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Table 5 PSI-MI assignments to annotated experimental techniques.

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

Techniques Statistics over the corpus Frequency per Decade
PSI-MI Class PSI-MI id PSI-MI name Freq Mean Std VMR 1970 1980 1990 2000
MI:0659 experimental feature detection MI:0659 experimental feature detection* 55% 2.44 2.76 2 64% 65% 67% 67%
  MI:0833 autoradiography 25% 1.65 1.4 1 29% 35% 22% 22%
  MI:0113 western blot 21% 4.95 3.38 2.25 - 13% 18% 44%
  MI:0074 mutation analysis 20% 3.34 3.24 3 14% 20% 27% 32%
  MI:0114 x-ray crystallography 4% 1.63 1.46 1 - - 2% 8%
  MI:0811 insertion analysis 4% 1.14 0.38 0 - - 7% 4%
MI:0045 experimental interaction detection MI:0091 chromatography technology 50% 4.23 4.14 4 100% 85% 55% 64%
  MI:0254 genetic interference 42% 2.68 2.35 2 - 28% 69% 64%
  MI:0807 comigration in gel electrophoresis 37% 2.51 2.13 2 21% 48% 51% 49%
  MI:0045 experimental interaction detection* 36% 3.1 3.12 3 14% 45% 47% 41%
  MI:0808 comigration in sds page 27% 2.02 1.61 0.5 7% 23% 33% 29%
  MI:0099 scintillation proximity assay 24% 1.94 1.65 1 64% 35% 20% 15%
  MI:0051 fluorescence technology 16% 1.84 1.8 1 7% 20% 5% 22%
  MI:0071 molecular sieving 15% 2.25 3.19 4.5 29% 13% 15% 13%
  MI:0217 phosphorylation reaction 13% 2.72 3.74 4.5 7% 8% 16% 14%
  MI:0415 enzymatic study 12% 1.96 2.11 4 7% 8% 11% 19%
  MI:0008 array technology 10% 8.47 7.47 6.13 - - - 22%
  MI:0928 filter trap assay 9% 2.24 2.47 2 36% 13% 4% 6%
  MI:0004 affinity chromatography technology 8% 2.33 2.44 2 - 5% 5% 13%
  MI:0428 imaging technique 7% 1.57 1.41 1 - 8% 4% 11%
  MI:0047 far western blotting 6% 1.5 0.82 0 - 3% 7% 8%
  MI:0435 protease assay 6% 3.92 4.01 5.33 - 5% 5% 8%
  MI:0017 classical fluorescence spectroscopy 6% 1.08 0.29 0 - - 5% 11%
  MI:0089 protein array 6% 1.64 1.62 1 - 3% 2% 11%
  MI:0029 cosedimentation through density gradient 5% 5.22 3.94 1.8 43% 10% - 2%
  MI:0040 electron microscopy 4% 2.57 1.31 0.5 - 10% - 4%
  MI:0676 tandem affinity purification 3% 3.8 5.18 8.33 - - - 7%
  MI:0054 fluorescence-activated cell sorting 3% 5.8 4.6 3.2 - - 4% 4%
  MI:0413 electrophoretic mobility shift assay 3% 1.6 0.77 0 - - 5% 2%
  MI:0012 bioluminescence resonance energy transfer 2% 6.25 5.68 4.17 - - 4% 2%
  MI:0018 two hybrid 2% 2 1.41 0.5 - - - 7%
  MI:0053 fluorescence polarization spectroscopy 2% 5 2.94 0.8 - 3% - 2%
  MI:0397 two hybrid array 2% 2 1.41 0.5 - - 2% 2%
  MI:0227 reverse phase chromatography 2% 3.25 2.87 1.33 - - 5% 1%
  MI:0226 ion exchange chromatography 1% 1 0 0 - - - 1%
  MI:0031 protein cross-linking with a bifunctional reagent 1% 7 4 2.29 - 3% - 1%
  MI:0052 fluorescence correlation spectroscopy 1% 1 0 0 - - - 1%
  MI:0416 fluorescence microscopy 1% 2.5 0.71 0 - - - 2%
  MI:0016 circular dichroism 1% 1.5 0.71 0 - - - 2%
  MI:0225 chromatin immunoprecipitation array 1% 1 0 0 - - - 1%
  MI:0872 atomic force microscopy 1% 1 0 0 - - - 1%
  MI:0049 filter binding 1% 1 0 0 - 3% 2% -
  MI:0426 light microscopy 1% 1 0 0 - - - 2%
MI:0661 experimental participant identification MI:0088 primer specific pcr 40% 10.38 15.87 22.5 - 8% 29% 95%
  MI:0080 partial dna sequence identification by hybridization 27% 3.75 3.47 3 14% 30% 29% 26%
  MI:0078 nucleotide sequence identification 20% 1.77 1.26 1 - 15% 25% 22%
  MI:0103 southern blot 14% 3.04 2.05 1.33 - 8% 15% 19%
  MI:0929 nothern blot 8% 5.56 4.8 3.2 - 3% 11% 11%
  MI:0421 identification by antibody 6% 1.82 1.51 1 - 8% 5% 6%
  MI:0427 identification by mass spectrometry 5% 1.67 0.94 0 - - 4% 8%
  MI:0082 peptide massfingerprinting 2% 1.5 0.71 0 - - - 5%
  MI:0093 protein sequence identification 1% 1 0 0 - - 2%  
  MI:0411 enzyme linked immunosorbent assay 1% 4 2 1 - - 2% 1%
MI:0346 experimental preparation MI:0714 nucleic acid transduction 26% 2.22 2.82 2 14% 15% 31% 29%
  MI:0715 nucleic acid conjugation 6% 1.73 1.41 1 7% 3% 5% 7%
  MI:0308 electroporation 5% 1.89 1.56 1 - - 2% 9%
  MI:0343 cdna library 3% 1 0 0 - - - 6%
MI:0190 interaction type MI:0194 cleavage reaction 1% 1 0 0 - 3% - -
MI:0116 feature type MI:0373 dye label 5% 1.2 0.45 0 7% 8% 5% 4%
  1. Experimental techniques were evaluated considering the number of documents where these concepts were annotated and the number of annotations in the corpus. Moreover, the frequency of annotation of experimental techniques was also estimated for documents published in the four decades (from 1970 to 2009). Statistical measures are detailed in the Methods and Materials section.
  2. * These PSI-MI general classes were used to identify techniques that did not map into any particular technique within the class.