Partly harmful, certainly that's sore (5)
I believe the answer is:
ulcer
'sore' is the definition.
(I've seen this in another clue)
'partly harmful certainly that's' is the wordplay.
'partly' indicates the answer is hidden within the clue (part of the clue is used).
'ULCER' can be found hidden inside 'harmful certainly thats'.
(Other definitions for ulcer that I've seen before include "Continuing source of pain" , "Cruel kind of open sore" , "Cruel sort of open sore" , "Cruel sort of body sore" , "Stomach or mouth sore" .)