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

Table 3 Annotations of the small molecules in the corpus.

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

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.
^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.
VMR: variance-to-mean
Std: standard deviation