A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems

BMC Bioinformatics

Table 3 Evaluation results on the whole, abstract, and full paper collections from the training set of BioNLP-ST 2011 GE task

	Whole			Abstract			Full
	P	R	F	P	R	F	P	R	F
Whole set
Simple event	92.40	67.16	77.78	93.11	66.87	77.84	89.36	68.44	77.52
Gene_expression	92.27	69.18	79.07	93.01	68.82	79.11	89.86	70.43	78.96
Transcription	92.43	55.54	69.39	92.88	55.67	69.61	89.66	54.74	67.97
Protein_catabolism	91.01	71.05	79.80	93.10	71.05	80.60	–
Phosphorylation	97.42	77.44	86.29	97.78	76.74	85.99	95.00	82.61	88.37
Localization	90.43	70.03	78.94	91.24	70.46	79.52	76.92	62.50	68.97
Binding	90.83	50.77	65.14	90.76	50.68	65.04	91.43	51.61	65.98
Total	92.08	63.10	74.88	92.60	62.57	74.68	89.61	65.83	75.90
Subset with selected triggers
Simple event	92.29	79.08	85.18	92.98	78.92	85.38	89.36	79.79	84.31
Gene_expression	92.27	79.85	85.61	93.01	79.25	85.58	89.86	81.94	85.71
Transcription	92.00	76.52	83.55	92.37	77.93	84.54	89.66	68.42	77.61
Protein_catabolism	91.01	77.14	83.51	93.10	77.14	84.38	–
Phosphorylation	97.42	81.62	88.82	97.78	81.48	88.89	95.00	82.61	88.37
Localization	90.04	77.04	83.03	90.83	77.65	83.72	76.92	66.67	71.43
Binding	90.25	70.94	79.44	90.11	70.47	79.09	91.43	75.29	82.58
Total	91.88	77.32	83.97	92.35	76.95	83.95	89.61	79.22	84.09

ISSN: 1471-2105