Global ETD Search

1	COMPUTATIONAL TOOLS FOR THE DYNAMIC CATEGORIZATION AND AUGMENTED UTILIZATION OF THE GENE ONTOLOGY Hinderer, Eugene Waverly, III 01 January 2019 (has links) Ontologies provide an organization of language, in the form of a network or graph, which is amenable to computational analysis while remaining human-readable. Although they are used in a variety of disciplines, ontologies in the biomedical field, such as Gene Ontology, are of interest for their role in organizing terminology used to describe—among other concepts—the functions, locations, and processes of genes and gene-products. Due to the consistency and level of automation that ontologies provide for such annotations, methods for finding enriched biological terminology from a set of differentially identified genes in a tissue or cell sample have been developed to aid in the elucidation of disease pathology and unknown biochemical pathways. However, despite their immense utility, biomedical ontologies have significant limitations and caveats. One major issue is that gene annotation enrichment analyses often result in many redundant, individually enriched ontological terms that are highly specific and weakly justified by statistical significance. These large sets of weakly enriched terms are difficult to interpret without manually sorting into appropriate functional or descriptive categories. Also, relationships that organize the terminology within these ontologies do not contain descriptions of semantic scoping or scaling among terms. Therefore, there exists some ambiguity, which complicates the automation of categorizing terms to improve interpretability. We emphasize that existing methods enable the danger of producing incorrect mappings to categories as a result of these ambiguities, unless simplified and incomplete versions of these ontologies are used which omit problematic relations. Such ambiguities could have a significant impact on term categorization, as we have calculated upper boundary estimates of potential false categorizations as high as 121,579 for the misinterpretation of a single scoping relation, has_part, which accounts for approximately 18% of the total possible mappings between terms in the Gene Ontology. However, the omission of problematic relationships results in a significant loss of retrievable information. In the Gene Ontology, this accounts for a 6% reduction for the omission of a single relation. However, this percentage should increase drastically when considering all relations in an ontology. To address these issues, we have developed methods which categorize individual ontology terms into broad, biologically-related concepts to improve the interpretability and statistical significance of gene-annotation enrichment studies, meanwhile addressing the lack of semantic scoping and scaling descriptions among ontological relationships so that annotation enrichment analyses can be performed across a more complete representation of the ontological graph. We show that, when compared to similar term categorization methods, our method produces categorizations that match hand-curated ones with similar or better accuracy, while not requiring the user to compile lists of individual ontology term IDs. Furthermore, our handling of problematic relations produces a more complete representation of ontological information from a scoping perspective, and we demonstrate instances where medically-relevant terms--and by extension putative gene targets--are identified in our annotation enrichment results that would be otherwise missed when using traditional methods. Additionally, we observed a marginal, yet consistent improvement of statistical power in enrichment results when our methods were used, compared to traditional enrichment analyses that utilize ontological ancestors. Finally, using scalable and reproducible data workflow pipelines, we have applied our methods to several genomic, transcriptomic, and proteomic collaborative projects. Annotation Enrichment Analysis Biomedical Ontologies Information Retrieval Ontological Maintenance Semantic Correspondence Bioinformatics Genomics
2	The Perception of Lexical Similarities Between L2 English and L3 Swedish Utgof, Darja January 2008 (has links) <p>The present study investigates lexical similarity perceptions by students of Swedish as a foreign language (L3) with a good yet non-native proficiency in English (L2). The general theoretical framework is provided by studies in transfer of learning and its specific instance, transfer in language acquisition.</p><p>It is accepted as true that all previous linguistic knowledge is facilitative in developing proficiency in a new language. However, a frequently reported phenomenon is that students see similarities between two systems in a different way than linguists and theoreticians of education do. As a consequence, the full facilitative potential of transfer remains unused.</p><p>The present research seeks to shed light on the similarity perceptions with the focus on the comprehension of a written text. In order to elucidate students’ views, a form involving similarity judgements and multiple choice questions for formally similar items has been designed, drawing on real language use as provided by corpora. 123 forms have been distributed in 6 groups of international students, 4 of them studying Swedish at Level I and 2 studying at Level II. </p><p>The test items in the form vary in the degree of formal, semantic and functional similarity from very close cognates, to similar words belonging to different word classes, to items exhibiting category membership and/or being in subordinate/superordinate relation to each other, to deceptive cognates. The author proposes expected similarity ratings and compares them to the results obtained. The objective measure of formal similarity is provided by a string matching algorithm, Levenshtein distance.</p><p>The similarity judgements point at the fact that intermediate similarity values can be considered problematic. Similarity ratings between somewhat similar items are usually lower than could be expected. Besides, difference in grammatical meaning lowers similarity values significantly even if lexical meaning nearly coincides. Thus, the obtained results indicate that in order to utilize similarities to facilitate language learning, more attention should be paid to underlying similarities.</p> master master's programme language culture general linguistics linguistics foreign language acquisition similarity formal similarity semantic similarity functional similarity transfer transfer of learning language acquisition form form-based research crosslinguistic infuence one-year master english swedish lexical similarities false friends cognates deceptive cognates origin words of the same origin proto-germanic proto-indo-european competence performance comprehension corpus corpus-based data corpus-based research levenshtein distance objective similarity perceived similarity frequency prototype prototypicality proficiency context informed guess simchecker word recognition tachitoscopic experiments semantic correspondence similarity judgements eurocom surface transfer deep transfer lateral transfer English language Engelska språket Linguistic subjects Lingvistikämnen
3	The Perception of Lexical Similarities Between L2 English and L3 Swedish Utgof, Darja January 2008 (has links) The present study investigates lexical similarity perceptions by students of Swedish as a foreign language (L3) with a good yet non-native proficiency in English (L2). The general theoretical framework is provided by studies in transfer of learning and its specific instance, transfer in language acquisition. It is accepted as true that all previous linguistic knowledge is facilitative in developing proficiency in a new language. However, a frequently reported phenomenon is that students see similarities between two systems in a different way than linguists and theoreticians of education do. As a consequence, the full facilitative potential of transfer remains unused. The present research seeks to shed light on the similarity perceptions with the focus on the comprehension of a written text. In order to elucidate students’ views, a form involving similarity judgements and multiple choice questions for formally similar items has been designed, drawing on real language use as provided by corpora. 123 forms have been distributed in 6 groups of international students, 4 of them studying Swedish at Level I and 2 studying at Level II. The test items in the form vary in the degree of formal, semantic and functional similarity from very close cognates, to similar words belonging to different word classes, to items exhibiting category membership and/or being in subordinate/superordinate relation to each other, to deceptive cognates. The author proposes expected similarity ratings and compares them to the results obtained. The objective measure of formal similarity is provided by a string matching algorithm, Levenshtein distance. The similarity judgements point at the fact that intermediate similarity values can be considered problematic. Similarity ratings between somewhat similar items are usually lower than could be expected. Besides, difference in grammatical meaning lowers similarity values significantly even if lexical meaning nearly coincides. Thus, the obtained results indicate that in order to utilize similarities to facilitate language learning, more attention should be paid to underlying similarities. master master's programme language culture general linguistics linguistics foreign language acquisition similarity formal similarity semantic similarity functional similarity transfer transfer of learning language acquisition form form-based research crosslinguistic infuence one-year master english swedish lexical similarities false friends cognates deceptive cognates origin words of the same origin proto-germanic proto-indo-european competence performance comprehension corpus corpus-based data corpus-based research levenshtein distance objective similarity perceived similarity frequency prototype prototypicality proficiency context informed guess simchecker word recognition tachitoscopic experiments semantic correspondence similarity judgements eurocom surface transfer deep transfer lateral transfer Specific Languages Studier av enskilda språk General Language Studies and Linguistics

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