If yen was worth 0.0035 six month ago and is worth 0.0045 today how much the yen appreciated or depreciated?

Currencies are traded as a relative to another currency and I am not sure what your 'alternate' (terms) currency is, but assuming you mean 1 Japanese yen = 1 XXX, then the Yen has appreciated by 28.57% (0.0045/0.0035 - 1).