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Table 3 Annotations of the small molecules in the corpus.

From: Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Concept Number of Annotations Number of Documents % Frequency of annotation (Eq. 1)ψ Mean of annotation (Eq. 2) Std (Eq. 3) VMR (Eq. 4)
Amino acids 1557 160 82.90 9.730 13.83 18.78
Nucleotides 1230 145 75.13 8.480 9.290 10.13
ppGpp 4159 145 75.13 28.68 31.00 34.32
β-D-glucose 792 123 63.73 6.440 10.63 16.67
Pi 662 113 58.55 5.860 12.60 28.80
Guanosine 407 112 58.03 3.630 3.540 3.000
ATP 587 100 51.81 5.870 7.410 9.800
GTP 748 91 47.15 8.220 13.85 21.13
AMP 598 90 46.63 6.640 10.09 16.67
PPi 447 87 45.08 5.140 5.180 5.000
H2O 210 83 43.01 2.530 2.430 2.000
Tris 261 82 42.49 3.180 2.800 1.330
Carbon 288 80 41.45 3.600 4.850 5.330
Chloramphenicol 435 77 39.90 5.650 8.250 12.80
pppGpp 632 74 38.34 8.540 13.61 21.13
(p)ppGpp 3127 72 37.31 43.43 56.00 72.93
NaCl 189 67 34.72 2.820 2.790 2.000
L-lactate 413 65 33.68 6.350 20.84 66.67
Glycerol 145 65 33.68 2.230 1.850 0.5000
Ethanol 189 65 33.68 2.910 4.400 8.000
Na+ 145 63 32.64 2.300 2.100 2.000
Ampicillin 321 62 32.12 5.180 12.74 28.80
EDTA 142 60 31.09 2.370 1.680 0.5000
L-methionine 248 59 30.57 4.200 6.670 9.000
L-histidine 183 59 30.57 3.100 5.410 8.330
L-valine 396 57 29.53 6.950 11.90 20.17
Formate 136 57 29.53 2.390 2.360 2.000
  1. Individual small molecules were evaluated considering the number of documents where these entities were annotated and the number of annotations in the corpus. Statistical measurements are detailed in the Methods and Materials section.
  2. ψ A threshold of 30% of the frequency of annotation was set for compounds. However, lists of all annotated entities are provided in Additional file 7.
  3. VMR: variance-to-mean
  4. Std: standard deviation