I am trying to automate the opening of an excel file located in a jobs database within lotus notes. I have been able to open up a window in lotus notes using the url, but I can\
You'll need to use VBA to access Lotus Notes via COM. Then you can get at the NotesEmbeddedObject, save it using the ExtractFile method, and then launch that saved copy.
An example of VBA using Notes COM API: http://www.vbafin.com/Lotus-Notes-VBA-code.php
There's a document on IBM's site that will help you get started:
How to use LotusScript classes with Visual Basic