SPARQL Query Mediation for Data Integration

The Semantic Web provides a set of promising technologies to make sophisticated data integration much easier, because data on the semantic Web is allowed to be connected by links and complex queries can be executed against the dataset of those linked data. Although the Semantic Web techniques offer RDF/OWL to support schematic mappings between diverse data sources, large-scale data integration is still severely hampered by various types of data-level semantic heterogeneity among the data sources. In the paper, we show that SPARQL queries that are intended to execute over multiple heterogeneous data sources can be mediated automatically

Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

Complex correspondences for query patterns rewriting

International audienceThis paper discusses the use of complex alignments in the task of automatic query patterns rewriting. We apply this approach in SWIP, a system that allows for querying RDF data from natural language-based queries, hiding the complexity of SPARQL. SWIP is based on the use of query patterns that characterise families of queries and that are instantiated with respect to the initial user query expressed in natural language. However, these patterns are specific to the vocabulary used to describe the data source to be queried. For rewriting query patterns, we experiment ontology matching approaches in order to find complex correspondences between two ontologies describing data sources. From the alignments and initial query patterns, we rewrite these patterns in order to be able to query the data described using the target ontology. These experiments have been carried out on an ontology on the music domain and DBpedia ontology

Rewriting SELECT SPARQL queries from 1:n complex correspondences

This paper presents a mechanism for rewriting SPARQL queries based on complex ontology correspondences. While the usefulness of simple correspondences, involving single entities from both source and target ontologies, has long been recognized, query rewriting requires more expressive links between ontology entities expressing the true relationships between them. Here, complex correspondences, in the format 1:n, between overlapping ontologies are exploited for rewriting SELECT SPARQL queries, so that they can be expressed over different RDF data sets in the Linked Open Data. Our approach has been evaluated using two data sets, one from the agriculture domain and another based on a reduced set involving the ontologies from the OAEI Conference track

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

<p>Abstract</p> <p>Background</p> <p>The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.</p> <p>Results</p> <p>As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.</p> <p>Conclusions</p> <p>Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.</p

Rule-Based Intelligence on the Semantic Web: Implications for Military Capabilities

Rules are a key element of the Semantic Web vision, promising to provide a foundation for reasoning capabilities that underpin the intelligent manipulation and exploitation of information content. Although ontologies provide the basis for some forms of reasoning, it is unlikely that ontologies, by themselves, will support the range of knowledge-based services that are likely to be required on the Semantic Web. As such, it is important to consider the contribution that rule-based systems can make to the realization of advanced machine intelligence on the Semantic Web. This report aims to review the current state-of-the-art with respect to semantic rule-based technologies. It provides an overview of the rules, rule languages and rule engines that are currently available to support ontology-based reasoning, and it discusses some of the limitations of these technologies in terms of their inability to cope with uncertain or imprecise data and their poor performance in some reasoning contexts. This report also describes the contribution of reasoning systems to military capabilities, and suggests that current technological shortcomings pose a significant barrier to the widespread adoption of reasoning systems within the defence community. Some solutions to these shortcomings are presented and a timescale for technology adoption within the military domain is proposed. It is suggested that application areas such as semantic integration, semantic interoperability, data fusion and situation awareness provide the best opportunities for technology adoption within the 2015 timeframe. Other capabilities, such as decision support and the emulation of human-style reasoning capabilities are seen to depend on the resolution of significant challenges that may hinder attempts at technology adoption and exploitation within the 2020 timeframe

Integration of Web APIs and Linked Data Using SPARQL Micro-Services - Application to Biodiversity Use Cases

International audienceIn recent years, Web APIs have become a de facto standard for exchanging machine-readable data on the Web. Despite this success, however, they often fail in making resource descriptions interoperable due to the fact that they rely on proprietary vocabularies that lack formal semantics.The Linked Data principles similarly seek the massive publication of data on the Web, yet with the specific goal of ensuring semantic interoperability.Given their complementary goals, it is commonly admitted that cross-fertilization could stem from the automatic combination of Linked Data and Web APIs. Towards this goal, in this paper we leverage the micro-service architectural principles to define a SPARQL Micro-Service architecture, aimed at querying Web APIs using SPARQL. A SPARQL micro-service is a lightweight SPARQL endpoint that provides access to a small, resource-centric, virtual graph. In this context, we argue that full SPARQL Query expressiveness can be supported efficiently without jeopardizing servers availability.Furthermore, we demonstrate how this architecture can be used to dynamically assign dereferenceable URIs to Web API resources that do not have URIs beforehand, thus literally “bringing” Web APIs into the Web of Data. We believe that the emergence of an ecosystem of SPARQL micro-services published by independent providers would enable Linked Data-based applications to easily glean pieces of data from a wealth of distributed, scalable, and reliable services. We describe a working prototype implementation and we finally illustrate the use of SPARQL micro-services in the context of two real-life use cases related to the biodiversity domain, developed in collaboration with the French National Museum of Natural History

Knowledge hypergraph based-approach for multi-source data integration and querying : Application for Earth Observation domain

Early warning against natural disasters to save lives and decrease damages has drawn increasing interest to develop systems that observe, monitor, and assess the changes in the environment. Over the last years, numerous environmental monitoring systems and Earth Observation (EO) programs were implemented. Nevertheless, these systems generate a large amount of EO data while using different vocabularies and different conceptual schemas. Accordingly, data resides in many siloed systems and are mainly untapped for integrated operations, insights, and decision making situations. To overcome the insufficient exploitation of EO data, a data integration system is crucial to break down data silos and create a common information space where data will be semantically linked. Within this context, we propose a semantic data integration and querying approach, which aims to semantically integrate EO data and provide an enhanced query processing in terms of accuracy, completeness, and semantic richness of response. . To do so, we defined three main objectives. The first objective is to capture the knowledge of the environmental monitoring domain. To do so, we propose MEMOn, a domain ontology that provides a common vocabulary of the environmental monitoring domain in order to support the semantic interoperability of heterogeneous EO data. While creating MEMOn, we adopted a development methodology, including three fundamental principles. First, we used a modularization approach. The idea is to create separate modules, one for each context of the environment domain in order to ensure the clarity of the global ontology’s structure and guarantee the reusability of each module separately. Second, we used the upper-level ontology Basic Formal Ontology and the mid-level ontologies, the Common Core ontologies, to facilitate the integration of the ontological modules in order to build the global one. Third, we reused existing domain ontologies such as ENVO and SSN, to avoid creating the ontology from scratch, and this can improve its quality since the reused components have already been evaluated. MEMOn is then evaluated using real use case studies, according to the Sahara and Sahel Observatory experts’ requirements. The second objective of this work is to break down the data silos and provide a common environmental information space. Accordingly, we propose a knowledge hypergraphbased data integration approach to provide experts and software agents with a virtual integrated and linked view of data. This approach generates RML mappings between the developed ontology and metadata and then creates a knowledge hypergraph that semantically links these mappings to identify more complex relationships across data sources. One of the strengths of the proposed approach is it goes beyond the process of combining data retrieved from multiple and independent sources and allows the virtual data integration in a highly semantic and expressive way, using hypergraphs. The third objective of this thesis concerns the enhancement of query processing in terms of accuracy, completeness, and semantic richness of response in order to adapt the returned results and make them more relevant and richer in terms of relationships. Accordingly, we propose a knowledge-hypergraph based query processing that improves the selection of sources contributing to the final result of an input query. Indeed, the proposed approach moves beyond the discovery of simple one-to-one equivalence matches and relies on the identification of more complex relationships across data sources by referring to the knowledge hypergraph. This enhancement significantly showcases the increasing of answer completeness and semantic richness. The proposed approach was implemented in an open-source tool and has proved its effectiveness through a real use case in the environmental monitoring domain

Automatic generation of semantic Mashups in web portals

The Web has become an important source for information, which are created by independent providers. Web portals provide an unified point of access to content, data, services and web applications located throughout the enterprise. However, Web users have often only an insufficient available amount of time, to effectively use the available information resources. This thesis proposes a mashup framework that automatically mashes-up web portal content with related background information. The background information are derived from information web services that are composed by an evolutionary algorithm