Actually it depends on the mafacturer. Some like KHS and iron Horse measure from center og b.b to top of seat collar. Some like trek and GT measure from center of b.b to center of top tube. Some are measured from center of b.b top top of top tube. So with that pull those measurements and see where it ends up.
If the bike has a sloped top tube, then the figure is fairly meaningless. As far as standover height goes, you also have to factor in the height of the bottom bracket from the ground (which can be quite high in some MTBs).
A much more important measurement is the length of the bike, which is a combinbation of effective top-tube length (horizontal dist from seatpost centre to headtube centre), + stem (+ drop bar/brake style). NB some of that length is behind the bottom bracket, some of it is in front. This makes a difference to the fit.
Personally when comparing frame geometries for fit, I take a weighted string and a tape measure, and sketch a quick graph of the points of contact (saddle/pedals/handlebars)