@nafergo The
#COLLADA and also the
#X3D file format allows to add custom structured metadata fields (XML) within the model file itself.
If you need (semantic) annotation of parts of the 3D model, then probably a "Repository Infrastructure" as proposed by the
#3D-COFORM project would be the way to go (e.g. see
http://dx.doi.org/10.2312/VAST/VAST12/041-048).