392 research outputs found
Survey over Existing Query and Transformation Languages
A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability
of many current Semantic Web approaches to cope with data available in such diverging
representation formalisms as XML, RDF, or Topic Maps. A common query language is the first
step to allow transparent access to data in any of these formats. To further the understanding
of the requirements and approaches proposed for query languages in the conventional as well
as the Semantic Web, this report surveys a large number of query languages for accessing
XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from
all these areas. From the detailed survey of these query languages, a common classification
scheme is derived that is useful for understanding and differentiating languages within and
among all three areas
A semantic web framework to integrate cancer omics data with biological knowledge
BACKGROUND: The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. RESULTS: For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. CONCLUSIONS: We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily
Creating ontological metadata for digital library content and services
We create ontological content metadata by generating it from MARC (MAchine Readable Cataloging) data. MARC contains much information that is hard to exploit computationally. In particular, relationships between works are implicit in shared values and natural language notes. The conversion process involves specifying an ontological model, mapping MARC to the ontology, and reasoning about the data to create explicit links between works.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42334/1/799-2-1-20_80020020.pd
KA-SB: from data integration to large scale reasoning
<p>Abstract</p> <p>Background</p> <p>The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data.</p> <p>Methods</p> <p>KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning).</p> <p>Results</p> <p>In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts.</p> <p>Conclusion</p> <p>These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool <url>http://khaos.uma.es/KA-SB</url>, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.</p
Management of Knowledge Representation Standards Activities
This report describes the efforts undertaken over the last two years to identify the issues underlying the current difficulties in sharing and reuse, and a community wide initiative to overcome them. First, we discuss four bottlenecks to sharing and reuse, present a vision of a future in which these bottlenecks have been ameliorated, and describe the efforts of the initiative's four working groups to address these bottlenecks. We then address the supporting technology and infrastructure that is critical to enabling the vision of the future. Finally, we consider topics of longer-range interest by reviewing some of the research issues raised by our vision
Examining the Application of Modular and Contextualised Ontology in Query Expansions for Information Retrieval
This research considers the ongoing challenge of semantics-based search from the perspective of how to exploit Semantic Web languages for search in the current Web environment.
The purpose of the PhD was to use ontology-based query expansion (OQE) to improve search effectiveness by increasing search precision, i.e. retrieving relevant documents in the topmost ranked positions in a returned document list. Query experiments have required a novel search tool that can combine Semantic Web technologies in an otherwise traditional IR process using a Web document collection
Semantic Management of Location-Based Services in Wireless Environments
En los últimos años el interés por la computación móvil ha crecido debido al incesante uso de dispositivos móviles (por ejemplo, smartphones y tablets) y su ubicuidad. El bajo coste de dichos dispositivos unido al gran número de sensores y mecanismos de comunicación que equipan, hace posible el desarrollo de sistemas de información útiles para sus usuarios. Utilizando un cierto tipo especial de sensores, los mecanismos de posicionamiento, es posible desarrollar Servicios Basados en la Localización (Location-Based Services o LBS en inglés) que ofrecen un valor añadido al considerar la localización de los usuarios de dispositivos móviles para ofrecerles información personalizada. Por ejemplo, se han presentado numerosos LBS entre los que se encuentran servicios para encontrar taxis, detectar amigos en las cercanías, ayudar a la extinción de incendios, obtener fotos e información de los alrededores, etc. Sin embargo, los LBS actuales están diseñados para escenarios y objetivos específicos y, por lo tanto, están basados en esquemas predefinidos para el modelado de los elementos involucrados en estos escenarios. Además, el conocimiento del contexto que manejan es implícito; razón por la cual solamente funcionan para un objetivo específico. Por ejemplo, en la actualidad un usuario que llega a una ciudad tiene que conocer (y comprender) qué LBS podrían darle información acerca de medios de transporte específicos en dicha ciudad y estos servicios no son generalmente reutilizables en otras ciudades. Se han propuesto en la literatura algunas soluciones ad hoc para ofrecer LBS a usuarios pero no existe una solución general y flexible que pueda ser aplicada a muchos escenarios diferentes. Desarrollar tal sistema general simplemente uniendo LBS existentes no es sencillo ya que es un desafío diseñar un framework común que permita manejar conocimiento obtenido de datos enviados por objetos heterogéneos (incluyendo datos textuales, multimedia, sensoriales, etc.) y considerar situaciones en las que el sistema tiene que adaptarse a contextos donde el conocimiento cambia dinámicamente y en los que los dispositivos pueden usar diferentes tecnologías de comunicación (red fija, inalámbrica, etc.). Nuestra propuesta en la presente tesis es el sistema SHERLOCK (System for Heterogeneous mobilE Requests by Leveraging Ontological and Contextual Knowledge) que presenta una arquitectura general y flexible para ofrecer a los usuarios LBS que puedan serles interesantes. SHERLOCK se basa en tecnologías semánticas y de agentes: 1) utiliza ontologías para modelar la información de usuarios, dispositivos, servicios, y el entorno, y un razonador para manejar estas ontologías e inferir conocimiento que no ha sido explicitado; 2) utiliza una arquitectura basada en agentes (tanto estáticos como móviles) que permite a los distintos dispositivos SHERLOCK intercambiar conocimiento y así mantener sus ontologías locales actualizadas, y procesar peticiones de información de sus usuarios encontrando lo que necesitan, allá donde esté. El uso de estas dos tecnologías permite a SHERLOCK ser flexible en términos de los servicios que ofrece al usuario (que son aprendidos mediante la interacción entre los dispositivos), y de los mecanismos para encontrar la información que el usuario quiere (que se adaptan a la infraestructura de comunicación subyacente)
A semantic and agent-based approach to support information retrieval, interoperability and multi-lateral viewpoints for heterogeneous environmental databases
PhDData stored in individual autonomous databases often needs to be combined and
interrelated. For example, in the Inland Water (IW) environment monitoring domain,
the spatial and temporal variation of measurements of different water quality indicators
stored in different databases are of interest. Data from multiple data sources is more
complex to combine when there is a lack of metadata in a computation forin and when
the syntax and semantics of the stored data models are heterogeneous. The main types
of information retrieval (IR) requirements are query transparency and data
harmonisation for data interoperability and support for multiple user views. A
combined Semantic Web based and Agent based distributed system framework has
been developed to support the above IR requirements. It has been implemented using
the Jena ontology and JADE agent toolkits. The semantic part supports the
interoperability of autonomous data sources by merging their intensional data, using a
Global-As-View or GAV approach, into a global semantic model, represented in
DAML+OIL and in OWL. This is used to mediate between different local database
views. The agent part provides the semantic services to import, align and parse
semantic metadata instances, to support data mediation and to reason about data
mappings during alignment. The framework has applied to support information
retrieval, interoperability and multi-lateral viewpoints for four European environmental
agency databases.
An extended GAV approach has been developed and applied to handle queries that can
be reformulated over multiple user views of the stored data. This allows users to
retrieve data in a conceptualisation that is better suited to them rather than to have to
understand the entire detailed global view conceptualisation. User viewpoints are
derived from the global ontology or existing viewpoints of it. This has the advantage
that it reduces the number of potential conceptualisations and their associated
mappings to be more computationally manageable. Whereas an ad hoc framework
based upon conventional distributed programming language and a rule framework
could be used to support user views and adaptation to user views, a more formal
framework has the benefit in that it can support reasoning about the consistency,
equivalence, containment and conflict resolution when traversing data models. A
preliminary formulation of the formal model has been undertaken and is based upon
extending a Datalog type algebra with hierarchical, attribute and instance value
operators. These operators can be applied to support compositional mapping and
consistency checking of data views. The multiple viewpoint system was implemented
as a Java-based application consisting of two sub-systems, one for viewpoint
adaptation and management, the other for query processing and query result
adjustment
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