Table 5

The breakdown of the indirect expressions by ‘inference’ scheme
reaction ID
 reaction type
 n
 1
 2
 3
 4
 5
 6
a
 b
 a
 b
 a
 b
R1
 Binding
 56
56






R2
 Binding
 20

3
 15


2
R3
 phosphorylation
 1
1






+ site information
 5



4
 1


+ modifier information
 1





1

R5
 degradation
 1
1






+ modifier information
 3




1

2
R7
 Binding
 12
3
 2
 6
1


R8
 gene expression
 9
 3
4


2

R9
 gene expression
 10
 3
 2
 4


1

R10
 processing
 12
 11
 1






The indirect expressions were subdivided by ‘inference’ scheme. Biologists often build a pathway by ‘inference’ with their biological domain knowledge from indirect expressions in the text. There are nine inference schemes when regarding indirect expressions, which indicate specific reactions. The figures are the number of sentences in each ‘inference’ scheme. Class 1a: state(s) of entity(-ies) before reaction, 1b: state(s) of entity(-ies) after reaction, 2a: function(s) of entity(-ies) before reaction, 2b: function(s) of entity(-ies) after reaction, 3a: influence of state change(s) of entity(-ies), 3b: influence of functional change(s) of entity(-ies), 4: related reaction, 5: reverse reaction, 6:characteristic of reaction.

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