Semantically Enriched Text-Based Retrieval in Chemical Digital Libraries

During the last decades, the information gathering process has considerably changed in science, research and development, and the private life. Whereas Web pages for private information seeking are usually accessed using well-known text-based search engines, complex documents for scientific research are often stored in digital libraries and will usually be accessed through domain specific Web portals. Considering the specific domain of chemistry, portals usually rely on graphical user-interfaces allowing for pictorial structure queries. The difficulty with purely text-based searches is that information seeking in chemical documents is generally focused on chemical entities, for which current standard search relies on complex and hard to extract structures. In this thesis, we introduce a retrieval workflow for chemical digital libraries enabling text-based searches. First, we explain how to automatically index chemical documents with high completeness by creating enriched index pages containing different entity representations and synonyms. Next, we analyze different similarity measures for chemical entities. We further describe how to model the chemists’ implicit knowledge to personalize the retrieval process. Furthermore, since users often search for chemical entities occurring in a specific context, we also show how to use contextual information to further enhance the retrieval quality. Since, the annotated context terms will not help for contextual search if the users use different vocabulary, we present an approach that semantically enriches documents with Wikipedia concepts to overcome the vocabulary problem. Since for most queries a huge amount of possibly relevant hits are returned to the user, we further present an approach summarizing the documents’ content using Wikipedia categories. Finally, we present an architecture for a chemical digital library provider combining the different steps enabling semantically enriched text-based retrieval for the chemical domain.Über die letzten Jahre hat sich der Prozess der Informationssuche stark verändert. Während im privaten Bereich meistens über eine text-basierte Websuche auf Informationen zugegriffen wird, erfolgt der Zugriff auf Dokumente für den wissenschaftlichen Gebrauch in der Regel über domänenspezifische Web Portale. Betrachtet man beispielsweise die Domäne der Chemie, basieren Web Portale auf speziellen grafischen Benutzeroberflächen, die gezeichnete, strukturbasierte Anfragen ermöglichen. Da die Informationssuche für chemische Dokumente generell auf chemischen Entitäten basiert, die wiederum aus komplexen Strukturen bestehen, birgt eine reine text-basierte Suche eine Vielzahl von Herausforderungen. In dieser Arbeit entwickeln wir einen Retrieval Workflow für eine chemische digitale Bibliothek, der text-basierte Suchen ermöglicht. Als erstes erzeugen wir für chemische Dokumente semantisch angereicherte Indexseiten. Im Folgenden analysieren wir wie man Ähnlichkeit zwischen chemischen Entitäten bestimmen kann. Im Anschluss zeigen wir wie man das subjektive Relevanzempfinden der Chemiker modellieren kann, um ein personalisiertes Retrieval zu ermöglichen. Dann beschäftigen wir uns mit der Tatsache, dass Benutzer häufig nach chemischen Entitäten suchen, die in einem bestimmten Kontext auftreten. Allerdings sind die annotierten Kontext-Terme nutzlos, falls die Benutzer ein völlig anderes Vokabular verwenden. Deshalb reichern wir die Dokumente semantisch mit Wikipedia Konzepten an um das Problem des unterschiedlichen Vokabulars zu beheben. Da für die meisten Anfragen eine Vielzahl von relevanten Treffern zurückgeliefert wird, präsentieren wir eine Methode um den Inhalt der Dokumente auf übersichtliche Weise mit Hilfe von Wikipedia Kategorien darzustellen. Schlussendlich kombinieren wir die gewonnenen Erkenntnisse und stellen eine Architektur für eine chemische digitale Bibliothek vor, die semantisch angereicherte, text-basierte Suchen in der Chemie ermöglicht

Risk and protective factors for structural brain ageing in the eighth decade of life

Individuals differ markedly in brain structure, and in how this structure degenerates during ageing. In a large sample of human participants (baseline n = 731 at age 73 years; follow-up n = 488 at age 76 years), we estimated the magnitude of mean change and variability in changes in MRI measures of brain macrostructure (grey matter, white matter, and white matter hyperintensity volumes) and microstructure (fractional anisotropy and mean diffusivity from diffusion tensor MRI). All indices showed significant average change with age, with considerable heterogeneity in those changes. We then tested eleven socioeconomic, physical, health, cognitive, allostatic (inflammatory and metabolic), and genetic variables for their value in predicting these differences in changes. Many of these variables were significantly correlated with baseline brain structure, but few could account for significant portions of the heterogeneity in subsequent brain change. Physical fitness was an exception, being correlated both with brain level and changes. The results suggest that only a subset of correlates of brain structure are also predictive of differences in brain ageing

Preference-Driven Personalization for Flexible Digital Item Adaptation

Abstract The delivery of multimedia content often needs the adaptation of the content in order to satisfy user constraints. With the Digital Item Adaptation part, the MPEG-21 standard already defines a useful frame-work to handle this task. However, in modern service-oriented architectures the functionality of adaptation is split over several services. Hence, the central instantiation of a suitable service chain needs to tackle a complex multiobjective optimization problem. In this problem between content choice and possible adaptations the current preference model in the MPEG-7/21 standard still lacks expressiveness. In the course of this paper we demonstrate this shortcoming and how the integration of more powerful models can ease the instantiation problem. Furthermore we explain how to efficiently evaluate preference trade-offs by evaluating skyline queries as currently investigated in the field of information systems. As a running example we use preference-based content adaptation in a typical media streaming application with Web services as basic modules. The contribution of our framework is to enable a central coordinator to instantiate an executable service composition chain by integrating all needed Web services to adapt the multimedia content in the best possible fashion in the sense of Pareto optimality

Using Wikipedia Categories for Compact Representations of Chemical Documents

Today, Web pages are usually accessed using text search engines, whereas documents stored in the deep Web are accessed through domain-specific Web portals. These portals rely on external knowledge bases, respectively ontologies, mapping documents to more general concepts allowing for suitable classifications and navigational browsing. Since automatically generated ontologies are still not satisfactory for advanced information retrieval tasks, most portals heavily rely on hand-crafted domain-specific ontologies. This, however, also leads to high creation and maintaining costs. On the other hand, a freely available community maintained, if somewhat general, knowledge base is offered by Wikipedia. During the last years the coverage of Wikipedia has reached a large pool of information including articles from almost all domains. In this paper, we investigate the use of Wikipedia categories to describe the content of chemical documents in a compact form. We compare the results to the domain-specific ChEBI ontology and the results show that Wikipedia categories indeed allow useful descriptions for chemical documents that are even better than descriptions from the ChEBI ontology

Exposing the Hidden Web for Chemical Digital Libraries

In recent years, the vast amount of digitally available content has lead to the creation of many topic-centered digital libraries. Also in the domain of chemistry more and more digital collections are available, but the complex query formulation still hampers their intuitive adoption. This is because information seeking in chemical documents is focused on chemical entities, for which current standard search relies on complex structures which are hard t

A Service Oriented Architecture for Personalized Universal Media Access

Multimedia streaming means delivering continuous data to a plethora of client devices. Besides the actual data transport, this also needs a high degree of content adaptation respecting the end users’ needs given by content preferences, transcoding constraints, and device capabilities. Such adaptations can be performed in many ways, usually on the media server. However, when it comes to content editing, like mixing in subtitles or picture-in-picture composition, relying on third party service providers may be necessary. For economic reasons this should be done in a service-oriented way, because a lot of adaptation modules can be reused within different adaptation workflows. Although service-oriented architectures have become widely accepted in the Web community, the multimedia environment is still dominated by monolithic systems. The main reason is the insufficient support for working with continuous data: generally the suitability of Web services for handling complex data types and state-full applications is still limited. In this paper we discuss extensions of Web service frameworks, and present a first implementation of a service-oriented framework for media streaming and digital item adaptation. The focus lies on the technical realization of the services. Our experimental results show the practicality of the actual deployment of service-oriented multimedia frameworks