Table 3. Variant extraction results on the Variome corpus.
Results for exact and partial matching are present. Each row shows the performance of each method in terms of true positives (TP), false negatives (FN), false positives (FP), Precision, Recall and F1 measure (F1). The tools are Extractor of Mutations (EMU), OpenMutationMiner (OMM), MutationFinder (MF), tmVar and SNP Extraction Tool for Human Variations (SETH) and their combination (Combined).
| Exact | TP | FN | FP | Precision | Recall | F1 |
|---|---|---|---|---|---|---|
| EMU
OMM MF tmVar SETH |
66
7 7 51 81 |
52
111 111 67 37 |
25
56 10 17 10 |
0.7253
0.1111 0.4118 0.7500 0.8901 |
0.5593
0.0593 0.0593 0.4322 0.6864 |
0.6316
0.0773 0.1037 0.5484 0.7751 |
| Partial | TP | FN | FP | Precision | Recall | F1 |
| EMU
OMM MF tmVar SETH Combined |
90
64 16 65 90 106 |
28
54 102 53 28 12 |
3
1 1 2 1 3 |
0.9677
0.9846 0.9412 0.9701 0.9890 0.9725 |
0.7627
0.5424 0.1356 0.5508 0.7627 0.9060 |
0.8531
0.6995 0.2370 0.7027 0.8612 0.9381 |