Ontology Based Semantic Web Information Retrieval Enhancing Search Significance

The web contain huge amount of structured as well as unstructured data/information. This varying nature of data may yield a retrieval response that is expected to contain relevant response that is expected to contain relevant as well as irrelevant data while directing search. In order to filter out irrelevance in the search result, numerous methodologies have been used to extract more and more relevant search responses in retrieval. This work has adopted semantic search dealing directly with the knowledge base. The approach incorporates Query pattern evolution and semantic keyword matching with final detail to enhance significance of relevant data retrieval. The proposed method is implemented in open source computing tool environment and the result obtained thereof are compared with that of earlier used methodologies

Semantic Interaction in Web-based Retrieval Systems : Adopting Semantic Web Technologies and Social Networking Paradigms for Interacting with Semi-structured Web Data

Existing web retrieval models for exploration and interaction with web data do not take into account semantic information, nor do they allow for new forms of interaction by employing meaningful interaction and navigation metaphors in 2D/3D. This thesis researches means for introducing a semantic dimension into the search and exploration process of web content to enable a significantly positive user experience. Therefore, an inherently dynamic view beyond single concepts and models from semantic information processing, information extraction and human-machine interaction is adopted. Essential tasks for semantic interaction such as semantic annotation, semantic mediation and semantic human-computer interaction were identified and elaborated for two general application scenarios in web retrieval: Web-based Question Answering in a knowledge-based dialogue system and semantic exploration of information spaces in 2D/3D

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics.

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included

An informatics supported web-based data annotation and query tool to expedite translational research for head and neck malignancies

<p>Abstract</p> <p>Background</p> <p>The Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets.</p> <p>Results</p> <p>The various components of this annotation tool include the Development of Common Data Elements (CDEs) that are derived from College of American Pathologists (CAP) Checklist and North American Association of Central Cancer Registries (NAACR) standards. The Data Entry Tool is a portable and flexible Oracle-based data entry device, which is an easily mastered web-based tool. The Data Query Tool helps investigators and researchers to search de-identified information within the warehouse/resource through a "point and click" interface, thus enabling only the selected data elements to be essentially copied into a data mart using a multi dimensional model from the warehouse's relational structure.</p> <p>The SPORE Head and Neck Neoplasm Database contains multimodal datasets that are accessible to investigators via an easy to use query tool. The database currently holds 6553 cases and 10607 tumor accessions. Among these, there are 965 metastatic, 4227 primary, 1369 recurrent, and 483 new primary cases. The data disclosure is strictly regulated by user's authorization.</p> <p>Conclusion</p> <p>The SPORE Head and Neck Neoplasm Virtual Biorepository is a robust translational biomedical informatics tool that can facilitate basic science, clinical, and translational research. The Data Query Tool acts as a central source providing a mechanism for researchers to efficiently find clinically annotated datasets and biospecimens that are relevant to their research areas. The tool protects patient privacy by revealing only de-identified data in accordance with regulations and approvals of the IRB and scientific review committee.</p

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

Social and Semantic Contexts in Tourist Mobile Applications

The ongoing growth of the World Wide Web along with the increase possibility of access information through a variety of devices in mobility, has defi nitely changed the way users acquire, create, and personalize information, pushing innovative strategies for annotating and organizing it. In this scenario, Social Annotation Systems have quickly gained a huge popularity, introducing millions of metadata on di fferent Web resources following a bottom-up approach, generating free and democratic mechanisms of classi cation, namely folksonomies. Moving away from hierarchical classi cation schemas, folksonomies represent also a meaningful mean for identifying similarities among users, resources and tags. At any rate, they suff er from several limitations, such as the lack of specialized tools devoted to manage, modify, customize and visualize them as well as the lack of an explicit semantic, making di fficult for users to bene fit from them eff ectively. Despite appealing promises of Semantic Web technologies, which were intended to explicitly formalize the knowledge within a particular domain in a top-down manner, in order to perform intelligent integration and reasoning on it, they are still far from reach their objectives, due to di fficulties in knowledge acquisition and annotation bottleneck. The main contribution of this dissertation consists in modeling a novel conceptual framework that exploits both social and semantic contextual dimensions, focusing on the domain of tourism and cultural heritage. The primary aim of our assessment is to evaluate the overall user satisfaction and the perceived quality in use thanks to two concrete case studies. Firstly, we concentrate our attention on contextual information and navigation, and on authoring tool; secondly, we provide a semantic mapping of tags of the system folksonomy, contrasted and compared to the expert users' classi cation, allowing a bridge between social and semantic knowledge according to its constantly mutual growth. The performed user evaluations analyses results are promising, reporting a high level of agreement on the perceived quality in use of both the applications and of the speci c analyzed features, demonstrating that a social-semantic contextual model improves the general users' satisfactio