Table 5

Examples of Errors Examples of FPs, FNs and boundary errors. In some of the examples square brackets are used to indicate the differences between the classifier's output and the annotation in the gold standard.

False Positives

Classifier (CL)

Gold Standard (GS)

General Words

homolog gene





Possible Errors in GS

[ssDNA-] and [RNA-binding protein]

ssDNA- and [RNA-binding protein]

False Negatives

Classifier (CL)

Gold Standard (GS)


[YAP2 uORF1] and uORF2

[YAP2 uORF1] and [uORF2]

Missing Expansion

zinc-finger protein ([THZif-1])

[zinc-finger protein] ([THZif-1])

Boundary Errors

Classifier (CL)

Gold Standard (GS)

GS NE contains CL NE(s)

AP-1 complexes

high mobility AP-1 complexes


USH1C disease gene

partner of [Rac]

[partner of Rac]

CL NE contains GS NE(s)

regulator virF


Wnt pathway


CL and GS Overlap

Serum [Fibrin Degradation Products]

[Serum Fibrin] Degradation Products

Finkel et al. BMC Bioinformatics 2005 6(Suppl 1):S5   doi:10.1186/1471-2105-6-S1-S5

Open Data