A Topology-Based Metric for Measuring Term Similarity in the Gene Ontology

Table 2

Semantic similarity values between child-parent pairwise terms in Figure 3 from the Wang et al. and Zhang et al. approaches are compared to our approach. 𝑆_𝑊 refers to the semantic similarity between two GO terms obtained using the Wang semantic similarity approach from G-SESAME (Gene Semantic Similarity Analysis and Measurements) Tools. 𝐷 values, 𝑆_𝑍, 𝑆_𝑍𝑢𝑅, and 𝑆_𝑍𝐿 refer to the Zhang et al. approach and 𝑆_GO refers to the semantic similarity approach developed here.

Parent GO Id	Child GO Id	𝑆GO	𝑆𝑊	𝑆𝑍	𝑆𝑍𝑢𝑅	𝑆𝑍𝐿
GO:0042770	GO:0042772	0.97920	0.940	10.11006	0.71747	0.90199
GO:0042770	GO:0030330	0.97920	0.940	10.11006	0.71747	0.94847
GO:0042770	GO:0008630	0.32398	0.704	10.11006	0.71747	0.90199
GO:0042770	GO:0000077	0.79240	0.802	10.11006	0.71747	0.96144
GO:0042772	GO:0006978	0.49591	0.882	12.30729	0.87340	1.00000
GO:0030330	GO:0006978	0.49591	0.889	11.20867	0.79544	0.95328
GO:0030330	GO:0006977	0.36008	0.615	11.20867	0.79544	0.95328
GO:0030330	GO:0042771	0.24760	0.696	11.20867	0.79544	0.95328
GO:0008630	GO:0042771	0.74832	0.931	12.30729	0.87340	1.00000
GO:0000077	GO:0031571	0.70186	0.830	10.92099	0.77502	0.94032
GO:0000077	GO:0031572	0.69945	0.850	10.92099	0.77502	0.94032
GO:0000077	GO:0031573	0.98344	0.948	10.92099	0.77502	0.94032
GO:0000077	GO:0031574	0.70603	0.870	10.92099	0.77502	0.94032
GO:0031571	GO:0006977	0.63398	0.774	12.30729	0.87340	1.00000