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Table 1 Annotations of the genetic components in the corpus.

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

Class Concept Number of Annotations Number of Documents % Frequency (Eq. 1)ψ Mean (Eq. 2) Std (Eq. 3) VMR (Eq. 4)
Genes relA 3163 138 71.50 22.92 27.23 33.14
  spoT 1315 88 45.60 14.94 27.42 52.07
  lac 354 63 32.64 5.620 19.42 72.20
  lacZ 534 50 25.91 10.68 17.16 28.90
  thi 91 47 24.35 1.940 0.050 4.000
  rel 523 47 24.35 11.13 20.68 36.36
  recA 82 39 20.21 2.100 1.810 0.5000
  rpsL 95 36 18.65 2.640 3.530 4.500
  thr 84 36 18.65 2.330 3.760 4.500
  rpsG 103 34 17.62 3.030 7.250 16.33
  leu 98 34 17.62 2.880 6.800 18.00
  rpoS 205 33 17.10 6.210 10.83 16.67
  kan 308 33 17.10 9.330 16.61 28.44
  glnV 42 31 16.06 1.350 0.7400 0
  rpoB 389 30 15.54 12.97 17.60 24.08
  ptsG 240 30 15.54 8.000 21.54 55.13
  trp 144 25 12.95 5.760 14.73 39.20
  carA 60 20 10.36 3.000 3.810 3.000
  hsdR 23 19 9.840 1.210 0.5600 0
DNAs DNA 1839 137 70.98 13.42 16.31 19.69
  plasmid DNA 193 36 18.65 5.360 12.31 28.80
  chromosomal DNA 63 24 12.44 2.630 2.440 2.000
  cDNA 125 23 11.92 5.430 5.820 5.000
RNAs RNA 4193 140 72.54 29.95 38.21 49.79
  uncharged tRNA 1168 117 60.62 9.980 19.64 40.11
  rRNA 1116 97 50.26 11.51 25.97 56.82
  a mRNA 999 91 47.15 10.98 19.52 36.10
  rrnA 911 87 45.08 10.47 22.51 48.40
  stable RNA 430 87 45.08 4.940 8.030 16.00
  a charged tRNA 140 43 22.28 3.260 4.200 5.330
  rrnB 301 26 13.47 11.58 19.30 32.82
  rrn 321 26 13.47 12.35 30.42 75.00
  16s-rRNAs 156 25 12.95 6.240 9.090 13.50
  1. Individual genetic components (i.e. genes, DNAs and RNAs) were evaluated considering the number of documents where these entities were annotated and their number of annotations in the corpus. Statistical measurements are detailed in the Methods and Materials section.
  2. ψ A threshold of 10% of the frequency of annotation was set for each genetic component category. However, lists of all annotated entities are provided in Additional file 5.
  3. VMR: variance-to-mean
  4. Std: standard deviation