Pliny was a tool for working with annotations when conducting personal scholarly research, and can be used with both digital and print materials. It also had data manangement and organizational features, and was designed to facilitate reading, reacting to that reading and forming an interpretation. Pliny stored all data on the user's computer rather than remotely on the web.
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As of 2017, Pliny is no longer being developed. However, the site is still up and functioning, which can be found above.
Pliny was used in this research abstract available in XML format https://raw.githubusercontent.com/lehkost/ToolXtractor/master/data/xml/2015/BRADLEY_John_How_about_Tools_for_the_whole_range_of_sch.xml