Utopia Documents v2.0 is a free PDF reader that connects scientific articles to online content. It allows link-outs to the web directly from highlighted text in a PDF to a range of data sources, scientific information, and semantic search tools. Users can interact directly with curated database entries—play with molecular structures, edit sequence and alignment data, and plot and export tabular data. It also features article metrics, whenever available, that let researchers see how articles are doing in the blogosphere, twitter, news, etc. Utopia Documents is usable in all scientific disciplines, but its link-out resources are optimized for the biomedical/biochemical spectrum.