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I am currently taking Katy Borner's class via Indiana University's online system:
We are learning to use the Sci2 tool and next week we'll be covering GIS data. Sci2 content is exported as PDF and then marked up using InkScape, a free analog to Adobe Illustrator.
There is a nice book that goes with this class, $25 on Amazon.
Prior to this I have used Sentinel Visualizer for handling geospatial data, but this is an expensive commercial app focused on anti-fraud/LE/counter-insurgency uses. I've done a good bit over the years with Garmin's GIS tools for microwave data link install and some work with postal codes and geo coordinates. I haven't gone deep enough into Sci2 to be able to speak to its handling of such content yet.