Table 2.

Runtime of the Onto2Graph algorithm and semantic similarity computation over the GO-Plus ontology

Reasoner	Properties	Transitive reduction	Edges generated	Conversion runtime	Semantic similarity runtime
Elk reasoner	SubClassOf	True	146850	1 min 37 s	4 min 59 s
		False	146850	0 min 58 s	4 min 54 s
Elk reasoner	SubClassOf + PartOf	True	154583	10 min 50 s	5 min 42 s
		False	165457	10 min 37 s	5 min 44 s
Elk reasoner	SubClassOf + PartOf + Regulates	True	159261	16 min 34 s	6 min 21 s
		False	170112	16 min 10 s	6 min 15 s
Syntactic reasoner	SubClassOf	True	73692	0 min 48 s	3 min 25 s
		False	73692	0 min 46 s	3 min 30 s
Syntactic reasoner	SubClassOf + PartOf	True	82034	0 min 49 s	3 min 59 s
		False	82205	0 min 47 s	4 min 8 s
Syntactic reasoner	SubClassOf + PartOf + Regulates	True	85335	0 min 48 s	5 min 8 s
		False	85506	0 min 49 s	4 min 42 s

For the conversion and semantic similarity computation, we used a 3.20 GHz Intel i5-3470 CPU with 8 GB 1600 MHz DDR3 RAM and allowed Onto2Graph to use four threads