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I am considering using a custom Service Application to meet a feature requirement of one of my clients. There is also a requirement that the data stored by the Service Application be searchable.

Does anyone know if a custom service application can be indexed, and how to do it?

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If you have a custom service application it will presumably have a custom database. You can crawl that using BCS as you would any other (non-SharePoint) database. If the service application data is stored in some other way you could create a custom connector and again use BCS. More involved, but you are already in pretty deep if you are building a custom Service Application ;-)

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