<p>Researchers tend to use their own or favourite gene names in scientific literature, even though there are official names. Some names may even be used for more than one gene. This leads to problems with ambiguity when automatically mining biological literature. To disambiguate the gene names, gene normalization is used. In this thesis, we look into an existing gene normalization system, and develop a new method to find gene candidates for the ambiguous genes. For the new method a lexicon is created, using information about the gene names, symbols and synonyms from three different databases. The gene mention found in the scientific literature is used as input for a search in this lexicon, and all genes in the lexicon that match the mention are returned as gene candidates for that mention. These candidates are then used in the system's disambiguation step. Results show that the new method gives a better over all result from the system, with an increase in precision and a small decrease in recall.</p>

Researchers tend to use their own or favourite gene names in scientific literature, even though there are official names. Some names may even be used for more than one gene. This leads to problems with ambiguity when automatically mining biological literature. To disambiguate the gene names, gene normalization is used. In this thesis, we look into an existing gene normalization system, and develop a new method to find gene candidates for the ambiguous genes. For the new method a lexicon is created, using information about the gene names, symbols and synonyms from three different databases. The gene mention found in the scientific literature is used as input for a search in this lexicon, and all genes in the lexicon that match the mention are returned as gene candidates for that mention. These candidates are then used in the system's disambiguation step. Results show that the new method gives a better over all result from the system, with an increase in precision and a small decrease in recall.

Highbush blueberry (Vaccinium corymbosum L.) has one of the highest antioxidant capacities and flavonoid concentrations of any fruit or vegetable, and regular consumption of blueberries has been connected to a wide range of health benefits. A diversity of flavonoids (flavonols, anthocyanins, proanthocyanidins) are likely responsible for many of the health benefits, and these compounds also significantly contribute to the organoleptic properties of ripe blueberries. Despite the potential importance of these flavonoids in diet, there has been little investigation into the molecular genetics of blueberry flavonoid biosynthesis. Therefore, I developed a real-time quantitative PCR protocol to monitor expression of flavonoid genes throughout development and ripening. Following evaluation of five reference genes, expression profiling of biosynthetic genes revealed that flavonoid synthesis is tightly controlled at the transcriptional level in a biphasic developmental pattern. These results are discussed in relation to flavonoid metabolite accumulation profiles, which were produced as part of a collaboration. Finally, in conjunction with a second group of collaborating scientists, some promising preliminary evidence is provided suggesting that the hormone abscisic acid might have a role in regulating ripening initiation in blueberry. / Graduate