( ( Kidney stones ) ( ( ( is ( ( the term ) commonly ) ) ( used ( to ( ( refer ( to ( ( ( ( stones , ) or ) calculi ) , ) ) ) ( in ( the ( urinary system ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (JJ Kidney) (NNS stones)) (VP (VBZ is) (ADVP (NP (DT the) (NN term)) (RB commonly)) (VP (VBN used) (S (VP (TO to) (VP (VB refer) (PP (TO to) (NP (NP (NNS stones)) (, ,) (CC or) (NP (NNS calculi)) (, ,))) (PP (IN in) (NP (DT the) (JJ urinary) (NN system)))))))) (. .)))
Kidney stones is the term commonly used to refer to stones,  or calculi, in the urinary system.
(ROOT (S (NP (JJ Kidney) (NNS stones)) (VP (VBP are) (VP (VBN considered) (NP (NP (DT a) (NN disease)) (SBAR (WHNP (WDT that)) (S (VP (VBZ affects) (NP (DT the) (JJ urinary) (NN system)))))))) (. .)))