Analyzing the data produced by next-generation sequencing technologies relies on access to information synthesized based on previous research findings. The volume of data available in the literature is growing rapidly, and it is becoming increasingly necessary for researchers to use AI or other statistics-based approaches in the analysis of their datasets. In this project, knowledge graphs are explored as a tool for providing access to contextual gene-information available in scientific literature. The explorative method described in this thesis is based on the implementation and comparison of two approaches for knowledge graph construction, a rule-based statistical as well as a neural-network and co-occurrence based approach, -based on specific literature contexts. The results are presented both in the form of a quantitative comparison between approaches as well as in the form of a qualitative expert evaluation of the quantitative result. The quantitative comparison suggested that contrasting knowledge graphs constructed based on different approaches can provide valuable information for the interpretation and contextualization of key genes. It also demonstrated the limitations of some approaches e.g. in terms of scalability as well as the volume and type of information that can be extracted. The result further suggested that metrics based on the overlap of nodes and edges, as well as metrics that leverage the global topology of graphs are valuable for representing and comparing contextual information between knowledge graphs. The result based on the qualitative expert evaluation demonstrated that literature-derived knowledge graphs of gene-information can be valuable tools for identifying research biases related to genes and also shed light on the challenges related to biological entity normalization in the context of knowledge graph development. In light of these findings, automatic knowledge-graph construction presents as a promising approach for improving access to contextual information about genes in scientific literature. / För att analysera de stora mängder data som produceras med hjälp av next-generation sequencing krävs det att forskare har tillgång till och kan sammanställa information från tidigare forskning. I takt med att mängden data som finns tillgänglig i den vetenskapliga litteraturen ökar, så ökar även behovet av att använda AI och andra statistiska metoder för att få tillgång till denna data i analysen. I detta projekt utforskas kunskapsgrafer som verktyg för att tillgängliggöra kontextuell geninformation i vetenskapliga artiklar. Den explorativa metod som beskrivs i detta projekt är baserad på implementationen och jämförelsen av två olika tekniker för kunskapsgrafgenerering, en regelbaserad-statistisk metod samt en metod baserad på neurala-nätverk och co-occurrence, baserade på specifika kontexter inom litteraturen. Resultatet presenteras både i form av en kvantitativ jämförelse mellan metoder samt genom en kvalitativ expertutvärdering baserad på det kvantitativa resultatet. Den kvantitativa jämförelsen antydde att jämförelsen mellan kunskapsgrafer genererade med hjälp av olika metoder kan bidra med värdefull information för tolkningen och kontextualiseringen av viktiga gener. Resultatet visade även på begränsningar hos vissa metoder, till exempel gällande skalbarhet samt den mängd och typ av information som kan extraheras. Men även att metrics baserade på överlappning av hörn och kanter, samt metrics som tar hänsyn till den globala topologin i grafer kan vara användbara i jämförelsen av, samt för att representera skillnader mellan biologiska kunskapsgrafer. Resultatet från den kvalitativa expertutvärderingen visade att kunskapsgrafer baserade på geninformation extraherad från vetenskapliga artiklar kan vara värdefulla verktyg för att identifiera forskningsbias gällande gener, samt framhävde viktiga utmaningar gällande normalisering av biologiska entiteter inom området kunskapsgrafsutveckling. Baserat på dessa fynd framstår automatisk kunskapsgrafsgenerering som ett lovande tillvägagångssätt för att förbättra tillgängligheten av kontextuell geninformation i vetenskaplig litteratur.

Diese Arbeit fokussiert auf die Integration von Web Anfrageschnittstellen (Web Formularen). Wir identifizieren mehrere Schritte für den Integrationsprozess: Im ersten Schritt werden unbekannte Anfrageschnittstellen auf ihre Anwendungsdomäne hin analysiert. Im zweiten Schritt werden die Anfrageschnittstellen in ein maschinenlesbares Format transformiert (Extraktion). Im dritten Schritt werden Paare semantisch gleicher Elemente zwischen den verschiedenen zu integrierenden Anfragesschnittstellen identifiziert (Matching). Diese Schritte bilden die Grundlage, um Systeme, die eine integrierte Sicht auf die verschiedenen Datenquellen bieten, aufsetzen zu können. Diese Arbeit beschreibt neuartige Lösungen für alle drei der genannten Schritte. Der erste zentrale Beitrag ist ein Exktraktionsalgorithmus, der eine kleine Zahl von Designregeln dazu benutzt, um Schemabäume abzuleiten. Gegenüber früheren Lösungen, welche in der Regel lediglich eine flache Schemarepräsentation anbieten, ist der Schemabaum semantisch reichhaltiger, da er zusätzlich zu den Elementen auch Strukturinformationen abbildet. Der Extraktionsalgorithmus erreicht eine verbesserte Qualität der Element-Extraktion verglichen mit Vergängermethoden. Der zweite Beitrag der Arbeit ist die Entwicklung einer neuen Matching-Methode. Hierbei ermöglicht die Repräsentation der Schnittstellen als Schemabäume eine Verbesserung vorheriger Methoden, indem auch strukturelle Aspekte in den Matching-Algorithmus einfließen. Zusätzlich wird eine globale Optimierung durchgeführt, welche auf der Theorie der bipartiten Graphen aufbaut. Als dritten Beitrag entwickelt die Arbeit einen Algorithms für eine Klassifikation von Schnittstellen nach Anwendungsdomänen auf Basis der Schemabäume und den abgeleiteten Matches. Zusätzlich wird das System VisQI vorgestellt, welches die entwickelten Algorithmen implementiert und eine komfortable graphische Oberfläche für die Unterstützung des Integrationsprozesses bietet. / This thesis focuses on the integration of Web query interfaces. We model the integration process in several steps: First, unknown interfaces have to be classified with respect to their application domain (classification); only then a domain-wise treatment is possible. Second, interfaces must be transformed into a machine readable format (extraction) to allow their automated analysis. Third, as a pre-requisite to integration across databases, pairs of semantically similar elements among multiple interfaces need to be identified (matching). Only if all these tasks have been solved, systems that provide an integrated view to several data sources can be set up. This thesis presents new algorithms for each of these steps. We developed a novel extraction algorithm that exploits a small set of commonsense design rules to derive a hierarchical schema for query interfaces. In contrast to prior solutions that use mainly flat schema representations, the hierarchical schema better represents the structure of the interfaces, leading to better accuracy of the integration step. Next, we describe a multi-step matching method for query interfaces which builds on the hierarchical schema representation. It uses methods from the theory of bipartite graphs to globally optimize the matching result. As a third contribution, we present a new method for the domain classification problem of unknown interfaces that, for the first time, combines lexical and structural properties of schemas. All our new methods have been evaluated on real-life datasets and perform superior to previous works in their respective fields. Additionally, we present the system VisQI that implements all introduced algorithmic steps and provides a comfortable graphical user interface to support the integration process.

Informationsextraktions (IE) auf sehr großen Datenmengen erfordert hochkomplexe, skalierbare und anpassungsfähige Systeme. Obwohl zahlreiche IE-Algorithmen existieren, ist die nahtlose und erweiterbare Kombination dieser Werkzeuge in einem skalierbaren System immer noch eine große Herausforderung. In dieser Arbeit wird ein anfragebasiertes IE-System für eine parallelen Datenanalyseplattform vorgestellt, das für konkrete Anwendungsdomänen konfigurierbar ist und für Textsammlungen im Terabyte-Bereich skaliert. Zunächst werden konfigurierbare Operatoren für grundlegende IE- und Web-Analytics-Aufgaben definiert, mit denen komplexe IE-Aufgaben in Form von deklarativen Anfragen ausgedrückt werden können. Alle Operatoren werden hinsichtlich ihrer Eigenschaften charakterisiert um das Potenzial und die Bedeutung der Optimierung nicht-relationaler, benutzerdefinierter Operatoren (UDFs) für Data Flows hervorzuheben. Anschließend wird der Stand der Technik in der Optimierung nicht-relationaler Data Flows untersucht und herausgearbeitet, dass eine umfassende Optimierung von UDFs immer noch eine Herausforderung ist. Darauf aufbauend wird ein erweiterbarer, logischer Optimierer (SOFA) vorgestellt, der die Semantik von UDFs mit in die Optimierung mit einbezieht. SOFA analysiert eine kompakte Menge von Operator-Eigenschaften und kombiniert eine automatisierte Analyse mit manuellen UDF-Annotationen, um die umfassende Optimierung von Data Flows zu ermöglichen. SOFA ist in der Lage, beliebige Data Flows aus unterschiedlichen Anwendungsbereichen logisch zu optimieren, was zu erheblichen Laufzeitverbesserungen im Vergleich mit anderen Techniken führt. Als Viertes wird die Anwendbarkeit des vorgestellten Systems auf Korpora im Terabyte-Bereich untersucht und systematisch die Skalierbarkeit und Robustheit der eingesetzten Methoden und Werkzeuge beurteilt um schließlich die kritischsten Herausforderungen beim Aufbau eines IE-Systems für sehr große Datenmenge zu charakterisieren. / Information extraction (IE) on very large data sets requires highly complex, scalable, and adaptive systems. Although numerous IE algorithms exist, their seamless and extensible combination in a scalable system still is a major challenge. This work presents a query-based IE system for a parallel data analysis platform, which is configurable for specific application domains and scales for terabyte-sized text collections. First, configurable operators are defined for basic IE and Web Analytics tasks, which can be used to express complex IE tasks in the form of declarative queries. All operators are characterized in terms of their properties to highlight the potential and importance of optimizing non-relational, user-defined operators (UDFs) for dataflows. Subsequently, we survey the state of the art in optimizing non-relational dataflows and highlight that a comprehensive optimization of UDFs is still a challenge. Based on this observation, an extensible, logical optimizer (SOFA) is introduced, which incorporates the semantics of UDFs into the optimization process. SOFA analyzes a compact set of operator properties and combines automated analysis with manual UDF annotations to enable a comprehensive optimization of data flows. SOFA is able to logically optimize arbitrary data flows from different application areas, resulting in significant runtime improvements compared to other techniques. Finally, the applicability of the presented system to terabyte-sized corpora is investigated. Hereby, we systematically evaluate scalability and robustness of the employed methods and tools in order to pinpoint the most critical challenges in building an IE system for very large data sets.

The aim of this thesis is to determine to what extent aircraft-borne radar remote sensing can be used as the sole method for making recordings of the surface of the earth as a basis for compiling topographical and relief maps of mountainous areas. This is done using three test areas: the Edelsberg area in the Allgäu Alps and the Silvretta and Verwall Groups in the Central Alps. The basis for discussion is provided by examination of the interaction between the objects to be imaged and the radar signal, the sensor-specific characteristics thereby being taken into account. Following this some data processing and conditioning methods used for extracting information on the relief and surface coverage for preparation of cartographical products are presented. Analysis of the quality of the results shows that, measured against the requirements of mountain cartography, radar remote sensing is a practical and useful tool for making maps in Alpine regions. As the sole source of information, however, aircraft-borne radar remote sensing p roves to date to be inadequate for cartographical applications in high-mountain regions. / Ziel der vorliegenden Arbeit ist, festzustellen, inwieweit die flugzeuggetragene Radarfernerkundung als alleinige Erfassungsmethode der Erdoberfläche zur Erstellung von topographischen und reliefbeschreibenden Karten in Gebirgslandschaften dienen kann. Dies wird anhand von drei Testgebieten, dem Edelsberggebiet in den Allgäuer Alpen sowie der Silvretta- und Verwallgrupe in den Zentralalpen, untersucht. Die Betrachtung der Interaktion zwischen den abzubildenden Objekten und dem Radar-Signal unter Berücksichtigung der sensorspezifischen Charakteristika bildet dabei die Diskussionsgrundlage. Im weiteren werden Methoden zur Datenprozessierung und -aufbereitung vorgestellt, die eine Informa-tionsextraktion bezüglich des Reliefs und der Oberflächenbedeckung für die Erstellung kartographischer Produkte ermöglichen. Die Qualitätsanalyse der Ergebnisse zeigt, dass die Radarfernerkundung, gemessen an den Anforderungen der Gebirgskartographie, ein sinnvolles und nutzbringendes Werkzeug für die Kartenerstellung in alpinen Regionen ist. Für kartographische Anwendungen in Hochgebirgsregionen erweist sich die flugzeuggetragene Radarfernerkundung als einzige Informationsquelle bislang allerdings als nicht ausreichend.

Searching is a fundamental task to support research. Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason. This work provides a system for combining the classical keyword-based search engines with semantic annotation. Conventional search results are annotated using a customized annotation algorithm, which takes the textual properties and requirements such as speed and scalability into account. The biomedical background knowledge consists of the GeneOntology and Medical Subject Headings and other related entities, e.g. proteins/gene names and person names. Together they provide the relevant semantic context for a search engine for the life sciences. We develop the system GoWeb for semantic web search and evaluate it using three benchmarks. It is shown that GoWeb is able to aid question answering with success rates up to 79%. Furthermore, the system also includes semantic hyperlinks that enable semantic browsing of the knowledge space. The semantic hyperlinks facilitate the use of the eScience infrastructure, even complex workflows of composed web services. To complement the web search of GoWeb, other data source and more specialized information needs are tested in different prototypes. This includes patents and intranet search. Semantic search is applicable for these usage scenarios, but the developed systems also show limits of the semantic approach. That is the size, applicability and completeness of the integrated ontologies, as well as technical issues of text-extraction and meta-data information gathering. Additionally, semantic indexing as an alternative approach to implement semantic search is implemented and evaluated with a question answering benchmark. A semantic index can help to answer questions and address some limitations of GoWeb. Still the maintenance and optimization of such an index is a challenge, whereas GoWeb provides a straightforward system.

Each day, millions of people ask questions and search for answers on the World Wide Web. Due to this, the Internet has grown to a world wide database of questions and answers, accessible to almost everyone. Since this database is so huge, it is hard to find out whether a question has been answered or even asked before. As a consequence, users are asking the same questions again and again, producing a vicious circle of new content which hides the important information. One platform for questions and answers are Web forums, also known as discussion boards. They present discussions as item streams where each item contains the contribution of one author. These contributions contain questions and answers in human readable form. People use search engines to search for information on such platforms. However, current search engines are neither optimized to highlight individual questions and answers nor to show which questions are asked often and which ones are already answered. In order to close this gap, this thesis introduces the \\emph{Effingo} system. The Effingo system is intended to extract forums from around the Web and find question and answer items. It also needs to link equal questions and aggregate associated answers. That way it is possible to find out whether a question has been asked before and whether it has already been answered. Based on these information it is possible to derive the most urgent questions from the system, to determine which ones are new and which ones are discussed and answered frequently. As a result, users are prevented from creating useless discussions, thus reducing the server load and information overload for further searches. The first research area explored by this thesis is forum data extraction. The results from this area are intended be used to create a database of forum posts as large as possible. Furthermore, it uses question-answer detection in order to find out which forum items are questions and which ones are answers and, finally, topic detection to aggregate questions on the same topic as well as discover duplicate answers. These areas are either extended by Effingo, using forum specific features such as the user graph, forum item relations and forum link structure, or adapted as a means to cope with the specific problems created by user generated content. Such problems arise from poorly written and very short texts as well as from hidden or distributed information.

Konversationerna i ett kundforum rör sig över olika ämnen och språket är inkonsekvent. Texterna uppfyller inte de krav som brukar ställas på material inför automatisk nyckelordsextraktion. Uppsatsens undersöker hur nyckelord automatiskt kan extraheras ur ett kundforum trots dessa svårigheter. Fokus i undersökningen ligger på tre aspekter av nyckelordsextraktion. Den första faktorn rör hur den etablerade nyckelordsextraktionsmetoden TF*IDF presterar jämfört med fyra metoder som skapas med hänsyn till materialets ovanliga struktur. Nästa faktor som testas är om olika sätt att räkna ordfrekvens påverkar resultatet. Den tredje faktorn är hur metoderna presterar om de endast använder inläggen, rubrikerna eller båda texttyperna i sina extraktioner. Icke-parametriska test användes för utvärdering av extraktionerna. Ett antal Friedmans test visar att metoderna i några fall skiljer sig åt gällande förmåga att identifiera relevanta nyckelord. I post-hoc-test mellan de högst presterande metoderna ses en av de nya metoderna i ett fall prestera signifikant bättre än de andra nya metoderna men inte bättre än TF*IDF. Ingen skillnad hittades mellan användning av olika texttyper eller sätt att räkna ordfrekvens. För framtida forskning rekommenderas reliabilitetstest av manuellt annoterade nyckelord. Ett större stickprov bör användas än det i aktuell studie och olika förslag ges för att förbättra rättning av extraherade nyckelord. / Conversations in a customer forum span across different topics and the language is inconsistent. The text type do not meet the demands for automatic keyword extraction. This essay examines how keywords can be automatically extracted despite these difficulties. Focus in the study are three areas of keyword extraction. The first factor regards how the established keyword extraction method TF*IDF performs compared to four methods created with the unusual material in mind. The next factor deals with different ways to calculate word frequency. The third factor regards if the methods use only posts, only titles, or both in their extractions. Non-parametric tests were conducted to evaluate the extractions. A number of Friedman's tests shows the methods in some cases differ in their ability to identify relevant keywords. In post-hoc tests performed between the highest performing methods, one of the new methods perform significantly better than the other new methods but not better than TF*IDF. No difference was found between the use of different text types or ways to calculate word frequency. For future research reliability test of manually annotated keywords is recommended. A larger sample size should be used than in the current study and further suggestions are given to improve the results of keyword extractions.

Each day, millions of people ask questions and search for answers on the World Wide Web. Due to this, the Internet has grown to a world wide database of questions and answers, accessible to almost everyone. Since this database is so huge, it is hard to find out whether a question has been answered or even asked before. As a consequence, users are asking the same questions again and again, producing a vicious circle of new content which hides the important information. One platform for questions and answers are Web forums, also known as discussion boards. They present discussions as item streams where each item contains the contribution of one author. These contributions contain questions and answers in human readable form. People use search engines to search for information on such platforms. However, current search engines are neither optimized to highlight individual questions and answers nor to show which questions are asked often and which ones are already answered. In order to close this gap, this thesis introduces the \\emph{Effingo} system. The Effingo system is intended to extract forums from around the Web and find question and answer items. It also needs to link equal questions and aggregate associated answers. That way it is possible to find out whether a question has been asked before and whether it has already been answered. Based on these information it is possible to derive the most urgent questions from the system, to determine which ones are new and which ones are discussed and answered frequently. As a result, users are prevented from creating useless discussions, thus reducing the server load and information overload for further searches. The first research area explored by this thesis is forum data extraction. The results from this area are intended be used to create a database of forum posts as large as possible. Furthermore, it uses question-answer detection in order to find out which forum items are questions and which ones are answers and, finally, topic detection to aggregate questions on the same topic as well as discover duplicate answers. These areas are either extended by Effingo, using forum specific features such as the user graph, forum item relations and forum link structure, or adapted as a means to cope with the specific problems created by user generated content. Such problems arise from poorly written and very short texts as well as from hidden or distributed information.

Searching is a fundamental task to support research. Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason. This work provides a system for combining the classical keyword-based search engines with semantic annotation. Conventional search results are annotated using a customized annotation algorithm, which takes the textual properties and requirements such as speed and scalability into account. The biomedical background knowledge consists of the GeneOntology and Medical Subject Headings and other related entities, e.g. proteins/gene names and person names. Together they provide the relevant semantic context for a search engine for the life sciences. We develop the system GoWeb for semantic web search and evaluate it using three benchmarks. It is shown that GoWeb is able to aid question answering with success rates up to 79%. Furthermore, the system also includes semantic hyperlinks that enable semantic browsing of the knowledge space. The semantic hyperlinks facilitate the use of the eScience infrastructure, even complex workflows of composed web services. To complement the web search of GoWeb, other data source and more specialized information needs are tested in different prototypes. This includes patents and intranet search. Semantic search is applicable for these usage scenarios, but the developed systems also show limits of the semantic approach. That is the size, applicability and completeness of the integrated ontologies, as well as technical issues of text-extraction and meta-data information gathering. Additionally, semantic indexing as an alternative approach to implement semantic search is implemented and evaluated with a question answering benchmark. A semantic index can help to answer questions and address some limitations of GoWeb. Still the maintenance and optimization of such an index is a challenge, whereas GoWeb provides a straightforward system.

Seit Jahrhunderten wird menschliches Wissen in Form von natürlicher Sprache ausgetauscht und in Dokumenten schriftlich aufgezeichnet. In den letzten Jahren konnte man auf dem Gebiet der Lebenswissenschaften eine exponentielle Zunahme wissenschaftlicher Publikationen beobachten. Diese Dissertation untersucht die automatische Extraktion von Beziehungen zwischen Eigennamen. Innerhalb dieses Gebietes beschäftigt sich die Arbeit mit der Steigerung der Robustheit für die Relationsextraktion. Zunächst wird der Einsatz von Ensemble-Methoden anhand von Daten aus der "Drug-drug-interaction challenge 2013" evaluiert. Ensemble-Methoden erhöhen die Robustheit durch Aggregation unterschiedlicher Klassifikationssysteme zu einem Modell. Weiterhin wird in dieser Arbeit das Problem der Relationsextraktion auf Dokumenten mit unbekannten Texteigenschaften beschrieben. Es wird gezeigt, dass die Verwendung des halb-überwachten Lernverfahrens self training in solchen Fällen eine höhere Robustheit erzielt als die Nutzung eines Klassifikators, der lediglich auf einem manuell annotierten Korpus trainiert wurde. Zur Ermittlung der Robustheit wird das Verfahren des cross-learnings verwendet. Zuletzt wird die Verwendung von distant-supervision untersucht. Korpora, welche mit der distant-supervision-Methode erzeugt wurden, weisen ein inhärentes Rauschen auf und profitieren daher von robusten Relationsextraktionsverfahren. Es werden zwei verschiedene Methoden untersucht, die auf solchen Korpora trainiert werden. Beide Ansätze zeigen eine vergleichbare Leistung wie vollständig überwachte Klassifikatoren, welche mit dem cross-learning-Verfahren evaluiert wurden. Um die Nutzung von Ergebnissen der Informationsextraktion zu erleichtern, wurde die semantische Suchmaschine GeneView entwickelt. Anforderungen an die Rechenkapazität beim Erstellen von GeneView werden diskutiert und Anwendungen auf den von verschiedenen Text-Mining-Komponenten extrahierten Daten präsentiert. / For several centuries, a great wealth of human knowledge has been communicated by natural language, often recorded in written documents. In the life sciences, an exponential increase of scientific articles has been observed, hindering the effective and fast reconciliation of previous finding into current research projects. This thesis studies the automatic extraction of relationships between named entities. Within this topic, it focuses on increasing robustness for relationship extraction. First, we evaluate the use of ensemble methods to improve performance using data provided by the drug-drug-interaction challenge 2013. Ensemble methods aggregate several classifiers into one model, increasing robustness by reducing the risk of choosing an inappropriate single classifier. Second, this work discusses the problem of applying relationship extraction to documents with unknown text characteristics. Robustness of a text mining component is assessed by cross-learning, where a model is evaluated on a corpus different from the training corpus. We apply self-training, a semi-supervised learning technique, in order to increase cross-learning performance and show that it is more robust in comparison to a classifier trained on manually annotated text only. Third, we investigate the use of distant supervision to overcome the need of manually annotated training instances. Corpora derived by distant supervision are inherently noisy, thus benefiting from robust relationship extraction methods. We compare two different methods and show that both approaches achieve similar performance as fully supervised classifiers, evaluated in the cross-learning scenario. To facilitate the usage of information extraction results, including those developed within this thesis, we develop the semantic search engine GeneView. We discuss computational requirements to build this resource and present some applications utilizing the data extracted by different text-mining components.