A great example of a web-friendly, interactive view of a scientific paper is the eLife Lens, example here: http://lens.elifesciences.org/#00380 . They announced the open source project back in June (blog post http://www.elifesciences.org/lens/). This is the direction that web-based paper views are moving toward, and some publishers (notably PLOS) already have quite nice interactive components.
PubMed, the government-run biomedical abstract database, also recently introduced its PubReader app for reading biomedical papers (http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/). But my money's on eLife here — NCBI is better known for its databases than its user interface design (to say the least).
It would be great to see some innovation here (some publishers have absolutely awful web-based journal article views). But as the main format for paper publishing and dissemination, I think the PDF won't be going away anytime soon.
I really like plos, but one criticism I have of their interface is that the figure takes up the entire page, which destroys my easy reference to the rest of the content. e.g. at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fj... Figure 1 takes up the entire height of my screen on my laptop and then I have to scroll back to where it is in the text.
Lens reads JSON, and we convert from XML to JSON using this component: https://github.com/elifesciences/refract. We are working on updated documentation, and a getting started guide, our hope is to make the base system flexible enough to display any "component".
PubMed, the government-run biomedical abstract database, also recently introduced its PubReader app for reading biomedical papers (http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/). But my money's on eLife here — NCBI is better known for its databases than its user interface design (to say the least).
It would be great to see some innovation here (some publishers have absolutely awful web-based journal article views). But as the main format for paper publishing and dissemination, I think the PDF won't be going away anytime soon.