Table 3 Performance of text-based sequence extraction for cis-regulatory annotation
| Â | dm2 | hg18 | mm8 | ce2 | rn4 | All |
|---|---|---|---|---|---|---|
Number of ORegAnno annotations | 2,079 | 589 | 255 | 178 | 107 | 3,208 |
Number of PMIDs with ORegAnno annotation | 389 | 283 | 113 | 30 | 48 | 850 |
Number of PMIDs with Ensembl target gene name(s) | 388 | 253 | 107 | 29 | 42 | 819 |
Number of text hits from PMIDs with ORegAnno annotation | 188 | 128 | 51 | 16 | 32 | 415 |
Number of text hits that overlap ORegAnno annotation | 149 | 54 | 36 | 13 | 17 | 269 |
Percent text hits that overlap ORegAnno annotation (PPV) | 79.3% | 42.2% | 70.6% | 81.3% | 53.1% | 64.8% |
Number of ORegAnno annotations overlapped by a text hits | 681 | 133 | 149 | 22 | 64 | 1,049 |
Percent ORegAnno annotations overlapped by a text hits (SN) | 32.8% | 22.6% | 58.4% | 12.4% | 59.8% | 32.7% |
Number of PMIDs with text hits | 124 | 91 | 44 | 12 | 24 | 295 |
Percent PMIDs with text hits (coverage) | 31.9% | 32.2% | 38.9% | 40.0% | 50.0% | 32.2% |
Number of PMIDs with text hits to correct species | 123 | 84 | 37 | 12 | 18 | 274 |
Percent PMIDs with text hits to correct species (PPV) | 99.2% | 92.3% | 84.1% | 100.0% | 75.0% | 92.9% |
Number of PMIDs with text hits and Ensembl target gene name(s) | 122 | 77 | 33 | 11 | 16 | 259 |
Number of PMIDs with text hits and perfect match to correct target gene name(s) | 67 | 57 | 24 | 4 | 10 | 162 |
Number of PMIDs with text hits and partial match to correct target gene name(s) | 16 | 12 | 5 | 3 | 4 | 40 |
Percent PMIDs with text hits and match to correct target gene name (PPV) | 68.0% | 89.6% | 87.9% | 63.6% | 87.5% | 78.0% |
Number of PMIDs without ORegAnno annotation with text hits | 76 | 1,291 | 841 | 13 | 459 | 2,680 |
Number of text hits from PMIDs without ORegAnno annotation | 126 | 2,602 | 2,131 | 14 | 1,002 | 5,875 |
Number of text hits from PMIDs without ORegAnno annotation that overlap ORegAnno annotation | 59 | 202 | 58 | 1 | 18 | 338 |
Number of ORegAnno annotations overlapped by text hits from PMIDs without ORegAnno annotation | 200 | 347 | 139 | 3 | 33 | 722 |