The situation outlined above is simply unacceptable in today's technologically-advanced world. The limits imposed on the length of articles and their corresponding references derive almost entirely from the constraints of paper-based publication. While these made sense for most of the 20th century, they make no sense at all today, and they distort and even imperil the scientific process. In the 21st century, fewer and fewer scientists peruse paper copies of journals. While one might argue that supplementary material can help improve the presentation of articles, especially in electronic form, the excessive and largely unregulated use of supplementary material is harmful to science. As we discussed above, the scientific quality and validity of supplementary files is rarely evaluated during the review process. Furthermore, cross-referencing prior works is a vital component of the scientific endeavor, yet many scientists' contributions go unrecognized, buried deeply in supplementary files and not tracked by citation indices. This situation disproportionately affects scientists developing the analytical methods that have, in many respects, made the current scientific revolution possible. Authors, reviewers, and journals alike must ensure the adequate acknowledgment, within every scientific article, of all prior work relevant to the study being published.
The ubiquitous use of electronic media in modern scientific publishing provides an opportunity for the better integration of supplementary material with the primary article. Specifically, we propose that supplementary items, irrespective of format, be directly hyper-linked from the text itself. Such references should be to specific sections of the supplementary material rather than the full supplementary text. Mechanisms for providing such links are available in virtually all commonly used word processors, as well as in the commonly used display media (HTML, PDF, etc.), thereby requiring no additional infrastructure to be put into place. The availability of the supplementary information just 'one click away' would not only dramatically improve the utility of published scientific articles, but also increase the likelihood that supplementary material are adequately evaluated during the review process.
Some journals have already taken steps towards providing a rich interface to their articles, and in many cases the supplementary tables, figures, or other media are appropriately hyperlinked directly from the manuscript. In PNAS, for example, online articles are presented in a feature-rich format that includes several useful interactive items: (i) hovering on a citation retrieves the citation in a pop-up widget; (ii) figures and table references are hyperlinked to the actual display item; (iii) files containing supplementary tables and other data are directly hyperlinked from the manuscript, allowing readers to download these items with a single click. In PNAS, these features are also preserved in the PDF version of the articles, and furthermore the supplementary material is automatically included within the downloaded PDF. In most other journals supplementary material must be downloaded separately.
In addition, we believe that removing arbitrary article size limits, at least for the online versions of articles, would have an important impact on removing the artificial distinction between supplementary material and the main manuscript text. An interesting compromise in this direction is exemplified by Nature Methods, where articles are accompanied by an Online Methods section that appears in both the online version of the article and the downloaded PDF.
In our discussion above we have singled out two manuscripts published in Science, primarily because Science is one of the few journals that provides clear instructions to authors and reviewers on supplementary material, yet articles published in this journal frequently overuse supplements. A more extensive analysis of supplementary materials across journals is beyond the scope of this editorial, however interested readers can examine such an analysis recently done for environmental science journals , as well as our own survey of 70 highly cited genomics papers from 7 different journals (Additional file 1: Table S1).
Given the extensive use of supplementary material, and the potential harm it poses to science, it is critical that all scientific journals develop clear and consistent policies on the use and review of supplementary material. Some initial recommendations on the use of supplementary material were recently outlined in a report of the National Information Standards Organization and the National Federation of Advanced Information Services , but these recommendations still need to be implemented and refined to ensure the ethical and consistent use of supplementary material in our discipline. We hope our paper will motivate scientists and publishers to enact desperately needed changes in the way supplementary materials are evaluated and used in scientific publishing.