Medscape has a nice article on pharmacy integration techniques found here.
The article reviews the following four choices detailing the benefits and risks.
1.) an integrated all-in-one CPOE and pharmacy system
2.) a bidirectional interface between the pharmacy system and the CPOE medication-ordering system.
3.) a unidirectional interface between the CPOE and the pharmacy system.
4.) No interface between the CPOE and pharmacy system.
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