Wilkowski, Bartlomiej

Denne afhandling diskuterer mulige anvendelser af semantik i nyere litteraturbaserede informatik systemer til at søge ny viden, generere hypoteser, og finde litteratur i biomedicin. De metoder, der forelægges her gøre brug af semantisk oplysninger udtaget fra biomedicinske tekster ved hjælp af naturlig sprogbehandling systemer, der understøttes af biomedicinske ontologier. Afhandlingen er opdelt i to hoveddele: for det første et afsnit om litteraturbaseret opdagelse med en gennemgang af de seneste tiltag indenfor området; for det andet, indsamling af litteratur inden for neurobilleddannelse og neurovidenskab analyseret med vægt på koordinatbaseret søgning af relevante publikationer. Mit eget bidrag til den første del er en ny litteraturbaseret `opdagelse browsing' metodologi baseret på semantisk prædikationer og grafteori der kan facilitere forskerne til at finde relevante litteratur om et speciceret biomedicinsk fænomen. Yderligere analyser af denne metode, indikerer ligeledes en potentiel anvendelse i forbindelse med probabilistiske metoder indenfor litteratursøgning. I den anden del af afhandlingen introduceres BredeQuery plugin, som integrerer et koordinatbaseret litteratursøgesystem i et neurobilleddannelse statistisk analysemiljø. Det efterfølges af en detaljeret beskrivelse af en prototype for kontekstafhængig neurovidenskabelig litteratursøgning, som ved hjælp af ontologier, giver brugeren mulighed for at definere rammerne af interesse for en søgning. Afhandlingens forskningsartikler, inkluderet i appendiks, diskuterer de nærmere detaljer om udformningen af de præsenterede metoder, casestudier, og andre praktiske detaljer.This thesis discusses potential applications of semantics to the recent literaturebased informatics systems to facilitate knowledge discovery, hypothesis generation, and literature retrieval in the domain of biomedicine. The approaches presented herein make use of semantic information extracted from biomedical texts by natural language processing systems supported by biomedical ontologies. The thesis is divided into two main parts: First, a field of literature-based discovery is introduced, with a review of recent approaches of the field; second, literature retrieval in the domain of neuroimaging (neuroscience) is discussed with the emphasis put on the coordinate-based searching of related publications. My own contribution to the first part is a novel literature-based `discovery browsing' methodology incorporating semantic predications, graph theory and path analysis for guiding researchers through the relevant literature on a user-specied biomedical phenomenon. Moreover, the additional analyses of the methodology show its potential application as a support for the recent probabilistic retrieval methods. In the second part of the thesis, I present the BredeQuery plugin which integrates a coordinate-based literature retrieval system with the common in neuroimaging statistical analysis environment. It is followed by the detailed description of a prototype of context-dependent neuroscientic literature retrieval methodology, which thanks to the employment of ontologies, allows the user to define context of interest for a search. The peer reviewed research articles, included in the appendices, discuss further the details of the presented methods, case studies, and provide other related information

Online Research Database In Technology

Semantic Approaches for Knowledge Discovery and Retrieval in Biomedicine

http://orbit.dtu.dk/ws/files/6247297/phd261_bw.pdf

Semantic Approaches for Knowledge Discovery and Retrieval in Biomedicine

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Online Research Database In Technology