Table 3 Setup for Experiment II and contribution of the CVDO: The simple categorisation introduced (see ‘Setup of Experiment I and Experiment II for a gene/protein synonym detection task’) has been applied to the terms from PubMed abstract/title from the small-annotated corpus (first column) as well as to the target terms (second column). Each row of the third column contains the number of target terms for the experiment taking into account the categories that appear in the first and second column

Terms from PubMed titles/abstracts

Target terms

n

Terms added by CVDO to the target terms

Gene symbol appears

Gene symbol appears

6

Terms from protein name (R)

Gene symbol appears

Only protein name

1

Protein name (R)

Gene symbol appears

Refer protein name

1

Terms referring to the protein name (R)

Gene symbol appears

Terms from protein name

2

Terms from protein name (R)

Only gene symbol

Gene symbol appears

20

Terms from protein name (R)

Only gene symbol

Only protein name

4

Protein name (R)

Refer protein name

Gene symbol appears

27

Terms from protein name and gene symbol (R)

Refer protein name

Only gene symbol

2

Gene symbol (R)

Refer protein name

Only protein name

2

Protein name

Refer protein name

Refer protein name

1

Terms referring to the protein name

Refer protein name

Terms from protein name

2

Terms from protein name