Research paper 2.0 – how much longer do we have to wait?

February 16, 2009 at 8:46 pm Leave a comment

I was absolutely delighted this Friday when I clicked on the hyperlink pointing to a supplementary figure in a PDF version of a paper in PNAS. You will never guess what happened! Adobe Acrobat actually downloaded the whole of the supplementary information section and appended it to the current document, and, here’s the biggest surprise – it was NOT some half-assed, slightly upgraded version of “data not shown”, with figure legends separated from the actual figures, and a big “DRAFT” watermark in the background. It actually looked and felt like a legitimate part of the paper. Is this a sign of the times? Is it actually happening? Are we going to finally get SI sections whose reading is not akin to the Chinese water torture? Guess not…

I went to the Cell website and picked the first paper that came into sight, clicked on the supplement, and… same ol’, same ol’ – legends first, than legendless figures so large you have to resize them to see anything. In Science, they put a tiny bit of effort into their SI and actually managed to position figure legends under their (still page-size) figures. Same with Nature, except their pdf even lacks links to supplementary info inside of the PDF and you have to go to the website and look for the tiny “Supplementary information” link burried between “Figures and tables” and “Online methods”. Even in pdfs from PLOS Biology (sic!), the champions of online publishing, the bearers of the “new and cool” flag, there are no links inside of the article that would allow you to append supporting information to the file.

I say: Shame on you, top journals! How difficult is it to insert hyperlinks to supplementary information, which, when clicked, will download the specific figure, or, better yet all the printable SI and append it to the end of the pdf? How hard is it to hire a high school kid who will reformat the images and change the font of the legends, so that they feel like part of the paper and are more readable? How damn impossible is it to hyperlink reference number to the actual reference at the end of the article for easy look-up a la PNAS? We live in Web 2.0 era. Time to upgrade your on-line publishing process to 2.0 as well!

A lot has been said by better men and women then myself on the recent “New Year’s resolutions” editorial in Cell, so I won’t get into details, but the gist of it has been that they basically promised a radical rethinking of their publishing strategy in view of the changing requirements for a “publishable unit” in top-tier biomedical journals. Well, I guess instead of thinking so much, they ought to hire a few Web- and DTP-savvy geeks who will make their supplementary info into what it should be – an easily accessible, easily readable, and easily archivable part of an otherwise incomplete paper.

The last thing I want to say is that it is our responsibility to make this happen. If the editors don’t hear OUR, the scientific community’s, complaints, they will hardly even realize how much of a problem these issues are, let alone try to fix them. So please, leave your comments, give me your support and some of that highly coveted link love, and together we can make this happen! I promise I will personally e-mail the editorial staff of the top journals if only I get enough support and helpful suggestions from you, dear readers, and if I can show them that my ranting is not just a voice of one calling in the wilderness.

Update: Please see parts 2 (readers’ comments), 3 (multimedia), and 4 (summary) of this series.

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Entry filed under: Computers in science, Grantsmanship and biomedical writing. Tags: , , , , , , , , , , , , .

Teaching students stuff vs. teaching them to think Research paper 2.0 – Part 2 – Readers’ comments

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