Table 3 GROOLS statistics on pathways and functional units for Genome Properties and UniPathway. Statistics are computed for the 14 studied organisms
From: GROOLS: reactive graph reasoning for genome annotation through biological processes
Genome properties | UniPathway | ||||||
|---|---|---|---|---|---|---|---|
UniProtKB | UniProtKB | UniProtKB | MicroScope | UniProtKB | MicroScope | ||
falsehood | specific | specific | |||||
Pathway conclusions | Exp. / Pred. | ||||||
Confirmed presence | True / True | 195 | 195 | 241 | 277 | 339 | 393 |
Unexpected absence | True / False | 0 | 12 | 0 | 0 | 0 | 0 |
Contradictory absence | True / Both | 0 | 56 | 0 | 5 | 0 | 5 |
Missing | True / None | 68 | 0 | 232 | 191 | 137 | 80 |
Unexpected presence | False / True | 13 | 13 | 33 | 50 | 79 | 121 |
Confirmed absence | False / False | 0 | 66 | 0 | 0 | 0 | 0 |
Contradictory presence | False / Both | 0 | 40 | 0 | 0 | 0 | 0 |
Absent | False / None | 106 | 0 | 275 | 258 | 229 | 187 |
Ambiguous presence | Both / True | 15 | 15 | 47 | 68 | 121 | 178 |
Ambiguous absence | Both / False | 0 | 13 | 0 | 0 | 0 | 0 |
Ambiguous contradiction | Both / Both | 0 | 24 | 0 | 3 | 0 | 3 |
Ambiguous | Both / None | 37 | 0 | 243 | 218 | 172 | 120 |
Unconfirmed presence | None / True | 1222 | 1222 | 728 | 946 | 1130 | 1409 |
Unconfirmed absence | None / False | 0 | 3453 | 0 | 0 | 0 | 0 |
Unconfirmed contradiction | None / Both | 0 | 726 | 0 | 5 | 0 | 4 |
Unexplained | None / None | 4238 | 59 | 2359 | 2137 | 1951 | 1658 |
Pathway statistics | |||||||
True positive | 184 | 184 | 200 | 238 | 272 | 310 | |
True negative | 106 | 66 | 188 | 176 | 159 | 130 | |
False positive | 13 | 53 | 19 | 31 | 48 | 77 | |
False negative | 65 | 65 | 190 | 152 | 118 | 80 | |
Precision | 93.40% | 77.64% | 91.32% | 88.48% | 85.00% | 80.10% | |
Recall | 73.90% | 73.90% | 51.28% | 61.03% | 69.74% | 79.49% | |
Accuracy | 78.80% | 67.93% | 64.99% | 69.35% | 72.19% | 73.70% | |
F1 score | 82.51% | 75.72% | 65.68% | 72.23% | 76.62% | 79.79% | |
Functional unit statistics | |||||||
True positive | 1236 | 1236 | 969 | 1719 | 982 | 1742 | |
True negative | 710 | 710 | 568 | 505 | 568 | 504 | |
False positive | 117 | 117 | 100 | 139 | 100 | 140 | |
False negative | 396 | 396 | 511 | 342 | 465 | 283 | |
Precision | 91.35% | 91.35% | 90.65% | 92.52% | 90.76% | 92.56% | |
Recall | 75.74% | 75.74% | 65.47% | 83.41% | 67.86% | 86.02% | |
Accuracy | 79.14% | 79.14% | 71.55% | 82.22% | 73.29% | 84.15% | |
F1 score | 82.81% | 82.81% | 76.03% | 87.73% | 77.66% | 89.17% | |