Table 6

The example sentences of each ‘bio-inference’ scheme

class

example

inferred reaction IDs

1

a

ex1

p50 is translated as a precursor of 105 kDa.

R10

b

ex2

CD23-induced NF-kappaB is a heterodimer composed of p65/p50 subunits.

R1

2

a

ex3

RelA contains a high-affinity binding site for its cytoplasmic inhibitor, I kappa B alpha.

R2

b

ex4

I kappa B-alpha inhibits transcription factor NF-kappa B by retaining it in the cytoplasm.

R2

3

a

ex5

When either serine-32 or serine-36 of I kappa B-alpha was mutated, the protein did not undergo signal-induced phosphorylation.

R3

b

ex6

Pretreatment of the cells with the proteasome inhibitor N-Ac-Leu-Leu-norleucinal inhibits this ligand-induced degradation of the human I kappa B alpha protein.

R5

4

ex7

As observed with I kappa B alpha, nuclear RelA stimulates p100 mRNA and protein expression.

R8

5

ex8

Nuclear expression of NF-kappa B occurs after its induced dissociation from its cytoplasmic inhibitor I kappa B alpha.

R2

6

ex9

A failure to degrade IkappaB-alpha pretreated with PAO is not due to its inhibitory effect on proteasomal degradation.

R5

The example sentences of each class of ‘bio-inference’ scheme are shown with their inferred reaction IDs. The linguistic cues to infer some reaction are shown in boldface.

Oda et al. BMC Bioinformatics 2008 9(Suppl 3):S5   doi:10.1186/1471-2105-9-S3-S5