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answers:

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A client has a number of disparate systems that they are planning to link together and have asked for a set of system interface specifications that would document the data and protocols used to interface the different parts.

The interfaces are between processes not between users.

Any recommendations for a template that we could use to document the system interfaces?

+1  A: 

This book might have the sort of guidance you're looking for: Enterprise Integration Patterns: Designing, Building, and Deploying Messaging Solutions

Mitch Wheat