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Is there a freely available dataset (csv, geojson, topojson, etc.) with geocoordinates of ancient cities, for example of the Roman Empire? Ideally with additional information like population size?

I've searched GeoCommons and NaturalEarth but found nothing.

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I would suggest Pleiades as the best option to start with. Lots of data, open source implementation, and you can upload too. You can download in CSV, KML and other formats. You may need to work the links to get supporting data such as population size - I don't know of anything that does that kind of time-varying data across the ancient world.

If you particularly want maps, David Rumsey is worth a look. ECAI (wikipedia link, since primary site appears down) might also be worth checking for your particular domain needs.

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