Table 4.

Summary of positive and negative matches between the manual annotation set and the automated annotation set. There were a total of 160 manual annotations (gold-standard set) and 231 cTAKES annotations. True positives were defined as manual annotations with an exact or partial match in the cTAKES annotation set. False negatives were defined as manual annotations with no cTAKES match or those with a match that was assigned incorrect polarity by cTAKES. False positives were defined a cTAKES annotation that had no overlap with a manual annotation

	Number	Percentage
Manual annotations (gold standard)	160
Automated annotations (cTAKES)	231
True positives	137	85.6
Perfect cTAKES matches	93	58.1
Partial cTAKES matches	44	27.5
False negatives	23	14.4
Manual annotation with no cTAKES annotation	10	6.3
Incorrect polarity assigned by cTAKES	13	8.1
False positives	71	31
cTAKES annotation with no manual annotation	71	31