Table 4.
Some evaluation examples based on the sentences derived from BioCreative V BEL track sample set
| Example 1 | ||
|---|---|---|
|
The nuclear protein pigpen has an affinity for carbohydrate structures a carbohydrate-binding domain resides in the C terminus of the molecule and can be preferentially inhibited by saccharides, most notably N-acetyl-d-galactosamine and chondroitin sulphate. | ||
| Type | Result | BEL statement |
| Gold | – | a(CHEBI:"N-acetyl-D-galactosamine") -| p(HGNC:FUS) |
| – | a(CHEBI:"chondroitin sulfate") -| p(HGNC:FUS) | |
| BELIEF | True positive | a(CHEBI:"N-acetyl-D-galactosamine") -| p(HGNC:FUS) |
| False positive | a(CHEBI:"N-acetyl-D-galactosamine") -| a(CHEBI:"chondroitin sulfate") | |
|
Example 2 | ||
| 60 or 90 μM galangin induced AhR nuclear translocation in both cell type (Figure 11A, lanes 7, 8; Figure 11B, lane 6). | ||
| Type | Result | BEL statement |
| Gold | – | a(CHEBI:galangin) -> act(p(HGNC:AHR)) |
| BELIEF | True positive | a(CHEBI:galangin) -> tloc(p(HGNC:AHR)) |
|
Example 3 | ||
| In the absence of CdCl2 pre-treatment, ionizing radiation increased both expression and phosphorylation of c-Jun in MRC5CV1 cells but not in AT5BIVA cells. | ||
| Type | Result | BEL statement |
| Gold | – | bp(GOBP:"response to ionizing radiation") -> p(HGNC:JUN,pmod(P)) |
| – | bp(GOBP:"response to ionizing radiation") -> p(HGNC:JUN) | |
| BELIEF | False positive | p(PH:placeholder) -| (a(CHEBI:"cadmium dichloride") -> p(HGNC:JUN,pmod(P))) |
| False positive | p(PH:placeholder) -| (a(CHEBI:"cadmium dichloride") -> p(HGNC:JUN)) | |
| False positive | p(HGNC:JUN) −− a(CHEBI:"cadmium dichloride") | |
|
Example 4 | ||
| The sensitivity to Fas-induced cell death was reduced in HGF transfectants, which was reversed by the presence of anti-HGF antibody | ||
| Type | Result | BEL statement |
| Gold | – | p(HGNC:HGF) -| (act(p(HGNC:FAS)) -> bp(GOBP:"cell death")) |
| BELIEF | Partly true positive | p(PH:placeholder) -| (p(HGNC:FAS) -> bp(GOBP:"cell death")) |
| Partly true positive | p(HGNC:FAS) −− bp(GOBP:"cell death") | |
| False positive | p(HGNC:HGF) −− bp(GOBP:"cell death") | |
Every example contains a sentence with the gold standard and predicted BEL statements. In addition, the results of the predicted BEL statements are provided.