Use-cases on evolution

This report presents a set of use cases for evolution and reactivity for data in the Web and Semantic Web. This set is organized around three different case study scenarios, each of them is related to one of the three different areas of application within Rewerse. Namely, the scenarios are: “The Rewerse Information System and Portal”, closely related to the work of A3 – Personalised Information Systems; “Organizing Travels”, that may be related to the work of A1 – Events, Time, and Locations; “Updates and evolution in bioinformatics data sources” related to the work of A2 – Towards a Bioinformatics Web

A template-based approach for the specification of 3D topological constraints

Several different models have been defined in literature for the definition of 3D scenes that include a geometrical representation of objects together with a semantical classification of them. Such semantical characterization encapsulates important details about the object properties and behavior and often includes spatial relations that are defined only implicitly or through natural language, such as \u201can external access shall be in touch with the building only when it is classified as a direct access\u201d. The problem of ensuring the coherence between geometric and semantic information is well known in literature. Many attempts exist which try to extent the OCL to allow the representation of spatial integrity constraints in an UML model. However, this approach requires a deep knowledge of the OCL formalism and the implementation of ad-hoc procedures to validate the constraints specified at conceptual level. Therefore, a new approach is needed that helps designers to define complex OCL constraints and at the same time allows the automatic generation of the code to test them on a given dataset. The aim of this paper is to propose a set of predefined templates to express on the classes of an UML data model, a family of 3D spatial integrity constraints based on topological relations; all this without requiring the knowledge of any formal language by domain experts and supporting their automatic translation into validation procedures

Encoding, Storing and Searching of Analytical Properties and Assigned Metabolite Structures

Informationen über Metabolite und andere kleine organische Moleküle sind von entscheidender Bedeutung in vielen verschiedenen Bereichen der Naturwissenschaften. Sie spielen z.B. eine entscheidende Rolle in metabolischen Netzwerken und das Wissen über ihre Eigenschaften, hilft komplexe biologische Prozesse und komplette biologische Systeme zu verstehen. Da in biologischen und chemischen Laboren täglich Daten anfallen, welche diese Moleküle beschreiben, existiert eine umfassende Datengrundlage, die sich kontinuierlich erweitert. Um Wissenschaftlern die Verarbeitung, den Austausch, die Archivierung und die Suche innerhalb dieser Informationen unter Erhaltung der semantischen Zusammenhänge zu ermöglichen, sind komplexe Softwaresysteme und Datenformate nötig. Das Ziel dieses Projektes bestand darin, Anwendungen und Algorithmen zu entwickeln, welche für die effiziente Kodierung, Sammlung, Normalisierung und Analyse molekularer Daten genutzt werden können. Diese sollen Wissenschaftler bei der Strukturaufklärung, der Dereplikation, der Analyse von molekularen Wechselwirkungen und bei der Veröffentlichung des so gewonnenen Wissens unterstützen. Da die direkte Beschreibung der Struktur und der Funktionsweise einer unbekannten Verbindung sehr schwierig und aufwändig ist, wird dies hauptsächlich indirekt, mit Hilfe beschreibender Eigenschaften erreicht. Diese werden dann zur Vorhersage struktureller und funktioneller Charakteristika genutzt. In diesem Zusammenhang wurden Programmmodule entwickelt, welche sowohl die Visualisierung von Struktur- und Spektroskopiedaten, die gegliederte Darstellung und Veränderung von Metadaten und Eigenschaften, als auch den Import und Export von verschiedenen Datenformaten erlauben. Diese wurden durch Methoden erweitert, welche es ermöglichen, die gewonnenen Informationen weitergehend zu analysieren und Struktur- und Spektroskopiedaten einander zuzuweisen. Außerdem wurde ein System zur strukturierten Archivierung und Verwaltung großer Mengen molekularer Daten und spektroskopischer Informationen, unter Beibehaltung der semantischen Zusammenhänge, sowohl im Dateisystem, als auch in Datenbanken, entwickelt. Um die verlustfreie Speicherung zu gewährleisten, wurde ein offenes und standardisiertes Datenformat definiert (CMLSpect). Dieses erweitert das existierende CML (Chemical Markup Language) Vokabular und erlaubt damit die einfache Handhabung von verknüpften Struktur- und Spektroskopiedaten. Die entwickelten Anwendungen wurden in das Bioclipse System für Bio- und Chemoinformatik eingebunden und bieten dem Nutzer damit eine hochqualitative Benutzeroberfläche und dem Entwickler eine leicht zu erweiternde modulare Programmarchitektur

Visually querying object-oriented databases

Bibliography: pages 141-145.As database requirements increase, the ability to construct database queries efficiently becomes more important. The traditional means of querying a database is to write a textual query, such as writing in SQL to query a relational database. Visual query languages are an alternative means of querying a database; a visual query language can embody powerful query abstraction and user feedback techniques, thereby making them potentially easier to use. In this thesis, we develop a visual query system for ODMG-compliant object-oriented databases, called QUIVER. QUIVER has a comprehensive expressive power; apart from supporting data types such as sets, bags, arrays, lists, tuples, objects and relationships, it supports aggregate functions, methods and sub-queries. The language is also consistent, as constructs with similar functionality have similar visual representations. QUIVER uses the DOT layout engine to automatically layout a query; QUIVER queries are easily constructed, as the system does not constrain the spatial arrangement of query items. QUIVER also supports a query library, allowing queries to be saved, retrieved and shared among users. A substantial part of the design has been implemented using the ODMG-compliant database system O₂, and the usability of the interface as well as the query language itself is presented. Visual queries are translated to OQL, the standard query language proposed by the ODMG, and query answers are presented using O₂ Look. During the course of our investigation, we conducted a user evaluation to compare QUIVER and OQL. The results were extremely encouraging in favour of QUIVER

Content based retrieval of PET neurological images

Medical image management has posed challenges to many researchers, especially when the images have to be indexed and retrieved using their visual content that is meaningful to clinicians. In this study, an image retrieval system has been developed for 3D brain PET (Position emission tomography) images. It has been found that PET neurological images can be retrieved based upon their diagnostic status using only data pertaining to their content, and predominantly the visual content. During the study PET scans are spatially normalized, using existing techniques, and their visual data is quantified. The mid-sagittal-plane of each individual 3D PET scan is found and then utilized in the detection of abnormal asymmetries, such as tumours or physical injuries. All the asymmetries detected are referenced to the Talairarch and Tournoux anatomical atlas. The Cartesian co- ordinates in Talairarch space, of detected lesion, are employed along with the associated anatomical structure(s) as the indices within the content based image retrieval system. The anatomical atlas is then also utilized to isolate distinct anatomical areas that are related to a number of neurodegenerative disorders. After segmentation of the anatomical regions of interest algorithms are applied to characterize the texture of brain intensity using Gabor filters and to elucidate the mean index ratio of activation levels. These measurements are combined to produce a single feature vector that is incorporated into the content based image retrieval system. Experimental results on images with known diagnoses show that physical lesions such as head injuries and tumours can be, to a certain extent, detected correctly. Images with correctly detected and measured lesion are then retrieved from the database of images when a query pertains to the measured locale. Images with neurodegenerative disorder patterns have been indexed and retrieved via texture-based features. Retrieval accuracy is increased, for images from patients diagnosed with dementia, by combining the texture feature and mean index ratio value