Table 3.

Summary of second experiment

Diseases	Number of patients			Evaluation
	Annotations	MetaMap	cTAKES	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
Diabetesa	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
Hypercholesterolemiaa	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
Depressiona	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/Cholecystectomya	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 Insufficiencya	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

The values improved are in bold

^aDiseases formed by two or more UMLS concepts