1. Evolving the Scientific Article
Keith Wollman
VP of Web Development and
Operations, Cell Press
2. Cell Press Background
Cell founded in 1974 at MIT Press
Benjamin Lewin bought Cell in 1986: Cell Press is born
Over next 13 years, Cell Press launches 3 journals:
Neuron (1989), Immunity (1994), Molecular Cell (1997)
Elsevier buys Cell Press in April 1999
-acquired Current Biology, Structure, Chemistry & Biology
-launched Developmental Cell, Cancer Cell, Cell Metabolism,
Cell Stem Cell, Cell Host & Microbe
-merger with Trends journals in 2007
-Cell Press Society Journals:
AJHG (2008), Biophysical Journal (2009)
3. Project Goals
Rethink the online presentation of an article.
Develop a hierarchical presentation of text and figures so that
readers can elect to drill down through the layers of content
based on their level of expertise and interest.
Provide multiple mechanisms for conveying the core content
of the article
Redefine the unit of publication to address the problem of
burgeoning supplemental data
Involve the scientific community in developing and refining the
ideas
Integrate video, sound, and animation into the scientific article
4. Contributors
User Centered Design
Director of Disruptive Technology
XML experts
Cell Press scientific editors
Cell Press illustrators and designers
Cell Press authors
Developers
Supplier Partners – DJS and TnQ
5. Article of the Future Prototypes
INTRODUCTION
RESULTS
DISCUSSION
15. User Feedback Stage 3
Survey with > 500 respondents
80% positive
10% neutral
10% negative
Fantastic -- wish I thought of it!
It looks absolutely amazing.
It is simple and practical!
More transparent - less scrolling!
I like the graphical overviews.
Quickly understand concepts.
Finally a way to quickly distil the
essence of the research.
I like "clickable" summary figures.
This is a much-needed change in
article format.
Radically better than what I use
16. Timeline
Beta version launched in July 2009
Launched for research articles in a
production environment on cell.com in
January 2010
Apply format to review articles and introduce
Reflect in summer 2010.
1 and 2. Emilie Marcus, Editor of Cell, was dissatisfied with the online presentation of a scientific article which had essentially remained unchanged since journals started going online in the mid 90s. Her initial vision was of a graphic to capture the content of an article plus act as a mechanism for navigating through the content. We developed a smoke and mirrors presentation to demonstrate the concept – lots of moving parts and clicks but no real scientific content. Presented to editors and management within Elsevier and the concept generated lots of excitement 3. We then tried to see if we could pull it off with real scientific content. Two editors who had recently left the bench were given the task of applying the concept to two papers. Could all the content be linked? We told not to worry about navigation schemes; but just focus on linking the content. We would involve a user-centered design expert to develop the user interface. The two editors ignored our advice and working with designers at Cell Press came up with their own navigation scheme. You can see that their initial ideas differ from the initial vision and are a lot closer to the final prototype. 4. Handed over to a UCD expert who improved on the basic ideas and turned it into a working prototype. Subsequently refined and improved after feedback from end-user groups and one-on-one interviews. (One of the initial groups we hosted at Cell Press provided a wide range of participants including an emeritus professor in his 70s plus senior investigators plus lots of postdocs. Usage patterns obviously varied considerably depending on age and career stage. We used graduate students and post docs predominantly in the one-on-one testing as they are the main users of the content. We made the prototypes publicly available in July 2009 and encouraged feedback from the scientific community via an online survey and I’ll talk about the results of that survey later. Now I’m going to take you on a tour of the prototype to explain the rationale for the format.
The overall goal of this landing page is to convey the core content of the paper in a variety of ways Highlights provide a bulleted list of the key results of the article. A graphical abstract allows readers to quickly gain an understanding of the main take-home message of the paper. The graphical abstract is intended to encourage browsing, promote interdisciplinary scholarship and help readers identify more quickly which papers are most relevant to their research interests. This page integrates multimedia components in the form of a video abstract or an interview with the author of the paper to provide the context of the article.
The editor of the Journal of Number Theory came up with this idea. He started a YouTube channel and encouraged authors whose paper had been accepted to provide a video abstract of their paper. The idea was well received and resulted in the submission of a paper from a Field Medalist (the Mathematics equivalent of the Nobel Prize) solely because the mathematician wanted to do a video abstract. Cell decided to start asking authors of one paper per issue whether they would be interested in submitting an abstract. We had some concerns as the quality of the Journal of Number Theory videos had been variable and had required a lot of preprocessing. We have been delighted with the results and Elsevier has now automated the process of converting the source videos to a format that can be played in place so that we no longer have to use YouTube but can display them on ScienceDirect. Neuron, Current Biology, Developmental Cell and Cell Stem Cell have all started publishing video abstracts.
This tab provides a quick way for the reader to access the main results of the article. The reader can see the figure and caption at the same time. Also provided is the context of the article – the area in the text where the figure is referred to. One of the underlying goals of the project was to address the problem of burgeoning supplemental data. Every Cell Press article is currently published with a supplemental data pdf that contains many figures, tables and additional text. This presents a problem for both reviewers and readers to be able to easily assimilate all this extra material and in the molecular biology domain there has been increasing unrest about this. Cell Press published guidelines in September that help to structure and restrict supplemental information. Initial response from the community has been very positive (but we haven’t reached the point where we tell a nobel prize winner that we won’t publish their favourite piece of supplemental data.)
We implemented a new version of the results section in response to user feedback. This layout allows the reader to see the text, the figure and figure caption all in one screen.
Tables and videos are also incorporated into this format and the reader can see a movie play alongside the text that refers to the movie.
Two versions An overview that enables the reader to understand enough about the experiment so that they can comprehend the results. This is the section that traditionally appeared in print. The extended view contains enough details that a researcher can replicate the experiment. This content usually is contained in the pdf that accompanies the article. We are breaking that content out of the pdf and including it in the xml.
Goal is to be able to filter the reference section in as many ways of possible. The year widget shows the distribution of the references by year. You can sort by year and you can also filter by a a particular author.. The context of the reference is displayed in place as well as providing a link to the part of the text where the reference is cited.
We made the prototypes of this new format available on beta.cell.com in July 2009 and encouraged feedback via an online survey. Overall was very positive. There were some really good suggestions for improving the approach and we have been able to implement some of those in the production version. Two major negative comments are that we have not tried to implement any form of semantic enhancement and that we are not providing access to the underlying experimental data. We have continued to encourage feedback with the production launch in January 2010. Again the overall feedback is positive but there are godd suggestions for continuing to improve the Results section. We ran a pilot of Reflect, a semantic enhancement service which provides an overlay of information about proteins and small molecules, on cell.com in November and De4cember 2009. Reflect was the Elsevier Grand Challenge winner (Explain?). The goal was to see if automated text mining which is never 100% accurate provided enough useful information to the users that they ignore the incorrect matches. We will make Reflect available on cell.com in 2010.
SnapShots are one page graphical summaries of tables of nomenclature and glossaries, full signaling pathways, and cellular processes. Cell started publishing these a couple of years ago and they have become our most successful Review format with the articles being amongst the top 20 downloaded on ScienceDirect. We have just launched Enhanced SnapShots in which we incorporate features that are only available online – animations, embedded captions, and dynamic figures. I’ll give you an idea of the types of things that we’re able to offer in this format: Click on antibiotic name. Close box. Hover over Elongation to show caption, then move cursor away so the box disappers. Move cursor to top right chemical structure so that the 3d model is revealed Click on the animation arrow and then the play arrow to play the animation.
