15 April 2015

Quantum Earth and Paperscape: mapping arXiv

Copyright Roberto Salazar & Sebastian Pizarro

Above is a visualisation of Quantum Earth, a continent consisting of research articles in the field of quantum mechanics. The idea was originally conceived by Roberto Salazar after completing his PhD on quantum information at the University of ConcepciĆ³n in Chile. Roberto teamed up with Sebastian Pizarro a digital designer to bring his idea of a quantum mechanics continent to life. The result was a map reminiscent of Tolkein replete with geographic landmarks such as Teleportation Lake and Quantum Engineering Volcano.


We contacted Roberto for his thoughts on open access:
"I think open access publishing is the way that things should be done in science. That being said, I feel that this will happen only if we improve open access tools for finding the right paper for your research. In this sense I believe that Paperscape is a breakthrough in the field and hope that it will be the first of many more. I use it in my daily research and has been of great help in finding the right paper and saving time (I just love it).
Our little contribution with the "Quantum Earth" map, is to give a graphic idea of how to use Paperscape when you already have an insight in the field. Also the purpose is to give positive publicity to this great idea."

Copyright Damien George and Rob Knegjens. Downloaded here

Paperscape is a project developed by Damien George and Rob Knegjens, two post doctoral researchers who wanted to create a tool to visualise the huge volume of papers in the pre-print repository arXiv. Visually, Paperscape resembles a galaxy made up of over a million stars. Each of the 'stars' represent actual research articles in the arXiv repository. The positions of the articles are determined by references to other articles, and in effect the references act as a gravitational force in the Paperscape galaxy, pulling closely related articles together to form clusters. The way the tool structures the articles makes finding new and highly cited articles much easier as well. This is because highly cited articles appear larger and new articles appear brighter.

Posters of the Paperscape galaxy are freely available to download here in various sizes.
The full size Quantum Earth map can be viewed and downloaded here.

13 April 2015

Wellcome peer review report

Copyright Wellcome Trust CC BY 2.0


Copyright Research Information Network
A Wellcome Trust commissioned report centred around the issue of peer review was published last month. The report, conducted by the Research Information Network, sets out a detailed analysis of peer review, the critiques, and the new alternative systems for peer review that have appeared in recent years.

The report defines traditional peer review as 'the process of subjecting an author’s scholarly manuscript to the scrutiny of others who are experts in the same field’ (p.6) These experts must assess whether the research is of sufficient quality to be included in the journal. Many journals also require reviewers to assess the originality and significance of research, however it is worth noting that some open access mega-journals such as PLOS ONE and Collabra do not require this.

The report details many of the criticisms commonly made of peer review. One criticism is that peer review is not effective at weeding out unsound research. The report makes mention of the fact that retraction rates have increased in recent years, although the volume of retractions is a very small proportion of the 2 million papers published each year globally. Another criticism mentioned in the report is the burden faced by reviewers, the vast majority of whom are unpaid. Research suggests that around 3 million papers are submitted for review each year, and many are submitted and reviewed more than once. This represents a significant burden on reviewers, half of whom spend more than 6 hours on each review (see our recent blog post on the new journal Collabra that compensates reviewers by paying them a proportion of APC income). Other criticisms include potential for bias, expense, delays, and the potential for subversive behaviour.

Given the criticisms and the potential new avenues afforded by new digital technologies there have been many experiments with alternative forms of peer review. To take one example, open review sees both author's and reviewer's names disclosed from the outset (for example BMJ and PeerJ) and is designed to encourage constructive comments and avoid overly harsh reviews. Journals such as Frontiers (see previous blog post here) have expanded on this idea and introduced an interactive communication element to their open review process.

After investigating the various forms of peer-review the report concludes that peer review "remains a bedrock of the scholarly communications system", but reflects that there is likely to be increasing pressure on traditional peer review systems as the rate and volume of scholarly communication increases. It is this continuing pressure that will ensure experimentation with new forms of peer review will continue with cooperation between research and publishing communities:
'[W]e detect a sense in which while publishers will continue to explore new approaches in the ways we have described, they would welcome more guidance from key sections of the research community on the kinds of peer review services they want from publishers, and on the purposes that they should seek to fulfil. Unless the purposes are defined with greater clarity than they are at present, at least some of the current experimentation may prove to be of little point.' Scholarly Communication and Peer Review: The Current Landscape and Future Trends, p.30. CC BY

The full report, Scholarly Communication and Peer Review: The Current Landscape and Future Trends, can be found here.

9 April 2015

Open Access and content mining

We've previously blogged about the British Library Electronic Theses Online Service (EThOS) that stores theses metadata and, where possible, the full text of digitised theses. BL Labs now wants to explore EThOS metadata for content mining or analysis of trends and is currently inviting research questions that could be answered using this approach. The move follows on from its project providing data to Virginia Tech to develop algorithms for automated subject tagging of theses.

This is another example of an overlay project underpinned by large-scale data harvesting such as the successful Mechanical Curator project that released one million out of copyright images into the public domain for researcher use and re-use.

ChemSpider is an earlier project that brings together chemical structures from a variety of sources into a free database including data from St Andrews theses. This publishing platform provides opportunities to make good quality data public, re-use and preserve known compound data and related information to advance research, develop services and surface the data on the wider internet.

It's an exciting area of Open Access and Open data and there are likely to be further developments as efforts are made digitising older theses and other sources.


Image captured by the Mechanical Curator project.  No known copyright restrictions.


1 April 2015

Share My Thesis competition - update


Last week the British Library Ethos service announced the winner of the Share My Thesis competition. We posted about the competition back in January, see here for more information.
 
The entrants had to first tweet about why their research is/was important using the #ShareMyThesis hashtag. The 8 shortlisted entrants then had to write a short article to elaborate on their tweet. You can read the winning entries here: 1st, 2nd, and 3rd.

Although the competition is now closed, the British Library Ethos service still encourages PhD students past and present to use #ShareMyThesis to share their PhD research with a wider audience.

30 March 2015

5000th repository item - update

This is a quick update on the 5000th item in the repository we highlighted back in February: A phenomenological-enactive theory of the minimal self, by Brett Welch. We sent Brett a copy of Martin Paul Eve’s book Open Access and the Humanities as a prize. Last week he received the book and was kind enough to send us a picture (we especially like the Saltire in the background!)


You can read Brett's thesis here:  http://hdl.handle.net/10023/604

Martin Paul Eve's book is also freely available to download and read online through our library catalogue, here: http://library.st-andrews.ac.uk/record=b2173431~S5

26 March 2015

New open access inter-faith journal


We are delighted to announce the first volume of Convocamus, a new journal on the University of St Andrews Library journal hosting platform.


Journal Homepage Image

Conceived and produced by Samuel Mellish and a team of undergraduate students in St Mary's College, Convocamus is an inter-faith publication providing a platform for scholarly dialogue. Sam provided a case study for our recent event, Managing journals: challenges and opportunities.

Following the absence of opportunities to pursue research projects outside of the undergraduate structure, students of St Mary's College sought to form a platform for such study. As members of a religious college the students wanted to use this platform to bring together individuals from a number of religions. This led to the birth of Convocamus. 

The editorial staff hope the journal will encourage inter-faith dialogue, and provide a platform for academic debate. Also, we hope it encourages undergraduates to take their studies beyond their degree.
The first articles have already had significant interest, with over 500 PDF downloads of the current issue. The greatest usage was understandably at the point of publication (261 article downloads in December 2014), with usage continuing into 2015.


The journal's Editor-in-Chief, Sam Mellish, would like to thank all those who have contributed and read the journal so far.

Read the first issue of Convocamus at: http://ojs.st-andrews.ac.uk/index.php/convocamus/issue/view/98/showToc

You can also let your comments and thoughts be heard via the Convocamus Facebook page: https://www.facebook.com/convocamus

25 March 2015

New St Andrews membership with the Multidisciplinary Digital Publishing Institute (MDPI)

The University Library is delighted to announce that we now have a membership with MDPI - Open Access Publishing that publishes in disciplines ranging from Biology and Life Sciences to Social Sciences, Arts and Humanities. We hope that the choice of journals, an easy user interface for authors and system integration with central funding needs will make this an attractive Open Access publication venue choice for researchers.

Please note the eligibility criteria for the University of St Andrews central open access funds.

Central funds are available for:
  • Papers acknowledging funding from Arthritis Research UK, Breast Cancer Campaign, British Heart Foundation, Cancer Research UK, Leukaemia & Lymphoma Research and the Wellcome Trust, where the corresponding author is at the University of St Andrews
  • Papers acknowledging RCUK funding (AHRC, BBSRC, EPSRC, ESRC, MRC, NERC or STFC), where the corresponding author is at the University of St Andrews
  • Corresponding authors who are full St Andrews staff or research students and who have no other source of open access funding 

St Andrews authors who are not eligible under the above criteria will still receive the membership discount but will be requested to pay for Article Processing Charges from their own budgets, should the paper be accepted for publication.

In all cases authors must confirm eligibility with the University Library before agreeing to pay an APC.

For further information, please visit:

http://www.st-andrews.ac.uk/library/services/researchsupport/openaccess/oafunding/

or email open-access-support@st-andrews.ac.uk

From Valera, S. and Bode, B.E. (2014) Strategies for the synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR, Molecules 19(12), 20227-20256 doi 10.3390/molecules191220227
Distributed under the terms of the Creative Commons Attribution License.