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I have an Enterprise Search center configured as a web application in my farm having unique application pool identity. The search traffic across teh farm go to this search center. Now I need to access the top search keywords from here in a separate web application(with different application pool) and display them as a tag cloud. Please suggest a way to do this or a third party webpart for it.

I cannot have the same application pool for both applications. Neither can I keep the credentials in web.config

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In SharePoint 2010, the Web Analytics service is responsible for gathering search stats and storing them in the Logging database.

There are a number of custom ways to get access to this data including implementing a custom web service, or writing a custom web part that pulls the data from the Logging database directly (directly querying the logging database is supported).

There is an out-of-box Web Part called the Web Analytics Web Part that can be configured to display the Most Frequent Search Center Queries, and can be configured to enable an RSS Feed. Using this OOTB web part combined with some JavaScript should allow you to convert the rendered results client-side into a Tag Cloud, otherwise you could reverse-engineer the web part with Reflector and implement your own server-side web part from the same data.

My suggestion, take a look at the Webn Analytics Web Part and see how you can bend it to your purpose.

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