Table 3 Indexing comparison of GRAPES and GRAPES-DD of single PPI network in terms of RAM requirement, Storage requirement, and Building time
From: GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases
| Â | Â | Â | RAM req. (MB) | Storage req. (MB) | Build time (s) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
Species | |V| | |E| | GRAPES-DD | GRAPES | ratio | GRAPES-DD | GRAPES | ratio | GRAPES-DD | GRAPES |
S. cerevisiae | 4709 | 40,284 | 38.1 | 91.1 | 2.39 | 10.5 | 26.2 | 2.49 | 60.93 | 63.49 |
5,230 | 53,699 | 56.3 | 136.3 | 2.42 | 11.7 | 42.4 | 3.63 | 604.47 | 630.92 | |
5,762 | 76,482 | 61.1 | 150.9 | 2.47 | 12.7 | 47.5 | 3.73 | 846.24 | 879.90 | |
5,936 | 89,674 | 46.5 | 121.2 | 2.61 | 12.9 | 36.8 | 2.86 | 128.52 | 135.01 | |
C. elegans | 1557 | 2472 | 7.1 | 5.7 | 0.80 | 0.2 | 0.3 | 1.45 | 0.24 | 0.20 |
2421 | 3981 | 7.8 | 7.9 | 1.02 | 0.5 | 1.0 | 2.06 | 0.52 | 0.44 | |
3664 | 7005 | 10.4 | 14.6 | 1.40 | 1.0 | 2.8 | 2.65 | 1.33 | 1.13 | |
6173 | 26,184 | 25.1 | 58.5 | 2.33 | 4.3 | 16.0 | 3.75 | 34.16 | 34.19 | |
D. melanogaster | 1185 | 2008 | 8.0 | 12.1 | 1.51 | 0.6 | 1.5 | 2.30 | 0.31 | 0.26 |
2488 | 6151 | 12.1 | 32.1 | 2.65 | 1.9 | 6.6 | 3.47 | 3.28 | 3.21 | |
2729 | 7235 | 13.3 | 36.2 | 2.73 | 2.3 | 7.9 | 3.37 | 4.30 | 4.22 | |
7928 | 37,542 | 52.3 | 198.7 | 3.80 | 13.1 | 64.3 | 4.90 | 144.05 | 156.07 | |
M. musculus | 1810 | 2413 | 8.0 | 13.1 | 1.64 | 0.7 | 2.2 | 2.94 | 0.42 | 0.36 |
3255 | 5424 | 11.0 | 31.0 | 2.81 | 1.9 | 7.1 | 3.68 | 2.52 | 2.50 | |
3758 | 6853 | 13.1 | 43.6 | 3.33 | 2.6 | 11.2 | 4.30 | 4.47 | 4.61 | |
6875 | 23,779 | 41.1 | 193.6 | 4.71 | 12.4 | 62.1 | 5.02 | 76.64 | 81.56 | |
H. sapiens | 4638 | 10,665 | 17.3 | 55.0 | 3.18 | 3.6 | 14.6 | 4.07 | 5.60 | 5.36 |
8728 | 31,164 | 53.5 | 215.4 | 4.02 | 13.1 | 70.8 | 5.42 | 65.14 | 68.26 | |
9826 | 48,835 | 87.5 | 351.4 | 4.02 | 21.5 | 120.1 | 5.59 | 213.95 | 230.16 | |
10,186 | 51,484 | 89.2 | 391.8 | 4.39 | 22.0 | 134.1 | 6.10 | 191.63 | 209.63 | |