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The study of the metabolism of hyperthermophilic microorganisms is of great industrial im portance since these organisms’ enzymes catalyze reactions at elevated temperatures. Various hyperthermophiles of archaea (eg, Thermococcus, Pyrococcus, etc.) and bac teria (eg, Caldicellulosiruptor, Thermotoga, etc.) are established as laboratory models; their metabolic pathways undergo genetic engineering aiming at optimal production of fuels and chemicals at elevated temperatures in industrial scale.

This thesis aims to ease the literature study of the biological processes (and related meta bolites) of microorganisms of interest. The key contribution of the thesis is a framework to (a) identify mentions of chemical entities (metabolites, substrates, enzyme cofactors, etc.) in paper abstracts, and (b) retrieve cooccurrence associations between microorganisms and chemical entities, and among chemical entities.