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Table 1 Semantic entities, applicable level (sentence, S or word(s), W), definitions and examples

From: Semantic text mining support for lignocellulose research

Semantic entity Level Definition
ActivityAssayConditions S Conditions at which the activity assay is carried out Ex.: disodium hydrogen phosphate, citric acid, pH 4.0, 37°C
Assay W Name of the activity assay Ex.: Dinitrosalicylic Acid Method (Somogyi-Nelson)
Enzyme W Enzyme name Ex.: alpha-galactosidase
Gene W Gene name Ex.: mel36F
Glycosylation S Presence of glycosylation on protein Ex.: N-glycosylated
Host W Organism used to produce the recombinant protein Ex.: Escherichia coli
KineticAssayConditions S Buffer, pH, temp. for the kinetic parameters determination Ex.: 0.1 M (disodium hydrogen phosphate, citric acid), pH 4.0, 37°C
Organism W Organism name Ex.: Gibberella sp.
pH S pH mentions Ex.: The enzyme retained greater than 90% of its original activity between pH 2.0 and 7.0 at room temperature for 3 h.
ProductAnalysis S Products formed from enzyme reaction and identification method Ex.: HPLC, glucose, galactose
SpecificActivity S Specific activity of the enzyme Ex.: 11.9 U/mg
Strain W Strain name Ex.: F75
Substrate W Substrate name Ex.: stachyose
SubstrateSpecificity S Substrate specificity mentions Ex.: The Endoglucanase from Pyrococcus furiosus had highest activity on cellopentaose
Temperature S Temperature mentions Ex.: The enzyme stability at different pH values was measured by the residual activity after the enzyme was incubated at 25°C for 3 h.
  1. The list of the semantic entities along with the level they apply (sentence or word level), their definition and an instance example is provided in Table 1.