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I think Windchill is written in Java as the graphical user interface that works on any browsers or platforms. So JLink suggested by phoxeoy or perhaps ProToolKit can be the backbone for your HTML interface.
In addition, I'd think database knowledge (Oracle) is the essential skill beside Java and C for your idea since you no longer need ProE to drive the intructions. It can be very complicated to accomplish something very simple. PTC does not offer any JLink or PTK trainings. That says they don't really support those modules well.
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