FSA: Finite State Automata
There has been development of concepts and toolkits for n-ary finite automata, which might provide a useful model for expression, creation and search of multidimensional linguistic annotations. We can cite the following toolkits:
LADL, Xerox, AT&T, van Noord and Grail+ though as far as we know, these have not been used for general manipulation of speech annotations, and may not be suitable in detail for this purpose.
A comprehensive, albeit old list of finite-state machine software, products, and projects can be found on the Grail+ linkpage.