Table 3.

Performance of text-based sequence extraction for cis-regulatory annotation

	dm2	hg18	mm8	ce2	rn4	All
Number of ORegAnno annotations	2,079	589	255	178	107	3,208
Number of PMIDs with ORegAnno annotation	389	283	113	30	48	850
Number of PMIDs with Ensembl target gene name(s)	388	253	107	29	42	819
Number of text hits from PMIDs with ORegAnno annotation	188	128	51	16	32	415
Number of text hits that overlap ORegAnno annotation	149	54	36	13	17	269
Percent text hits that overlap ORegAnno annotation (PPV)	79.3%	42.2%	70.6%	81.3%	53.1%	64.8%
Number of ORegAnno annotations overlapped by a text hits	681	133	149	22	64	1,049
Percent ORegAnno annotations overlapped by a text hits (SN)	32.8%	22.6%	58.4%	12.4%	59.8%	32.7%
Number of PMIDs with text hits	124	91	44	12	24	295
Percent PMIDs with text hits (coverage)	31.9%	32.2%	38.9%	40.0%	50.0%	32.2%
Number of PMIDs with text hits to correct species	123	84	37	12	18	274
Percent PMIDs with text hits to correct species (PPV)	99.2%	92.3%	84.1%	100.0%	75.0%	92.9%
Number of PMIDs with text hits and Ensembl target gene name(s)	122	77	33	11	16	259
Number of PMIDs with text hits and perfect match to correct target gene name(s)	67	57	24	4	10	162
Number of PMIDs with text hits and partial match to correct target gene name(s)	16	12	5	3	4	40
Percent PMIDs with text hits and match to correct target gene name (PPV)	68.0%	89.6%	87.9%	63.6%	87.5%	78.0%
Number of PMIDs without ORegAnno annotation with text hits	76	1,291	841	13	459	2,680
Number of text hits from PMIDs without ORegAnno annotation	126	2,602	2,131	14	1,002	5,875
Number of text hits from PMIDs without ORegAnno annotation that overlap ORegAnno annotation	59	202	58	1	18	338
Number of ORegAnno annotations overlapped by text hits from PMIDs without ORegAnno annotation	200	347	139	3	33	722