Personalizable Knowledge Integration

Large repositories of data are used daily as knowledge bases (KBs) feeding computer systems that support decision making processes, such as in medical or financial applications. Unfortunately, the larger a KB is, the harder it is to ensure its consistency and completeness. The problem of handling KBs of this kind has been studied in the AI and databases communities, but most approaches focus on computing answers locally to the KB, assuming there is some single, epistemically correct solution. It is important to recognize that for some applications, as part of the decision making process, users consider far more knowledge than that which is contained in the knowledge base, and that sometimes inconsistent data may help in directing reasoning; for instance, inconsistency in taxpayer records can serve as evidence of a possible fraud. Thus, the handling of this type of data needs to be context-sensitive, creating a synergy with the user in order to build useful, flexible data management systems. Inconsistent and incomplete information is ubiquitous and presents a substantial problem when trying to reason about the data: how can we derive an adequate model of the world, from the point of view of a given user, from a KB that may be inconsistent or incomplete? In this thesis we argue that in many cases users need to bring their application-specific knowledge to bear in order to inform the data management process. Therefore, we provide different approaches to handle, in a personalized fashion, some of the most common issues that arise in knowledge management. Specifically, we focus on (1) inconsistency management in relational databases, general knowledge bases, and a special kind of knowledge base designed for news reports; (2) management of incomplete information in the form of different types of null values; and (3) answering queries in the presence of uncertain schema matchings. We allow users to define policies to manage both inconsistent and incomplete information in their application in a way that takes both the user's knowledge of his problem, and his attitude to error/risk, into account. Using the frameworks and tools proposed here, users can specify when and how they want to manage/solve the issues that arise due to inconsistency and incompleteness in their data, in the way that best suits their needs

RDF Querying

Reactive Web systems, Web services, and Web-based publish/ subscribe systems communicate events as XML messages, and in many cases require composite event detection: it is not sufficient to react to single event messages, but events have to be considered in relation to other events that are received over time. Emphasizing language design and formal semantics, we describe the rule-based query language XChangeEQ for detecting composite events. XChangeEQ is designed to completely cover and integrate the four complementary querying dimensions: event data, event composition, temporal relationships, and event accumulation. Semantics are provided as model and fixpoint theories; while this is an established approach for rule languages, it has not been applied for event queries before

A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.Peer Reviewe