Table 2 Statistics for the concept annotation classes used in the training (67-document) and evaluation (30-document) data sets and for those added as additional training data for concept normalization for all ontologies
Ontology | # training set annotation classes | Avg/median # training set annotation classes per article | # classes added to training set | # evaluation set annotation classes | Avg/median # evaluation set annotation classes per article |
|---|---|---|---|---|---|
ChEBI | 1463 | 22/18 | 58,214 | 627 | 21/20 |
ChEBI_EXT | 2852 | 43/38 | 58,439 | 1167 | 39/39 |
CL | 581 | 9/7 | 2163 | 253 | 8/9 |
CL_EXT | 651 | 10/8 | 2168 | 286 | 10/10 |
GO_BP | 1586 | 24/21 | 29,213 | 682 | 23/23 |
GO_BP_EXT | 2511 | 37/33 | 29,301 | 1090 | 36/37 |
GO_CC | 677 | 10/9 | 4052 | 212 | 7/6 |
GO_CC_EXT | 896 | 13/12 | 4086 | 296 | 10/9 |
GO_MF | 49 | 1/1 | 10951 | 19 | 1/1 |
GO_MF_EXT | 738 | 11/11 | 10,031 | 377 | 13/12 |
MOP | 85 | 1/1 | 3574 | 32 | 1/1 |
MOP_EXT | 108 | 2/1 | 3578 | 40 | 1/1 |
NCBITaxon | 690 | 10/9 | 1,175,661 | 315 | 11/9 |
NCBITaxon_EXT | 757 | 11/10 | 1,175,682 | 346 | 12/10 |
PR | 1278 | 19/18 | 213,371 | 466 | 16/16 |
PR_EXT | 1534 | 23/22 | 213,531 | 588 | 20/19 |
SO | 1216 | 18/18 | 2256 | 544 | 18/19 |
SO_EXT | 3172 | 47/47 | 2405 | 1409 | 47/48 |
UBERON | 2048 | 31/24 | 14,057 | 1040 | 35/31 |
UBERON_EXT | 2409 | 36/29 | 14,113 | 1217 | 41/38 |