Table 1 Queries used for the KB evaluation.

Q1

Find the proteins that are in the context of gene expression.

SELECT DISTINCT ?s1 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?e1 a genia:Gene_expression .

  ?t1 genia:themeOf ?e1.

}

Q2

Find the proteins that are in the context of localization.

SELECT DISTINCT ?s1 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?e1 a genia:Localization .

  ?t1 genia:themeOf ?e1.

}

Q3

Find the protein that are in the context of binding.

SELECT DISTINCT ?s1 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?e1 a genia:Binding .

  ?t1 genia:themeOf ?e1.

}

Q4

Find the protein pairs that bind to each other.

SELECT DISTINCT ?s1 ?s2 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?t2 a genia:Protein; tao:denoted_by ?s2 .

  ?e1 a genia:Binding .

  ?t1 genia:themeOf ?e1 .

  ?t2 genia:themeOf ?e1 .

FILTER (?s1 < ?s2)

}

Q5

Find the protein pairs of which one regulates the other.

SELECT DISTINCT ?s1 ?s2 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?t2 a genia:Protein; tao:denoted_by ?s2 .

  ?t1 genia:themeOf ?e1.

  ?t2 genia:causeOf ?e1.

}

Q6

Find the protein pairs of which one regulates the other (transitive).

SELECT DISTINCT ?s1 ?s2 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?t2 a genia:Protein; tao:denoted_by ?s2 .

  ?t1 genia:themeOf+ ?e1.

  ?t2 genia:causeOf ?e1.

}

Q7

Find the protein pairs of which one regulates expression of the other.

SELECT DISTINCT ?s1 ?s2 WHERE {

  ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?t2 a genia:Protein; tao:denoted_by ?s2 .

  ?e1 a genia:Gene_expression .

  ?t1 genia:themeOf ?e1.

  ?e1 genia:themeOf ?e2.

  ?t2 genia:causeOf ?e2.

}

Q8

Find the protein pairs of which one regulates expression of the other (transitive).

SELECT DISTINCT ?s1 ?s2 WHERE

{ ?t1 a genia:Protein; tao:denoted_by ?s1 .

  ?t2 a genia:Protein; tao:denoted_by ?s2 .

  ?e1 a genia:Gene_expression .

  ?t1 genia:themeOf ?e1.

  ?e1 genia:themeOf+ ?e2.

  ?t2 genia:causeOf ?e2.

}