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 |
Maximum F-measure for each system on each ontology. Bolded systems produced the highest F-measure.