This week saw the launch of BMJ Open, a new online journal from the BMJ Group. BMJ Open is fully open access and exists to publish research from across all medical disciplines. It offers authors the option to have their work peer reviewed thoroughly for appropriate methods and transparent reporting, but without judgement being applied about novelty or importance. If after peer review the article is deemed worthy of publication, it will be published and deposited in PubMed Central.

The open access is supported by levying an article processing charge (APC) of £1200 for any accepted article (although discounts and waivers are available).

Innovative features

Among BMJ Open’s firsts for BMJ Group journals is use of the Disqus commenting and rating system, as explained in a previous post. As of April we will be publishing article-level metrics to show article usage.

The journal is also the first in the group to publish reviewers’ comments for accepted articles. Reviewers’ comments and the previous versions of the article that those comments apply to are published alongside the final copy-edited and typeset HTML and PDF versions. This gives credit to reviewers, many of whom play a considerable role in improving papers, as well as providing a more transparent publication process.

Data sharing

How to store and share raw data is one of the hottest topics in publishing at the moment. We are currently working with data curation and publication experts to provide authors with a simple and efficient way of storing their data and linking to it from their article. In particular we are working with the Dryad UK project, part of the UK JISC’s Managing Research Data programme. Watch this space for further developments.

Sharing raw data helps bring the complete research record in to the open. Another way of doing this is through publication of research protocols. We encourage authors to submit their original research protocol with their article, but we will also be publishing protocols themselves, and two were published this week. We will also consider ‘pre-protocols’; innovative study designs yet to receive funding/approval.

To encourage this joined-up approach, authors can publish ‘two articles for the price of one’, by receiving a 50% discount on the APC when the protocol is published and a further 50% discount if they publish the resulting research in BMJ Open.

More information

Trish Groves, editor-in-chief of BMJ Open and deputy editor of the BMJ, explains more about the aims and scope of the journal and its place in the BMJ Group’s open access offerings here; the journal’s first published papers are here and you can submit here.

Naturally the journal has a presence in the blogosphere, on Twitter and on Facebook, so you can let us know what you think, comment on articles and spread the word about the journal or papers that catch your eye.

Facebook has once again been busy redesigning its site, this time focusing on the fan pages used by brands, organisations and specialist medical journals! The Facebook page makeover essentially makes Facebook’s public pages look more like personal profiles, which themselves were redesigned about two months ago .

So what’s new?

Facebook pages, like their profile counterparts, now show a line of photos at the top of their main wall (see screenshot below). For pages, these photos include any images posted by the page owner.

Aside from that, page elements are shifted around a bit: the navigation area, which allows you to toggle through different tabs, is now on the left-hand column of the page instead of the top. The other update Facebook is adding is an “Everyone” filter that brings the most interesting and engaging posts from a page’s community to the top of the page.

The posts displayed on the wall are now filtered through an algorithmic process similar to what’s done in the “Top News” option on the main Facebook stream. Previously, posts were shown in a purely chronological order.  This makes it easier for users and admins to easily find the most “liked” and commented-on conversations on a particular page. The new Facebook Pages are also smart enough to filter out posts that are not in a language you speak.

New social media links on our journal sites

By coincidence, new Facebook and Twitter links have also gone live on each of our journal websites. As mentioned in a previous post, each of our journals has a dedicated Twitter account and Facebook fan page, where users can keep up to date with the latest Editor’s choice and Unlocked articles, podcasts, blogs and mentions in the press. These accounts are now directly linked to from the right-hand column of each journal website (see below).

Users can either navigate to an individual journal website to access the Facebook and Twitter pages, or they can use this central list of all journal social media accounts:

https://group.bmj.com/products/journals/social-media

With Amazon claiming a breakthrough success for its Kindle, having announced that eBooks now exceed paperback sales on its US site, the BMJ Group is developing its offerings on this platform. Since the beginning of 2010 “for every 100 paperback books Amazon sold, the company sold 115 Kindle books”.

One of the neat little sub-features of Amazon’s Kindle is being able to subscribe to blogs on it. You have to pay a token amount for the privilege, but for Kindle users, it makes sense as the content is delivered to you wirelessly for your favourite blogs. BJSM (British Journal of Sports Medicine) has recently released its popular blog onto the Kindle. The BJSM blog provides the sports medicine, physical activity and exercise performance communities with a forum to interact about a range of relevant issues.

Kindle blogs are fully downloaded onto your Kindle so you can read them even when not wirelessly connected. And unlike RSS readers which often only provide headlines, blogs on Kindle give you full text content and images, and are updated wirelessly throughout the day. More of the BMJ blogs will be making their way on to Kindle in the near future so let us know which you’d like to see first!

According to the 2010 International Communications Market report by OfCom, the UK saw the highest growth in smartphone ownership, with numbers increasing by a whopping 70% between January 2009 and January 2010. Over in the US, 72% of physicians used smartphones in 2010, which is up from 64% in 2009, according to the Manhattan Research’s Taking the Pulse report. By 2012, that number is predicted to rise to 81%.

Given this astonishing growth in usage, BMJ Group has been investing in a variety of mobile technology solutions, including the iPad App for the BMJ, and now a ‘mobile friendly’ web interface for Emergency Medicine Journal.

The new mobile web browser for EMJ detects when a user is accessing http://emj.bmj.com via a mobile device. Regardless of the type of smartphone, all mobile users are automatically forwarded to an optimised template. The new system offers streamlined content and display for web-enabled, smaller screens with low bandwidth networks. It has been specifically designed to accommodate the mobile behaviour of “keeping up” and “looking up” and works across all devices, including Blackberry, Android and iPhone.

What does it look like?

Homepage

  

Archive

Email a friend

 

PDF view

From the end of last year, BMJ blogs became fully open access using the creative commons license. They have always been free to access, and it is likely that most of our readers will not immediately notice any change, but there is a subtle difference.

The term “open access” implies much more than just “free”. According to the Wellcome Trust, articles to be listed as open access must be freely available immediately, and publishers must also allow for their free reuse. This means that articles can be copied, distributed, displayed, performed and modified into derivative works by any user.

So although readers have always been able to freely access our blogs, they can now reuse our blog content, as long as they credit the original BMJ blog in any derivative works they produce. It is also useful for our blog authors who can now post their own blogs elsewhere, for example on their institutional websites.

The hope is that this will increase the readership of our blogs, as they are highlighted elsewhere and bought to the attention of more people. It is also in keeping with the “social” aspect of blogging. We have found that using Twitter and Facebook to promote our blogs has had a huge impact on traffic to the site. Users like to share links and comment on blogs, and this encourages others to take a look at the site as well.

It is also fits in with the BMJ publishing model, as all our research articles are formally open access.

Have a look at the various BMJ blogs at https://stg-blogs.bmj.com/bmj/

N.B. Please note that this change does not apply to the BMJ Journal blogs or those that do not contain the creative commons logo.

by Juliet Dobson, Assistant web editor and blogs editor for bmj.com

Following on from last week’s discussion of information-seeking behaviour, today we’ll be exploring one way of transforming individual articles into portals to greater information; Utopia Documents .

What is Utopia Documents?

At its most basic level, Utopia Documents is a PDF reading tool that allows articles to be augmented with interactive content, and helps the reader explore data associated with a particular paper. It’s a desktop application for reading and exploring papers, and functions in many respects like a normal PDF reader. Its real potential becomes  clear when configured with appropriate domain-specific ontologies and plugins. Once these are in place, the software transforms PDF versions of articles from static facsimiles of their printed counterparts into dynamic gateways to additional knowledge, linking both explicit and implicit information embedded in the articles to online resources, as well as providing access to auxiliary data and interactive visualisation and analysis tools. For a thorough demonstration of the software, take a look at the video below:

Why concentrate on PDF’s and not HTML?

Given the huge investment in XML/HTML versions of articles, are we taking a step backwards by semantically-tagging our PDF’s? Professor Teresa K. Attwood, who led the bio-informatics component of the EPSRC/DTI-funded UTOPIA(d) project, argues that:

“Utopia Documents was developed in response to the realization that, in spite of the benefits of ‘enhanced HTML’ articles online, most papers are still read, and stored by researchers in personal archives, as PDF files. Several factors likely contribute to this reluctance to move entirely to reading articles online: PDFs can be ‘owned’ and stored locally, without concerns about web sites disappearing, papers being withdrawn or modified, or journal subscriptions expiring; as self-contained objects, PDFs are easy to read offline and share with peers (even if the legality of the latter may sometimes be dubious); and, centuries of typographic craft have led to convergence on journal formats that (on paper and in PDF) are familiar, broadly similar, aesthetically pleasing and easy to read.”

Further authors have responded to reservations regarding the semantically-limited nature of PDF’s as being a non-issue.

“We argue that PDFs are merely a mechanism for rendering words and figures, and are thus no more or less ‘semantic’ than the HTML used to generate web pages. Utopia Documents is hence an attempt to provide a semantic bridge that connects the benefits of both the static and the dynamic online incarnations of published texts.”

What are the main features of Utopia Documents?

In an interview at the Guardian, Utopia’s Phillip McDermott says:

“Utopia Documents links scientific research papers to the data and to the community. It enables publishers to enhance their publications with additional material, interactive graphs and models. It allow the reader to access a wealth of data resources directly from the paper they are viewing, makes private notes and start public conversations. It does all this on normal PDFs, and never alters the original file. We are targeting the PDF, since they still have around 80% readership over online viewing.”

Discover published metadata

If a publisher has invested in the appropriate domain-specific ontologies and plugins,  Utopia Documents can provide access to additional context, from database entries to golssary definitions. All new articles in the Semantic Biochemical Journal, for example, include publisher-curated annotations of the most salient facts.

Comment on articles

The software allows readers to annotate their PDF’s, either privately for personal reference or publicly as part of an online discussion.

At the HighWire Publisher meeting in California this week, a number of key trends in research behaviour were revealed. The Libraries and Academic Research division of Stanford University has carried out 45 interviews to ascertain the information-seeking behaviours of its own researchers, with some enlightening results.

General patterns of behaviour
Many respondents described using “more automated” alerts to stay up-to-date with new material in their field of study. Some reported reading 5-10 journals per week. However, what is interesting is that users defined ‘reading a journal’ as simply browsing through an electronic table of contents or email alert, rather than scanning it from cover to cover. On these eTOCs, researchers would like to see greater annotation. Ideally, they pointed to the inclusion of ‘take home messages’ for each article, so that they might ascertain the suitability of the article to their needs before clicking through to the abstract.

“I don’t review journals, I search databases”. Researchers admitted to only swatting up on the current literature in their field when writing a specific paper or applying for a grant. Research is therefore often driven by necessity and not habit. “I read for a purpose, always with a goal”. This means that users are often missing out on discovery, browsing and serendipitous findings when working in online environments. Interviewees also felt that online journals were missing thematic connections. They reported that whilst these used to be present in print journals through editorial curation, the same context was not usually available through online journal sites.

Context
Context is key and was enthusiastically advocated as one of the major benefits of researching within an online environment. During a panel session at the conference, one researcher suggested that articles should be viewed as portals to greater information rather than the end product. The respondents would like to see more ‘similar articles’ and recommendations on particular topics, instead of browsing archives by issue or year, which would be an obvious benefit of semantic technology.

Annotation tools
Another panel member at the conference who participated in the study, argued that highlighting and annotating tools are imperative for researchers online and need to be as easy to use as in print. A great deal of time and effort is wasted on keeping track of what a researcher has read rather than exploring the subject matter. This process is multi-level, piecemeal and often involves individual systems with no interoperability. Kindle was offered as a solution to this problem. Not only can users add comments and highlighting to articles and ebooks, but they can then log-in to their account and pull off all of these notes into one central document. The device can also be used to see which sections of text other users are focusing on.

Discovery tools
PubMed was listed as the top discovery tool of choice. The second most popular was Web of Science, followed by Google Scholar (mentioned by a third of respondents), Wikipedia (to obtain initial overviews of new topics) and Google. One interviewee confided that they, “use Google to vacuum around the edges of the carpet”. Most databases only contain formal articles but researchers are sometimes eager to find additional context, and that is where Google comes into play.

Reading patterns
Unsurprisingly, there is a common tendency to print the PDF of an article when reading in-depth. On-screen reading is associated with retrieving snippets of information and following links, but many prefer to read significant chunks of text offline. Abstracts, figures, introductions, conclusions and subheadings were all identified as skimmers’ touchpoints. Supplemental data was regarded as important but inconvenient due to it’s fragmented and inconsistent nature. Some publishers, such as The Journal of Neuroscience, are getting rid of supplemental material completely. Their thinking is that if a figure is essential to the article body, it should embedded within the text and not tagged onto the side as an afterthought.

Conclusions
The researchers in this study were conservative towards change. They were only interested in new concepts that could significantly increase their productivity. HighWire highlighted a number of key areas for journal publishers to focus on:

• Facilitate selection of what to read
• Information extraction and skimming
• Supplemental data management
• Portable annotation
• Integrated literature management

Publishers should be working with the tools researchers are using externally. To be in a position to fully achieve this, we should be investing more time in semantic technologies and initiatives such as data mining and linked data. The study is not yet complete so watch this space for updates in the coming year.

Following a recent ethical and transparency audit by Liz Wager, Chair of COPE (Committee on Publication Ethics), the specialist journals have revamped their editorial boards. As well as tidying up the structure of these pages and correcting any stylistic errors, we have collected each journal Editor’s competing interests and made them publicly available.

New design and comprehensive listings

Each journal now has a complete and up to date editorial board, which includes the full names, institutions and locations of all board members. In addition, the email addresses of the core editors are included to promote interaction with our authors and users. The layout has been cleaned up and as a result is much more user-friendly.

Competing interests

Editor’s conflicts of interest are a fundamental principle of transparency. If authors and reviewers are expected to declare their competing interests, then Editors should do the same. Please see below an example of the competing interest form each of our Editors is asked to complete:

1) Have you in the past five years accepted the following from an organisation that may in any way gain or lose financially from the publication of papers in *insert journal name*?

a) Reimbursement for attending a symposium?
b) A fee for speaking?
c) A fee for organising education?
d) Funds for research?
e) Funds for a member of staff?
f) Fees for consulting?

2) Have you in the past five years been employed by any organisation that may in any way gain or lose financially from the publication of papers in the *insert journal name*?

a) Do you hold any stocks or shares in an organisation?
b) Do you have any other competing financial interests?
c) Do you have any other financial competing interests? If so, please specify.

To view a specific Editor’s competing interests, simply navigate to a journal editorial board (e.g. http://bjsm.bmj.com/site/about/edboard.xhtml) and click on the “Competing interests” link underneath the Editor’s name. You will then be taken to the BMJ Editorial Advisory Board or the Group site, where all of our competing interest statements are hosted, often accompanied by brief biographies of the Editors in question.

The BMJ Group’s first dedicated palliative and supportive care journal went live online this week, in preparation for the impending launch in April next year. Check out the new blog site here – https://stg-blogs.bmj.com/spcare/ and show your support by following the journal on Twitter and Facebook.

Introducing BMJ Supportive & Palliative Care

BMJ Supportive and Palliative Care is our newest, peer-reviewed journal with international reach. It aims to link many disciplines and specialties throughout the world; promoting an exchange of evidence based research and innovative practice by publishing high quality transitional research, clinical trials, epidemiology, behavioural sciences, health service research, reviews, and comment.

Following the launch in 2011, BMJ Supportive & Palliative Care will be published quarterly in print and continuously online. It will aim to target not only doctors, but different categories of clinician and healthcare workers associated with palliative medicine, specialist or generalist palliative care, supportive care, psychosocial-oncology and end-of-life care.

The journal’s broad scope makes it a relevant and important resource for palliative care specialists, as well as doctors and nurses in medical and surgical specialties including cardiology, gastroenterology, neurology, oncology, paediatrics, primary care, psychiatry, psychology, renal medicine, respiratory medicine.

A world-class editorial team, which will be lead by Dr Bill Noble, Macmillan senior lecturer in palliative medicine at the University of Sheffield and honorary consultant physician in palliative medicine at Sheffield Teaching Hospitals NHS Foundation Trust, will ensure a high standard of practice-changing research and education.

The new BMJ Supportive & Palliative Care website – scheduled to coincide with the first edition – will play an important role in the overall journal and feature all content ahead of print, as well as offering regular news updates, podcasts, blogs, polls, and eventually, interactive educational features.

Look out for more posts and updates on the BMJ Supportive & Palliative Care blog in the build up to the official launch of the journal at COMPASS, April 2011.

Following a previous post on the Semantic Web, this week we’ll be exploring the implications of this web of data for the publishing world. Semantic web technologies, as opposed to the grander idea of the Semantic Web itself, offer tools that can help publishers assemble and distribute their content more efficiently.

What is semantic publishing?

Fundamentally, semantic web publishing refers to information published on the web, accompanied by semantic markup. Semantic publication makes information search and data integration more effective by equipping computers with the ability to understand the structure and even the meaning of the published information. In the Semantic Web, published information is accompanied by metadata describing the information, thereby providing a ‘semantic’ context.

What difference could this make to the publishing world?

Many believe that semantic publishing has the potential to revolutionise scientific publishing. Tim Berners-Lee predicted in 2001 that the Semantic Web “will likely profoundly change the very nature of how scientific knowledge is produced and shared, in ways that we can now barely imagine”. Revisiting the Semantic Web in 2006, he and his colleagues argued that it “could bring about a revolution in how, for example, scientific content is managed throughout its life cycle”. Researchers could directly self-publish their experiment data in ‘semantic’ format on the web and semantic search engines could then make these data widely available.

Creating richer metadata – the technical bit

Metadata is used by most publishers in some capacity. The majority also use taxonomies (a hierarchy of terms used to categorise content), although they might not be aware of this name. The next step towards richer metadata is the use of ontologies. Mimicking the relationship between taxonomies and metadata, ontologies make taxonomies look ‘flat’. Ontologies describe more detailed relationships among concepts and provide a higher level of richness in the metadata.

Taxonomies are very similar to the animal and plant kingdom taxonomies, in which every species is located in a particular branch. However, more conceptual objects don’t always fit so nicely into this basic lineage. If a publisher created a taxonomy based on colours with the following—red, yellow, and blue—as the top nodes, purple would need to be related to both red and blue. In a simple taxonomy, the term ‘purple’ would probably be repeated under both, but in a technical sense they would actually be two distinct nodes that have the same name.

In an ontology, however, purple can be represented as the same concept appearing in multiple nodes on the tree. However, rather than being tree-like, ontologies are a complex mapping of concepts with defined relationships between those concepts (such as ‘subclass of’ or ‘part of’).

In the video below, Louise Tutton, COO at Publishing Technology, talks about the Semantic Web and its opportunities at Online Information, London (30th November).

http://www.youtube.com/watch?v=Ky_JUDWXEDU