As a vehicle for disseminating scientific knowledge, the PDF gets a lot of bad press. In this article, we argue that there are more important things to be worrying about.
S. Pettifer, P. McDermott, J. Marsh, D. Thorne A. Villeger and T.K. Attwood Ceci n’est pas un hamburger: modelling and representing the scholarly article. Learned Publishing, 24:3, July 2011.

The paper that started it all! This non-technical article is a review of various initiatives (primarily from the Life Sciences) to link published articles to their underlying data sets. It culminates by introducing Utopia Documents, and is itself a demonstration of the software’s features. Read it using Utopia Documents for the best experience! It’s an Open Access publication, and is free to download.

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Calling international rescue: knowledge lost in literature and data landslide! Biochemical Journal, Dec 2009.

This more technical introduction to Utopia Documents was presented at ECCB10 on September the 26th.
T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents: linking scholarly literature with research data. In Proceedings of 9th European Conference on Computational Biology, Ghent, Belgium, Sep 2010.

Another Open Access publication, describing the technology/architecture and philosophy of the the Utopia system.
S. R. Pettifer, D. Thorne, P. McDermott, J. Marsh, A. Villéger, D. B. Kell, and T. K. Attwood. Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 16, Jun 2009.

A fairly non-technical review of tools for managing and interacting with digital literature. Not a Utopia-specific paper, but useful background to our work. Open Access.
D. Hull, S. R. Pettifer, and D. B. Kell. Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Comput Biol, 4(10):e1000204, Oct 2008.