Base of chalk, a limestone extract (6)
I believe the answer is:
alkali
'base' is the definition.
(I know this)
'of chalk a limestone extract' is the wordplay.
'of' says the answer is hidden in the clue.
'ALKALI' is hidden within 'chalk a limestone extract'.
(Other definitions for alkali that I've seen before include "Substance that neutralises acid" , "Substance such as lime or caustic soda" , "Basic stuff" , "Opposite of acid" , "Substance turning litmus paper blue" .)