An Overview of Biomolecular Event Extraction from Scientific Documents

Table 6

Event enrichment performance comparison. BioNLP shared task comparison results in recall/precision/F-score (%) on the test set for Task 2 (event enrichment). (A) abstracts only and (F) full papers. Data extracted from BioNLP-ST 2009, BioNLP-ST 2011, and BioNLP-ST 2013 overviews [51, 52, 109].

Year	System		Site	Localization	Total
2009	UTurku + DBCLS09; Björne et al. [86]	(A)	71.43/71.43/71.43	23.08/88.24/36.59	32.14/72.41/44.52
2011	FAUST; Riedel et al. [111]	(A); (F)	43.51/71.25/54.03; 17.58/69.57/28.07	36.92/77.42/50.00; —	41.33/72.97/52.77; 17.39/66.67/27.59
	UMass; Riedel and McCallum (b) [104]	(A); (F)	42.75/70.00/53.08; 16.48/75.00/27.03	36.92/77.42/50.00; —	40.82/72.07/52.12; 16.30/75.00/26.79
2013	TEES-2.1; Björne and Salakoski [97]	(F)	20.68/59.82/30.73	36.67/78.57/50.00	22.03/61.90/32.50
	EVEX; Hakala et al. [91]	(F)	19.44/59.43/29.30	36.67/78.57/50.00	20.90/61.67/31.22

Only phosphorylation sites were considered.
The results are for overall binding and phosphorylation sites.
The task included the prediction of sites for other protein modification and regulation events.