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Now scientists from the universities of St Andrews and Edinburgh are using ground-penetrating radar equipment to map out what else may lie beneath. The waves bounce off cavities or tunnels carved into the rock below.
The team has discovered that the subterranean network is at least double the size originally thought. Simon Shackley, from Edinburgh University's School of Geosciences, said: "On the other side of Gilmerton Road there is a rather large chamber that is probably about 4m [13ft] deep."
"There also appear to be cavities in front of the cove and behind it - both about 2m deep".
Dr Richard Bates, of St Andrews University, told BBC Scotland the tunnels were "strange places" with very little detail about who used them or why they were built in the first place.
"Perhaps by the work we're doing - if we're getting a bigger picture we're mapping in a more extensive way the footprint of it - then what we're hoping is that will tell us something about the use," he said.
"If it's got lots more passageways or maybe it's only got these two single passageways, but they might be leading somewhere else. And where they're leading to could potentially tell us what these were used for."