to academic institutions around the globe. Hojoki pulls updates from Mendeley and other productivity tools like Evernote and Basecamp into a common newsfeed. Kleenk allows users to create free-form semantic links between documents in their Mendeley library and share them publicly. OpenSNP, winner of Mendeley’s $10,001 Binary Battle prize, makes the connection between raw genetic data and published research.

Bastian Greshake, co-founder of openSNP, explained: “We started openSNP to crowdsource the discovery of genotype-phenotype associations. In less than a year, our users have uploaded over 200 genetic testing results and more than 3400 phenotypic annotations for over 100 different genetically influenced traits, which is a great success. Mendeley’s API enables our users to find the latest scientific literature – including thousands of Open Access articles – relevant to their own genetic testing results.”

Dario Taraborelli, Senior Research Analyst at the Wikimedia Foundation and creator of ReaderMeter.org, said: “By sharing a large corpus of open-licensed data, Mendeley is laying the foundation for a whole new science of the making and spreading of scientific knowledge. This offers coders and researchers alike an unprecedented opportunity to map and measure the real-time impact of scientific research. Mendeley’s API is a mountain of data just waiting to be mined.” Jason Priem and Heather Piwowar, co-founders of Total-Impact.org, added: “Using Mendeley’s data, we can show how papers are making a difference long before they show up in the citation record, as well as which papers are making a difference to student readers, or readers in developing countries. Of course, this wouldn’t be possible without Mendeley’s commitment to releasing this data openly, under the CC-BY license.  A lot of us in the Open Science community are convinced that the we’re on the way to a system built on this kind of openness. In the future, researchers will interact with the literature via a web of interlocking, third-party applications for sorting, filtering, and conversing. By opening its valuable data to developers, Mendeley is helping us get there, today.”

Tim O’Reilly, founder of O’Reilly Media and also a Mendeley Binary Battle judge, added: “This milestone shows how the future of science is being built, app by app, data source by data source. Open data is the biggest science story of the 21st century.”

Dr. Victor Henning, CEO & Co-Founder of Mendeley, said: “Our vision was always to make science more open. The Mendeley API liberates data that has been locked behind paywalls for decades – enabling app developers to reinvent academic workflows, research data discovery, even scientific publishing. Max Planck said: Science progresses funeral by funeral. I think we’ve found a better method.”

Mendeley API graphs and app screenshots:
http://www.flickr.com/photos/mendeley/sets/72157631195319638/

Making Openness Work: An interview with Barry Bunin of Collaborative Drug Discovery

I recently had the chance to sit down with Barry Bunin to talk about his new drug discovery platform, Collaborative Drug Discovery. As you may guess from the title, he’s taking a novel approach to drug discovery. Modern drug discovery faces huge challenges due to the economic inefficiency of the process where hundreds of millions of dollars must be spent to discover one new drug. The current model also makes it difficult to capitalize on all the interesting but not immediately drug-relevant data that’s generated in the process. CDD’s approach promotes collaboration as opposed to the traditional approach where different teams at different companies repeat much of the same work and suggests that companies will actually share information that leads to a mutual benefit, provided there’s a easy and secure way to do so. I’m delighted to share this interview with you of yet another company showing how openness and collaboration works for business.Read More »

Leading universities adopt Mendeley data to accelerate research analytics by 3 years

This week, leading academic institutions in North America, Europe, and Asia signed up to Mendeley’s new data dashboard, the Mendeley Institutional Edition. The dashboard analyses their research activity and impact on the global research community in real time – down from the 3-5 year time lag of the “Impact Factor”, the current gold standard for such evaluations. This allows academic institutions to react faster to their faculty’s research needs and provide them with quicker, more personalised support during the research process – thus accelerating the pace of scientific discovery for all of us.

Readership statitics in Mendeley Institutional EditionThe Impact Factor, a measure of the number of citations an academic journal receives, is a pivotal metric of science: Academics have to publish in high-Impact Factor journals to receive promotions, tenure, or grant funding, and universities allocate their million-dollar library budgets to those same high-Impact Factor journals. This is despite the Impact Factor’s many known flaws – the most limiting of which is that the citations it is based on take 3-5 years to accumulate.

This week’s release of Mendeley’s Institutional Edition, distributed by leading Dutch library subscriptions agent Swets, brings research impact measurement to real-time speed, while also providing more granular and social metrics of how academic research is consumed, discussed, and annotated. It allows research institutions to see detailed analytics of the journals their academics are reading, the journals they are publishing in, and how many readers those publications have. This data is built on Mendeley’s global research community of more than 1.8 million academics who are using the startup’s tools for document management, discovery, and collaboration.

The first customers of Mendeley’s data dashboard are premier international research institutions: Two prominent universities on the East Coast and in the Bay Area, the University of Pittsburgh, the University of Western Ontario, the University of Nevada, Reno, the VTT Technical Research Centre of Finland, the Korea Advanced Institute of Science and Technology, and the Agriculture, Forestry and Fisheries Research Council Japan.

Speaking of the announcement, Dr. Tod Colegrove, Head of DeLaMare Science & Engineering Library at University of Nevada, Reno, said: “Rather than spending vast amounts of staff resources attempting to quantify usage of existing library resources – remaining largely unaware of past and present use outside of the library’s current subscribed offerings – Mendeley offers a unique and immediate lens into the library’s researchers’ information behaviours. Purchase decisions can be informed directly by past and present actual use of potential library resources, rather than being left to the increasingly less relevant the-way-we’ve-always-done–it model of serials management.” His colleague Lisa Kurt added: “The collaborative nature of Mendeley is a game changer for our institution where departments and colleges are working to break through their silos and focus on the best parts of the work they do. Mendeley is solving a very real problem in a rather elegant way.”

At the University of Western Ontario, Head Librarian Joyce Garnett commented: “Western Libraries is proud to be an early adopter of Mendeley Institutional Edition, a significant addition to our digital toolbox. It will facilitate citation management for individual researchers, collaboration for research groups, and, through its analytics capacity, enable librarians to assess the relevance and use of our collections. Mendeley is unique, growing its database organically through the choices and preferences of researchers as they create and disseminate new knowledge.”

In a bid to develop alternatives to the Impact Factor, new research metrics startups such as altmetric.com and total-impact.org have already turned to Mendeley’s readership data, and several peer-reviewed studies have recently highlighted its positive correlation with the Impact Factor. Dr. Victor Henning, CEO and co-founder of Mendeley, said: “I’m excited that after receiving scientific validation from the research community, our data is now helping some of the world’s best universities work more efficiently and get to life-changing discoveries faster. My inner nerd is going: Wow, this is freaking amazing.”

Mendeley Institutional Edition screenshots: http://www.flickr.com/photos/mendeley/sets/72157630651813190/

Papers aren't just for people




Image via klausonline

There should be copyright exemptions for text mining in research.

There is a fundamental shift happening now in how research is conducted and it is affecting all fields of academic endeavor. Some fields have already shifted and some are just beginning to, but the shift has a common cause, and that cause is the growing amount of research output. At a certain point, the amount of research output exceeds the ability for researchers to consume it all as it is published. In biological sciences, the shift has already begun, but the difficulties reach all the way to the (digital) humanities.

At Mendeley, we’re building tools to address this problem. Mendeley Suggest is designed to suggest relevant research to you, in effect showing you the results of searches you haven’t run yet. Searching the Mendeley catalog allows you to find papers in smarter ways than just keywords, by ranking the results according to how widely read the paper is and by showing you groups and other concepts related to the paper. At the end, though, there has to be a researcher reading the paper and using the knowledge to inform their research, and this just doesn’t scale. We need to be smarter about this. However useful these tools are, they only stem the flood, when what we should be doing is building boats. Read More »

Winners of the first Binary Battle Apps for Science Contest

We, along with PLoS, have been overwhelmed by the huge response that academics and the developer community have given to open up science. When we announced this contest to develop science applications on top of the Mendeley and PLoS platforms last March, we were not totally sure that anyone would even be interested. Boy, were we wrong!

Tim O’Reilly, Founder and CEO of O’Reilly Media and one of five all-star judges, said this about the Binary Battle –

“I always tell developers to work on stuff that matters. It’s time to stretch beyond the consumer internet, and what better place to focus than on furthering the cutting edges of science?”

Mendeley launched the API platform in April of 2010 with the hope that it would 1) spur innovation in the science ecosystem and 2) send a signal to others that opening up data benefits everyone. To date, more than 1000 developers have applied for API keys to build on top of that data. With the Binary Battle announcement, we hoped to carry open science further and by all accounts we did.

Today we announce the winners of the 2011 Mendeley-PLoS Binary Battle. We narrowed the Binary Battle entries down to the Top 10+1, and then handed the voting over to our list of expert judges (Werner Vogels, Juan Enriquez, Tim O’Reilly, James Powell, and John Wilbanks. We also opened the vote up to the public to count as 1/6 and combined with the judges. It was great to see that both the public voting and the judges voting correlated very well. It was so close for many of the apps, but one stood out to both the judges and the public….Read More »