An analysis of the present system of scientific publishing: What’s wrong and where to go from here

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The Format:
One of the main strengths of our framework is the possibility of creating a homogenous body of scientific literature that will allow for thorough searching and data mining48. To this end it is imperative that a set of universal standards for the formatting of scientific articles be established. In addition it is also important to create a standardized language to describe the information contained within the articles18, 60.
With all of the text of each article available online large scale literature searchers, similar to database searches, will allow users to integrate and incorporate disparate information for analyses. Large scale global searches will allow users to pick out key words or gene names from the entire body of scientific literature. To facilitate more powerful searches, we envision a standardization of formats and key words – similar to MESH terms in the NCBI’s Entrez/Pubmed system61.
Within the potentially unlimited extant of cyberspace, articles will expand and provide not only more information, but more information in a more efficient manner. One potential way of setting a internet journal format is to have the data presented in multiple different layers; articles are accessed by a wide variety of readers (e.g. experts, non-experts and casual readers), all of which have different information requirements which could be satisfied by different layers of the article. (The concept of different layers within an article has been suggested by Dr. Paul Ginsparg, founder of the arXiv physics pre-print archive 7.) For example, the first layer might include the primary data, the information on which the article is based with little or no textual information, thus allowing experts to quickly scan and retrieve data. A second layer would provide more information regarding the material and methodology. The third layer would resemble a short article providing, succinctly the data, methods, and some discussion and conclusion. Finally a fourth layer might include information that might be necessary for the uninitiated reader, including a longer introduction, methods, discussion, conclusion and supplementary materials. While presently space limitations force authors to either leave out information or publish it as supplementary material, a wholly online format would allow researchers to incorporate all their data and textual information into the article.
In addition to the extra space an online format would allow authors and editors to integrate hyperlinks into the papers providing readers with access to further information on the subject at hand, both within the article itself, to other sites, gray information, articles, and, importantly, erratum62. Furthermore, a list of citations as well as links to derivative works can be continuously and dynamically updated63. Moreover, readers should have the opportunity to post comments on individual articles, organically growing what on paper would have been an inert document.
Present paper-based articles have static tables and figures. An online literature will allow for interactive vibrant and informative figures where users will be able to zoom in on parts that they may be interested in or rotate 3D protein structures. Additionally, the internet allows for dynamically updatable tables that will be available for bulk downloads64
As all new ideas take time to be accepted, some scientists may balk at the idea of “layering” their articles, but in the end such formats would benefit themselves when they need to access other people’s work. Such formatting also requires an integrity of work, laying bare all research and results for scrutiny, allowing for no ambiguity.
Moreover, some authors may be averse to having to carefully structure their articles to conform to some seemingly arbitrary standards. These authors must understand that computers are much more capable of parsing and handling structured and well designed information, and their minimal efforts will go a long way in providing significantly more functionality. In the long run, it is in the interests of the author when her works can be communicated more widely65.

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