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what is your own application from a technical point of view. Is it a VB app, a C# app? Does it run on the same workstation as the Notes client?
what does it do?
what type of communication between your own app and Lotus Notes do you want to establish, i.e. what would you like to achieve?
what version of Lotus Notes are you running?
In general here are a few things you could do:
In Lotus Notes you can create a button and attach some logic to it. This could be a button in your Toolbar or an action button that is attached to a form or view within a Notes application (for example within your email database). These buttons can trigger the execution of LotusScript code which can manipulate any Notes object (including emails) and also talk to external applications (for example via COM). You need the Domino Designer to do this.
In your VB app you could setup logic to talk to the Lotus Domino Objects via COM.