Why is scientific data so badly communicated?

Ross Mounce and I are starting to extract content (“content-mining”) from BMC journals. [Why BMC only? Because most of the other major publishers refuse to let us do it even when we subscribe.] [Why not PLoS? For technical informatics reasons which I have communicated to PLoS and which they have taken on board.]

I am going to appeal frequently for like-minded people to form a community of Open Content Miners, so if you are interested, let us know.

Anyway we are going through BMC Evolutionary Biology and looking at data types. We are optimistic in general.

DISCLAIMER: I shall use examples from BMC because this is all I can access. I shall frequently be critical – BMC is no better or worse in most of these. My criticism of Elsevier, Wiley, Springer, Nature, RSC, ACS, etc. is an order of magnitude worse.

Anyway – here’s the first diagram I came across. I’ll say later HOW we extract, but for the moment look how badly the information is presented. That’s partly because of the slavery of the printed page (and “print” is the evil word because authors and publishers expect reader to print the page). Tell ME what you think is suboptimal about this figure (I have at least 3 complaints, some of which are very common). The diagram should scale to a size where the text is (just) readable.


People have been reading this – I’d value your comments.


Wiley Open Access journals now indexed by DOAJ

DOAJWe are pleased to annouce that a number of Wiley Open Access titles have recently be added to the Directory of Open Access Journals (DOAJ). This directory currently lists 8092 open access journals, with more titles being regularly added. The recently added Wiley Open Access journals are: MicrobiologyOpen, Evolutionary Applications, Cancer Medicine, EMBO Molecular Medicine and ChemistryOpen. All of these journals are freely available to read on Wiley Online Library.  These are in addition to the earlier launched journals Brain and Behavior and Ecology and Evolution which have been indexed since February 2012.

Inclusion in DOAJ  increases visibility by enabling potential authors and readers to navigate to them directly within the directory. Many librarians have commented that they see inclusion in DOAJ as a sign of a quality open access journal. Wiley Open Access will continue to work with DOAJ to have all new journals in our program included.

Latest Article Alert from BMC Infectious Diseases

The latest articles from BMC Infectious Diseases, published between 30-Jul-2012 and 29-Aug-2012

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Study protocol
Doxycycline-mediated effects on persistent symptoms and systemic cytokine

Latest Article Alert from BMC Medical Research Methodology

The latest articles from BMC Medical Research Methodology, published between 30-Jul-2012 and 29-Aug-2012

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Study protocol
Learning from Failure – Rationale and Design for a Study about

The Advantage of Veins

Locust wing

Desert locusts are known to travel great distances, experiencing substantial mechanical stress along the way, however little is understood about their wings ability to resist damage during these long flights. Using a tensile test machine, Trinity College researchers Dr. Dirks and Dr. Taylor investigated the toughness of these insect’s extremely thin wings, specifically looking into the function of the network of veins running through the wing membrane, shown in Figure 1 above, as barriers to crack propagation. As the title, “Veins Improve Fracture Toughness of Insect Wings” suggests, the study found these veins increased the effective structural toughness of the wing significantly, causing cracks to slow or stop and helps explain how the insects manage to withstand damage incurred over long flights. Check out Video 1 of the article to see the veins impede cracks.


Image citation:

Dirks J-H, Taylor D (2012) Veins Improve Fracture Toughness of Insect Wings. PLoS ONE 7(8): e43411. doi:10.1371/journal.pone.0043411

JKUAT IR Sensitization workshops


JKUAT Library plans to sensitize the JKUAT community on the JKUAT OA policy and IR. The first workshop will be held on 14th September 2012 and will be targeting Teaching staff and researchers, editors, ICT staff JKUSO representatives, BPS representative, JKUAT IR policy committee, Campus representatives. The second workshop will be targeting JKUAT management and will be combined with a launch of the repository by the Vice Chancellor and is scheduled tentatively for 19th September 2012. The issues to be covered are

  • An introduction to OA institutional repositories initiatives: What they are and their benefits
  • A historical background of the JKUAT IR
  • An overview of the JKUAT IR Policy
  • Copyright issues and IRs
  • Implementation experience of other institutions
  • Demonstration of the JKUAT IR

The library looks forward to this important milestone    


Molecular Informatics Presents—New Open Access Special Issue: Open Innovation in Drug Discovery

Molecular Informatics CoverThe exponentially growing availability of open data and its exploitation in drug discovery and development has a significant impact on the way how Pharmaceutical Sciences are progressing. Semantic-web technologies for flexible integration of databases, web-based tools which allow the mining of large life science data sets, mobile apps for instant availability of information, new approaches for classifying targets and assays are just a few examples of the immense opportunities offered by the concept of openness. In this special issue devoted to “Open Innovation in Drug Discovery” a few snapshots in this area are highlighted, demonstrating how the whole community will benefit from applications built upon open data.

Articles include:
REVIEW: Taking Open Innovation to the Molecular Level – Strengths and Limitations
COMMUNICATIONS: PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery

This entire special issue is available open access, thanks to financial support from Open PHACTS  and Wiley-VCH.

About the Journal
Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computerassisted molecular design. Having commenced publication in 2010, it just received a first Impact Factor of 2.390 – straight into the top quartile of the Mathematics & Computational Biology category**!

**2011 Journal Citation Reports® (Thomson Reuters, 2012)

Latest Article Alert from Particle and Fibre Toxicology

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Invitation: Learn more about e Life, the funder-researcher collaboration for the best in science

P.S. on the following: Mark Patterson (eLife Managing Executive Editor), Ian Mulvany (our head of technology), and I will also be on hand. We look forward to having you!

eLife is holding an online Open House to share news on the development of its anticipated open-access journal for the very best in life science and biomedical research. Join us.
eLife is the new researcher-driven initiative to reshape science communication launched in collaboration by three prestigious biomedical research funders: the Howard Hughes Medical Institute (USA), Max Planck Society (Germany), and the Wellcome Trust (UK). Announced in June 2011, the first aim of the initiative is to launch an open-access journal for the most important advances in the life sciences and biomedicine. The eLife journal will showcase papers identified through a new rapid, fair, and constructive review process, and serve as a platform for innovation in the presentation and use of research content.
While eLife presses toward launch of the journal by the end of 2012, interest in how this unique funder-researcher collaboration could change science and scientific publishing grows. Media coverage has been extensive and has included detailed stories on one of eLife’s first accepted papers – just weeks after we opened for submissions.
On September 12, please join us for an online Open House to learn more about what the initiative aims to do, the scope of the journal, how the review process is different, the papers that have been accepted, the status of launch, and more. eLife Editor-in-chief Randy Schekman – Professor of Molecular and Cell Biology at the University of California (Berkeley), and an Investigator at the Howard Hughes Medical Institute – will host. Scientists, students, potential reviewers, members of the eLife community, librarians, research funders, publishers, open-access advocates – all – are welcome.
The eLife online Open House will be held:
Wednesday, September 12, 2012
9:00 – 10:00AM U.S. Pacific time
(12:00 – 1:00PM U.S. Eastern | 5:00 – 6:00PM UK)
To determine the time in another world region, visit http://www.worldtimeserver.com/convert_time_in_US-CA.aspx?y=2012&mo=9&d=12&h=9&mn=0
Please register to attend by September 10 at http://www.elifesciences.org/crm/civicrm/event/info?id=7&reset=1. (Phone and Web access will be required to participate).
To share your questions in advance, post to the eLife Web site (http://www.elifesciences.org/open-house), Tweet #eLifeopen, or email d.clarke@elifesciences.org.
To learn more about eLife and the growing momentum behind the initiative, visit elifesciences.org.

To receive news directly from eLife, feel free to sign up at http://www.elifesciences.org/crm/civicrm/profile/create?reset=1&gid=11
About eLife
eLife is a unique collaboration between the funders and practitioners of research to communicate ground-breaking discoveries in the life and biomedical sciences in the most effective way. Set for launch in late 2012, the eLife journal will be a platform for maximising the reach and influence of new discoveries and to showcase new approaches to the presentation, use, and assessment of research. As an open-access journal, eLife will deliver access to content for free, online, immediately on publication, and will encourage maximum possible reach and utility of the content by publishing under the terms of the Creative Commons Attribution License, which is emerging as the gold standard for open-access publishing. Learn more at elifesciences.org.


Jennifer McLennan?Communications, eLife
+1-202-631-8854 (c)
eLife Sciences Publications, Ltd is a limited liability non-profit non-stock corporation incorporated in the State of Delaware, USA, with company number 5030732, and is registered in the UK with company number FC030576 and branch number BR015634 at the address Suite 203, Sheraton House, Castle Park, Cambridge CB3 0AX.