A P2P Integration Architecture for Protein Resources

The availability of a direct pathway from a primary sequence (denovo or DNA derived) to macromolecular structure to biological function using computer-based tools is the ultimate goal for a protein scientist. Today\u27s state of the art protein resources and on-going research and experiments provide the raw data that can enable protein scientists to achieve at least some steps of this goal. Thus, protein scientists are looking towards taking their benchtop research from the specific to a much broader base of using the large resources of available electronic information. However, currently the burden falls on the scientist to manually interface with each data resource, integrate the required information, and then finally interpret the results. Their discoveries are impeded by the lack of tools that can not only bring integrated information from several known data resources, but also weave in information as it is discovered and brought online by other research groups. We propose a novel peer-to-peer based architecture that allows protein scientists to share resources in the form of data and tools within their community, facilitating ad hoc, decentralized sharing of data. In this paper, we present an overview of this integration architecture and briefly describe the tools that are essential to this framework

Online Analysis of Dynamic Streaming Data

Die Arbeit zum Thema "Online Analysis of Dynamic Streaming Data" beschäftigt sich mit der Distanzmessung dynamischer, semistrukturierter Daten in kontinuierlichen Datenströmen um Analysen auf diesen Datenstrukturen bereits zur Laufzeit zu ermöglichen. Hierzu wird eine Formalisierung zur Distanzberechnung für statische und dynamische Bäume eingeführt und durch eine explizite Betrachtung der Dynamik von Attributen einzelner Knoten der Bäume ergänzt. Die Echtzeitanalyse basierend auf der Distanzmessung wird durch ein dichte-basiertes Clustering ergänzt, um eine Anwendung des Clustering, einer Klassifikation, aber auch einer Anomalieerkennung zu demonstrieren. Die Ergebnisse dieser Arbeit basieren auf einer theoretischen Analyse der eingeführten Formalisierung von Distanzmessungen für dynamische Bäume. Diese Analysen werden unterlegt mit empirischen Messungen auf Basis von Monitoring-Daten von Batchjobs aus dem Batchsystem des GridKa Daten- und Rechenzentrums. Die Evaluation der vorgeschlagenen Formalisierung sowie der darauf aufbauenden Echtzeitanalysemethoden zeigen die Effizienz und Skalierbarkeit des Verfahrens. Zudem wird gezeigt, dass die Betrachtung von Attributen und Attribut-Statistiken von besonderer Bedeutung für die Qualität der Ergebnisse von Analysen dynamischer, semistrukturierter Daten ist. Außerdem zeigt die Evaluation, dass die Qualität der Ergebnisse durch eine unabhängige Kombination mehrerer Distanzen weiter verbessert werden kann. Insbesondere wird durch die Ergebnisse dieser Arbeit die Analyse sich über die Zeit verändernder Daten ermöglicht

Developing tools and models for evaluating geospatial data integration of official and VGI data sources

PhD ThesisIn recent years, systems have been developed which enable users to produce, share and update information on the web effectively and freely as User Generated Content (UGC) data (including Volunteered Geographic Information (VGI)). Data quality assessment is a major concern for supporting the accurate and efficient spatial data integration required if VGI is to be used alongside official, formal, usually governmental datasets. This thesis aims to develop tools and models for the purpose of assessing such integration possibilities. Initially, in order to undertake this task, geometrical similarity of formal and informal data was examined. Geometrical analyses were performed by developing specific programme interfaces to assess the positional, linear and polygon shape similarity among reference field survey data (FS); official datasets such as data from Ordnance Survey (OS), UK and General Directorate for Survey (GDS), Iraq agencies; and VGI information such as OpenStreetMap (OSM) datasets. A discussion of the design and implementation of these tools and interfaces is presented. A methodology has been developed to assess such positional and shape similarity by applying different metrics and standard indices such as the National Standard for Spatial Data Accuracy (NSSDA) for positional quality; techniques such as buffering overlays for linear similarity; and application of moments invariant for polygon shape similarity evaluations. The results suggested that difficulties exist for any geometrical integration of OSM data with both bench mark FS and formal datasets, but that formal data is very close to reference datasets. An investigation was carried out into contributing factors such as data sources, feature types and number of data collectors that may affect the geometrical quality of OSM data and consequently affect the integration process of OSM datasets with FS, OS and GDS. Factorial designs were undertaken in this study in order to develop and implement an experiment to discover the effect of these factors individually and the interaction between each of them. The analysis found that data source is the most significant factor that affects the geometrical quality of OSM datasets, and that there are interactions among all these factors at different levels of interaction. This work also investigated the possibility of integrating feature classification of official datasets such as data from OS and GDS geospatial data agencies, and informal datasets such as OSM information. In this context, two different models were developed. The first set of analysis included the evaluation of semantic integration of corresponding feature classifications of compared datasets. The second model was concerned with assessing the ability of XML schema matching of feature classifications of tested datasets. This initially involved a tokenization process in order to split up into single words classifications that were composed of multiple words. Subsequently, encoding feature classifications as XML schema trees was undertaken. The semantic similarity, data type similarity and structural similarity were measured between the nodes of compared schema trees. Once these three similarities had been computed, a weighted combination technique has been adopted in order to obtain the overall similarity. The findings of both sets of analysis were not encouraging as far as the possibility of effectively integrating feature classifications of VGI datasets, such as OSM information, and formal datasets, such as OS and GDS datasets, is concerned.Ministry of Higher Education and Scientific Research, Republic of Iraq