August 2007
The Coming Revolution in Scholarly Communications & Cyberinfrastructure
J. Lynn Fink, University of California, San Diego
Philip E. Bourne, University of California, San Diego

SciVee: Pioneering New Methods of Scientific Communication

In addition to the BioLit tools for authoring and data integration, we want to use cyberinfrastructure to the fullest advantage. Due to the increasing availability of high bandwidth and consumer-level video recording equipment, internet video is now wildly popular. We want to take advantage of this trend and use this medium to communicate science more effectively. It is important, however, to bear in mind the need for quality content. To this end, we have developed SciVee, 11 which allows authors to upload an article they have already published (open access, naturally) with a video or podcast presentation (about 10 minutes long) that they have made that describes the highlights of the paper. The author can then synchronize the video with the content of the article (text, figures, etc.) such that the relevant parts of the article appear as the author discusses them during the video presentation. We call the result a pubcast. Figure 2 shows a typical view of a SciVee pubcast.

Figure 2

Figure 2. A SciVee pubcast. This figure shows how a video presentation is integrated with a published article. While the speaker is discussing a point from the article, the relevant figure or text is highlighted. The viewer can also download the original paper as a companion to the pubcast.

Anyone can visit SciVee and view the pubcast. It is similar to attending a conference to hear a particular speaker, except that the pubcast is available on demand, can be viewed any number of times, and explicitly refers to the content of the original article. Another important feature of SciVee is the ability of any user to add or read comments on pubcasts. This allows a community to be established around an article and encourages discussion about the results and their impact on the field. We believe this activity will transform what has traditionally been a static document into a dynamic exchange.

SciVee makes it easier and faster to keep up with current literature by delivering the key points of articles in a portable and enjoyable medium. A reader can interact with several articles using this website in the time it would take to read a single full article in the traditional way.


We believe revitalizing journal articles will have a significant impact on the scientific community. The traditional article format no longer effectively supports the research in the electronic age. The number of articles researchers need to read in order to keep up with their field has increased significantly in the last decades. In addition, there is an increasing number of articles that report data generated in a high-throughput manner and the primary method of exploring these data is through a database, not through the article itself. In part, these phenomena are due to the increasing reliance on cyberinfrastructure to perform research. It is thus a natural response to use cyberinfrastructure to address this situation. Indeed, our initial tests have proven quite successful. A large group of students in the UCSD School of Pharmacy and Pharmaceutical Sciences were shown an eight minute pubcast of a recently published paper and were then quizzed on their comprehension. Their results were compared to students who were given the paper and eight minutes in which to read it. The pubcast group largely outperformed the paper group and, perhaps more importantly, greatly enjoyed the experience.

SciVee and the BioLit tools will complement similar efforts such as the Stuctured Digital Abstract,12 MutationFinder,13 and BioCreAtIvE.14 We hope that the scientific community will embrace these efforts and use cyberinfrastructure to its fullest capacity to make scientific communication more enjoyable and effective.

This work is supported by grants 0544575 and 0732706 from the National Science Foundation
1Public Library of Science – www.plos.org
2RCSB Protein Data Bank – www.pdb.org
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6Creative Commons Attribution License - www.plos.org/journals/license.html
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9Harris, M. A., Clark, J., Ireland. A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C. et al. "The Gene Ontology (GO) database and informatics resource," Nucleic acids research 2004, Vol. 32(Database issue), pp. D258-261.
10Medical Subject Headings - www.nlm.nih.gov/mesh
11SciVee - www.scivee.com
12Gerstein, M., Seringhaus, M., Fields, S. "Structured digital abstract makes text mining easy," Nature 2007, Vol. 447, no. 7141, pp.142.
13Caporaso, J. G., Baumgartner, W. A., Jr., Randolph, D. A., Cohen, K. B., Hunter, L. "MutationFinder: A high-performance system for extracting point mutation mentions from text," Bioinformatics (Oxford, England) 2007.
14Hirschman, L., Yeh, A., Blaschke, C., Valencia, A. "Overview of BioCreAtIvE: critical assessment of information extraction for biology," BMC bioinformatics 2005, Vol. 6, suppl. 1, pp. S1.

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Reference this article
Bourne, P., Fink, L. "Reinventing Scholarly Communication for the Electronic Age," CTWatch Quarterly, Volume 3, Number 3, August 2007. http://www.ctwatch.org/quarterly/articles/2007/08/reinventing-scholarly-communication-for-the-electronic-age/

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