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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

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

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
  1. 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