Table 1.
Gold standard corpora (GSCs) used in this work
| Entity type | Corpus | Text genre | Text type | No. sentences | No. tokens | No. unique tokens | No. annotations | No. unique annotations |
|---|---|---|---|---|---|---|---|---|
| Chemicals | BioSemantics (Akhondi et al., 2014) | Patent | Full-text | 163219 | 6608020 | 173193 | 386110 | 72782 |
| CDR (Li et al., 2016) | Scientific Article | Abstract | 14166 | 326506 | 22083 | 15915 | 2623 | |
| CHEMDNER patent (Krallinger et al., 2015a,b) | Patent | Abstract | 35679 | 1495524 | 60850 | 65685 | 20630 | |
| Diseases | Arizona Disease (Leaman et al., 2009) | Scientific Article | Abstract | 2804 | 74346 | 8133 | 3425 | 1266 |
| CDR | Scientific Article | Abstract | 14166 | 326506 | 22083 | 12617 | 3113 | |
| miRNA (Bagewadi et al., 2014) | Scientific Article | Abstract | 2676 | 66419 | 7638 | 2159 | 606 | |
| NCBI Disease (Doğan et al., 2014) | Scientific Article | Abstract | 7645 | 173283 | 12534 | 6881 | 2136 | |
| Variome (Verspoor et al., 2013) | Scientific Article | Full-text | 6274 | 177119 | 12307 | 5904 | 451 | |
| Species | CellFinder (Neves et al., 2012) | Scientific Article | Full-text | 2234 | 66519 | 7584 | 479 | 42 |
| Linneaus (Gerner et al., 2010) | Scientific Article | Full-text | 19048 | 491253 | 33132 | 4259 | 419 | |
| LocText (Goldberg et al., 2015) | Scientific Article | Abstract | 956 | 22756 | 4335 | 276 | 37 | |
| miRNA | Scientific Article | Abstract | 2676 | 66419 | 7638 | 722 | 41 | |
| S800 (Pafilis et al., 2013) | Scientific Article | Abstract | 8356 | 198091 | 19992 | 3708 | 1503 | |
| Variome | Scientific Article | Full-text | 6274 | 177119 | 12307 | 182 | 8 | |
| Genes/proteins | BioCreative II GM (Smith et al., 2008) | Scientific Article | Abstract | 20384 | 514146 | 49365 | 24596 | 15841 |
| BioInfer (Pyysalo et al., 2007) | Scientific Article | Abstract | 1147 | 34187 | 5200 | 4378 | 1041 | |
| CellFinder | Scientific Article | Full-text | 2234 | 66519 | 7584 | 1750 | 734 | |
| DECA (Wang et al., 2010) | Scientific Article | Abstract | 5492 | 139771 | 14053 | 6324 | 2127 | |
| FSU-PRGE (Hahn et al., 2010) | Scientific Article | Abstract | 35361 | 914717 | 453634 | 59489 | 27363 | |
| IEPA (Ding et al., 2001) | Scientific Article | Abstract | 241 | 15365 | 2871 | 1110 | 130 | |
| LocText | Scientific Article | Abstract | 956 | 22756 | 4335 | 1395 | 549 | |
| miRNA | Scientific Article | Abstract | 2676 | 66419 | 7638 | 1058 | 370 | |
| Variome | Scientific Article | Full-text | 6274 | 177119 | 12307 | 4617 | 458 |