I would like to ask you to have a look at the Linguistic Annotation Framework, which provides a graph-based "pivot format" which is intended to serve as the lingua franca for annotations schemes (in terms of form, not content). The idea is that everyone uses his/her own format, provided it conforms to an abstract data model, and then there is a tool that can transform this into the generic graph format (GrAF). In this form, annotations can be easily merged and compared, and -- most interestingly for your group -- transduced to any other format that a given tool needs. Or, one would assume, someday tools might all use GrAF as input. GrAF is designed to be perfectly generic, and has been shown to be able to handle all kinds of annotations. We already have "Proff of concept" tools to transduce many formats into GrAF and tools to export GrAF to a wide variety of formats.

Even if you do not use LAF/GrAF itself, please look at the LAF documents (links to them on the wiki pages of Working Groups 1 and 7) because the ideas and principles are the result of 20 years of thinking on this topic.

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