I'd like to contribute to use cases and examples in our Beyond the PDF discussions. Reading is an activity that has been heavily studied in the library & information science and usability communities. It's also key to our preference for the scientific paper over other forms (i.e. the fact-based database, the oral presentation). My goal is to translate these findings into ideas for future prototypes.
At the moment, three main topics stand out in my mind: active reading, just-in-time reading, and reading avoidance. By "active reading", I mean purposeful often non-linear reading, often accompanied by skimming, scanning, highlighting, and note-taking. By "just-in-time" reading, I mean delving into the literature at the end-stages of the writing process, to scan for omitted literature or new findings. "Reading avoidance" means assessing and exploiting content with as little actual reading as possible.
Renear & Palmer call for ontologies to be used not only for retrieval, but also for "ontology-aware reading tools". In order to envision the reading tools of the future, we need to look at what is known about what scientists actually do when they read, their underlying reasons for reading, and the ways in which the PDF (and other forms of the scientific paper) are meeting and falling short of their needs.
Renear, Allen H., and Carole L. Palmer. 2009. “Strategic Reading, Ontologies, and the Future of Scientific Publishing.” Science 325:828-832.
Tenopir, Carol, Donald W. King, Sheri Edwards, and Lei Wu. 2009. “Electronic journals and changes in scholarly article seeking and reading patterns.” Aslib Proceedings 61:5-32.
Marshall, Catherine C. 2009 Reading and Writing the Electronic Book. Morgan and Claypool Publishers.