Comparison of MetaMap and cTAKES for entity extraction in clinical notes

Table 3 Summary of second experiment

Diseases	Number of patients			Evaluation
	Annotations	MetaMap	cTAKES	MetaMap			cTAKES
	Annotations	MetaMap	cTAKES	Recall	Precision	F-score	Recall	Precision	F-score
Hypertension	325	336	340	0.99	0.96	0.98	0.99	0.95	0.97
Diabetes^a	259	254	266	0.89	0.91	0.90	0.92	0.89	0.91
Atherosclerotic Cardiovascular Disease (CAD)^a	181	130	205	0.60	0.83	0.69	0.92	0.81	0.87
Congestive Heart Failure (CHF)	172	175	183	0.89	0.87	0.88	0.92	0.86	0.89
Hypercholesterolemia^a	172	159	146	0.88	0.96	0.92	0.81	0.96	0.88
Obstructive Sleep Apnea (OSA)	127	105	102	0.78	0.94	0.85	0.76	0.94	0.84
Osteoarthritis (OA)	87	76	61	0.76	0.87	0.81	0.67	0.95	0.78
Depression^a	83	109	116	0.93	0.706	0.802	0.99	0.71	0.82
Asthma	81	83	92	0.93	0.90	0.91	1.00	0.88	0.94
Gastroesophageal Reflux Disease (GERD)	76	83	85	0.97	0.89	0.93	0.99	0.88	0.93
Gallstones/Cholecystectomy^a	74	65	68	0.865	0.99	0.92	0.89	0.97	0.93
Gout	56	58	58	0.98	0.95	0.96	0.98	0.95	0.96
Peripheral Vascular Disease (PVD)	37	37	32	0.97	0.97	0.97	0.84	0.97	0.90
Venous Insufficiency^a	21	27	30	0.905	0.704	0.792	1	0.7	0.824
AVERAGE				0.88	0.89	0.88	0.91	0.89	0.89

ISSN: 1472-6947