Semantic text mining support for lignocellulose research

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

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.

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.

ISSN: 1472-6947