Query Migration from Object Oriented World to Semantic World

— In the last decades, object-oriented approach was able to take a large share of databases market aiming to design and implement structured and reusable software through the composition of independent elements in order to have programs with a high performance. On the other hand, the mass of information stored in the web is increasing day after day with a vertiginous speed, exposing the currently web faced with the problem of creating a bridge so as to facilitate access to data between different applications and systems as well as to look for relevant and exact information wished by users. In addition, all existing approach of rewriting object oriented languages to SPARQL language rely on models transformation process to guarantee this mapping. All the previous raisons has prompted us to write this paper in order to bridge an important gap between these two heterogeneous worlds (object oriented and semantic web world) by proposing the first provably semantics preserving OQLto-SPARQL translation algorithm for each element of OQL Query (SELECT clause, FROM clause, FILTER constraint, implicit/ explicit join and union/intersection SELECT queries)

Structuring research methods and data with the research object model:genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e. g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. Availability: The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/r

MneMojno - Design and deployment of a Semantic web service and a mobile application

In this paper we discuss our experience with the design, development and deployment of MneMojno Semantic Web Service and Mobile Application. MneMojno makes use of Semantic Web Technologies to create a Web service and a mobile application for rating and providing detail information about food products. This paper introduces the main components of the system: a framework to capture information about food products from various sources, a semantic web service and a framework to visualize and analyze usage statistics. Finally, we discuss challenges and problems we faced during the development and present our conclusions and future directions for exploration in terms of developing MneMojno further

Debugging scripts in SPipes editor

Jazyk SPipes je technologie umožňující zpracování strukturovaných dat Sémantického webu. Tato diplomová práce se zabývá zlepšením stavu stávajícího editoru SPipes skriptů. V práci jsou nejprve představeny principy Sémantického webu a relevantní technologie. Na základě zevrubné analýzy již existujícího editoru a provedené rešerše byla navržena úprava architektury aplikace a definovány funkční a nefunkčí požadavky na editor. Hlavní přínosy práce jsou převedení backendové části z jazyka Scala do Javy za účelem odstranění problémů vyplývajících z nekompatibility mezi jazykem Scala a Spring frameworkem, který je použit. Dále pak vytvoření testů, které zjednodušují odhalení potenciálních chyb v aplikaci, rozdělení původně monolytické aplikace na několik oddělených služeb využívajících Docker a docker-compose, čímž se výrazně sníží práce spojená se správnou konfigurací a spouštěním aplikace. V neposlední řadě přináší tato práce nové a netriviální funkce editoru - možnost validovat a ladit editované skripty a moduly.The SPipes language is a technology that enables the processing of structured data in the form of the Semantic Web. This thesis attempts to improve the existing SPipes script editor. The thesis first introduces the principles of the Semantic Web and related technologies. Based on a thorough analysis of the existing editor and conducted survey, the application architecture was redesigned and functional and non-functional requirements for the editor were defined. Main contributions of this work are re-implementation of the backend part from Scala to Java, which eliminates the compatibility issues arising from the incompatibility between Scala and the Spring framework that is used. Special attention was paid to writing tests for most parts of the application, which simplifies the detection of potential bugs in the application. Major change in architecture was to split the originally monolithic application into several separate services with the use of Docker and docker-compose, leading to simpler configuration and easier deployment of the application. Last but not least, this thesis introduces new non-trivial features of the editor - the capability of validating and debugging of SPipes scripts and modules

prototypical implementations ; working packages in project phase II

In this technical report, we present the concepts and first prototypical imple- mentations of innovative tools and methods for personalized and contextualized (multimedia) search, collaborative ontology evolution, ontology evaluation and cost models, and dynamic access and trends in distributed (semantic) knowledge. The concepts and prototypes are based on the state of art analysis and identified requirements in the CSW report IV

Knowledge formalization in experience feedback processes : an ontology-based approach

Because of the current trend of integration and interoperability of industrial systems, their size and complexity continue to grow making it more difficult to analyze, to understand and to solve the problems that happen in their organizations. Continuous improvement methodologies are powerful tools in order to understand and to solve problems, to control the effects of changes and finally to capitalize knowledge about changes and improvements. These tools involve suitably represent knowledge relating to the concerned system. Consequently, knowledge management (KM) is an increasingly important source of competitive advantage for organizations. Particularly, the capitalization and sharing of knowledge resulting from experience feedback are elements which play an essential role in the continuous improvement of industrial activities. In this paper, the contribution deals with semantic interoperability and relates to the structuring and the formalization of an experience feedback (EF) process aiming at transforming information or understanding gained by experience into explicit knowledge. The reuse of such knowledge has proved to have significant impact on achieving themissions of companies. However, the means of describing the knowledge objects of an experience generally remain informal. Based on an experience feedback process model and conceptual graphs, this paper takes domain ontology as a framework for the clarification of explicit knowledge and know-how, the aim of which is to get lessons learned descriptions that are significant, correct and applicable