There are special magma vents in certain levels, which you can deploy a Robo Miner on top of, once the required tech has been researched. The result is a rare ore mine.
You can't mine lava flows in general, only the special magma vents.
The Eden Starship Colony game can have a random magma vent to the lower right of the starting base. You can restart the level a few times until you see it.
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