There are some Java libraries available that can work with PDF files. You could use these within Integration Server, exposing services to retrieve data from a PDF and then map/process that data as needed. Do a search on the 'net for available tools and pick one that looks to fill the need you have.
I’ll reiterate Mark’s caution: this will likely be a fragile solution, highly susceptible to breaking due to even minor changes in the PDF. You’d be wise to explore other alternatives first.
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