HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

BMC Bioinformatics

Table 11 Overall running time in seconds (s) and average speed in protein pairs per second (prot. pairs/s) obtained by four groupwise GO-based similarity measures (GO, 2020-05-02 version) implemented by HESML in the evaluation of the pairwise protein similarity between the Homo Sapiens and Canis lupus familiaris organisms

Pairwise protein comparison between two large organisms
Measure	Type	HESML Time (s)	Avg. speed (prot. pairs/s)
SimLP [100]	Common ancestors ratio	28243	12038
SimUI [100]	Common ancestor max depth	31922	10651
SimGIC-Seco [105, 110]	IC-based	30754	11055
BMA-Lin-Seco [87, 104, 110]	IC-based	7981	42604

We used the 542193 and 120720 GO annotations for both organisms provided by the “goa_human.gaf” and “go_dog.gaf” files, respectively. Approximately 340 million protein pairs and \(33.5 \times 10^9\) GO-annotation pairs are compared

ISSN: 1471-2105