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There are a number of middleware solutions which allow some form of common access to heterogeneous data. There are many data formats, and there is a large amount of scope to provide translation between different types of database, and different file formats. Some of these translations would be very specific, but there may be some more generic patterns which have not been developed.
A large innovation would be to develop a common query language for searching and retrieving information from arbitrary sources. Currently there are systems which allow access to relational style databases and files or to xml databases. Extending these to work in a more generic way could provide a very powerful abstraction on top of the data. Unfortunately xml and relational models for databases do not match well with each other, so a general query language would have performance problems to solve.
Another solution to the problems of heterogeneous data is to provide data warehousing, where an intermediate data store is used. All input data is transferred to the warehouse, and transformed in to one common format to make the data easier to query.