When it comes to 2D-data it seems there are a couple standards out there to represent it in a semantic way (GeoSPARQL, NeoGeo, ...). However I couldn't really find one to do that for 3D-data. I have some CityGML-data but that does not seem to be an appropriate format to do formal reasoning of a geometry level. Do you know of any current standard or groups that work on that problem?
In the field of geology there are some standards evolving:
RESQML is being developed by the Energistics Group which is a consortium of geomodelling software vendors (Paradigm, Schlumberger etc.) and users of this software (Total, CCG, BP etc.). They try to put all the information of their softwares into this standard.
GeoSciML is quite generic standard for geologic data. The OGC is trying to develop this standard in order to make the exchange of geologic data easier. Because it is based on GML (actually it is an application schema of GML) you can also use it to carry 3D models although there is no geo modelling software currently understanding the semantics of 3D GML.
EarthResourceML is related to GeoSciML and more focusing on resources. I have not worked with it so far.
BoreholeML is a standard being developed by the geological surveys of Germany in order to be able to describe boreholes. It also features a 3D geometry.