Table 10. COSMIC variant extraction coverage result when only articles with variants in the reference set as well as at least one result identified by the information extraction tool are considered.

The table shows the number of common articles (PMIDs), the number of variants in the reference set (Total), the number of matched variants by the mutation extraction tool (Matched), the proportion of matched variants (Recall), the number of variants matched when the gene is not considered (M NG) and the proportion of matched variants when the gene is not considered (Rec NG). The data sets considered are MEDLINE abstracts (medline), Open Access PMC articles (pmc.ft), PDF articles when no Open Access PMC articles are available (pdf), PDF representation for all the articles (pdf.all), tables available from the Open Access PMC Articles’ XML (table), supplementary material (sup) and the combination from all the sources (all). The tools are Extractor of Mutations (EMU), OpenMutationMiner (OMM), MutationFinder (MF), tmVar and SNP Extraction Tool for Human Variations (SETH). The row with tool value as All indicates the result when the variants extracted by all the tools are merged.

Data set	Tool	PMIDs	Total	Matched	Recall	M NG	Rec NG
medline medline medline medline medline	EMU OMM MF SETH tmVar	128 109 104 16 114	627 483 498 80 515	146 140 126 25 139	0.2329 0.2899 0.2530 0.3125 0.2699	157 147 137 26 145	0.2504 0.3043 0.2751 0.3250 0.2816
medline	All	137	676	156	0.2308	169	0.2500
pmc.ft pmc.ft pmc.ft pmc.ft pmc.ft	EMU OMM MF SETH tmVar	339 299 282 67 308	31742 31405 30415 1425 31391	726 697 632 141 655	0.0229 0.0222 0.0208 0.0989 0.0209	758 726 658 148 682	0.0239 0.0231 0.0216 0.1039 0.0217
pmc.ft	All	351	31848	814	0.0256	853	0.0268
pdf pdf pdf pdf pdf	EMU OMM MF SETH tmVar	61 8 16 2 32	474 64 131 10 294	34 1 5 6 4	0.0717 0.0156 0.0382 0.6000 0.0136	47 1 6 6 5	0.0992 0.0156 0.0458 0.6000 0.0170
pdf	all	64	505	34	0.0673	47	0.0931
pdf.all pdf.all pdf.all pdf.all pdf.all	EMU OMM MF SETH tmVar	439 341 330 83 379	33134 32428 31774 1555 32745	1094 1132 989 246 1049	0.0330 0.0349 0.0311 0.1582 0.0320	1114 1137 996 247 1060	0.0336 0.0351 0.0313 0.1588 0.0324
pdf.all	All	446	33295	1304	0.0392	1327	0.0399
table table table table table	EMU OMM MF SETH tmVar	197 166 146 38 90	1946 1765 1505 509 1128	580 597 462 179 176	0.2980 0.3382 0.3070 0.3517 0.1560	681 699 564 207 233	0.3499 0.3960 0.3748 0.4067 0.2066
table	All	211	2019	694	0.3437	831	0.4116
sup sup sup sup sup	EMU OMM MF SETH tmVar	77 86 76 37 73	27888 31156 30897 28088 30285	19177 20054 1286 21052 7763	0.6876 0.6437 0.0416 0.7495 0.2563	19217 20116 1308 21089 7782	0.6891 0.6457 0.0423 0.7508 0.2570
sup	All	106	31564	22756	0.7209	22829	0.7233
all all all all all	EMU OMM MF SETH tmVar	450 353 344 109 388	33409 32887 32623 29047 33008	20203 20960 2087 21335 8724	0.6047 0.6373 0.0640 0.7345 0.2643	20284 21040 2133 21379 8762	0.6071 0.6398 0.0654 0.7360 0.2655
all	All	458	33676	23859	0.7085	23969	0.7118