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I am making a chat bot that requires the use of 3 external APIs to be used as responses. When wanting to call an external API from within Watson Assistant, webhooks would be required to connect to one API either locally or on the cloud (IBM functions). How would I connect more than one API to the assistant if possible ?

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Unfortunately no, not at this time. The design was meant to have a middleware app that orchestrated the apis, formats the data, etc just like the video in the docs.