Table 5 Best performance for each ontology-system pair
Cell Type Ontology (CL) | ||||||
|---|---|---|---|---|---|---|
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.32 | 0.76 | 0.20 | 1169 | 379 | 4591 |
MetaMap | 0.69 | 0.61 | 0.80 | 4590 | 3010 | 1170 |
ConceptMapper | 0.83 | 0.88 | 0.78 | 4478 | 592 | 1282 |
Gene Ontology - Cellular Component (GO_CC) | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.40 | 0.75 | 0.27 | 2287 | 779 | 6067 |
MetaMap | 0.70 | 0.67 | 0.73 | 6111 | 2969 | 2341 |
ConceptMapper | 0.77 | 0.92 | 0.66 | 5532 | 452 | 2822 |
Gene Ontology - Molecular Function (GO_MF) | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.08 | 0.47 | 0.04 | 173 | 195 | 4007 |
MetaMap | 0.09 | 0.09 | 0.09 | 393 | 3846 | 3787 |
ConceptMapper | 0.14 | 0.44 | 0.08 | 337 | 425 | 3834 |
Gene Ontology - Biological Process (GO_BP) | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.25 | 0.70 | 0.15 | 2592 | 1120 | 14321 |
MetaMap | 0.42 | 0.53 | 0.34 | 5802 | 4994 | 11111 |
ConceptMapper | 0.36 | 0.46 | 0.29 | 4909 | 5710 | 12004 |
Sequence Ontology (SO) | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.44 | 0.63 | 0.33 | 7056 | 4094 | 14231 |
MetaMap | 0.50 | 0.47 | 0.54 | 11402 | 12634 | 9885 |
ConceptMapper | 0.56 | 0.56 | 0.57 | 12059 | 9560 | 9228 |
ChEBI | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.56 | 0.7 | 0.46 | 3782 | 1595 | 4355 |
MetaMap | 0.42 | 0.36 | 0.50 | 4424 | 8689 | 3717 |
ConceptMapper | 0.56 | 0.55 | 0.56 | 4583 | 3687 | 3554 |
NCBI Taxonomy | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.04 | 0.16 | 0.02 | 157 | 807 | 7292 |
MetaMap | 0.45 | 0.31 | 0.88 | 6587 | 14954 | 862 |
ConceptMapper | 0.69 | 0.61 | 0.79 | 5857 | 3793 | 1592 |
Protein Ontology (PRO) | ||||||
System | F-measure | Precision | Recall | # TP | # FP | # FN |
NCBO Annotator | 0.50 | 0.49 | 0.51 | 7958 | 8288 | 7636 |
MetaMap | 0.36 | 0.39 | 0.34 | 5255 | 8307 | 10339 |
ConceptMapper | 0.57 | 0.57 | 0.57 | 8843 | 6620 | 6751 |