Ozone: An Insulating Layer Between Ontologies, Databases and Object Oriented Applications

Recent research shows that ontologies are a prominent tool for the semantic integration of heterogeneous data sources. However, in existing ontology-based systems the ontologies are tightly coupled with the rest of the system components. As a result, large parts of the system have to be developed in a logic programming language, typically used in describing ontologies, and adhere to the ontological knowledge model and representation. This eventually impedes the use of ontologies in industrial integrated systems. In this paper, we present an architecture that isolates the ontologybased components, waives the representation and programming language constraints and simplifies the knowledge model that components outside the ontology have to be aware of. The architecture makes it possible to access the ontological information and the federated data using exclusively object-oriented structures and interfaces. We show that it allows new databases to easily join the federation by implementing a standard database interface. The architecture has been implemented and evaluated in the field of information retrieval for e-commerce. We review the principal results and limitations of this case study

A messaging system to handle semantic dissonance

Enterprises have been compelled to share their data internally and externally, but creating a consistent view of enterprise data has been challenging. Within a typical enterprise, each division uses its own domain specific data model and schema, and different enterprises obviously use their own data models and schema. Integrating these diverse data models and schemas, which have both syntactic and semantic differences, tends to be complex, slow, and inaccurate. Syntactic differences, i.e., differences in names or layout, have received substantial attention in research. Semantic dissonance simply means that the structure may be similar (or even the same) but the meaning associated with the attributes that define each structure are different, has received less attention in the world of practical software development. A practical messaging system for handling semantic dissonance has been developed. The system utilizes the Resource Description Framework (RDF) and SOAP XML Messaging Specification. It is implemented using Jena, a Java API for RDF, and the Apache SOAP, an Open Source SOAP server and client. This report describes the messaging system, its implementation, its strengths and limitations in handling semantic dissonance

Design and Implementation of Information Retrieval using Ontology

An approach is proposed that can be used to make these arch adaptive according to each user2019;s need using ontology .Our approach is distinct because it allows each user to perform more fine-grained search by capturing changes of each user2019;s preferences without any user effort. Such a method is not performed in typical search engines

The Semantic and Syntactic Model of Metadata

As more information becomes “born digital”, metadata creation is increasingly becoming part of the information creation process. Current metadata schemes inherit much of the library cataloging tradition, which has shown limitations on representing “born digital” type of resources. Through analysis of issues of metadata schemes and review of metadata research and projects, the authors propose an ontology-based approach to building a modular metadata model in which semantics and syntax may be integrated to suit the needs for representing “born digital” resources. The authors use an learning object ontology as an example to demonstrate how the semantics and syntax may be built into a modular model for metadata

Semantic Integration in MADS Conceptual Model

Our vision of a viable way for transparent and meaningful processing of heterogeneous spatio-temporal data is to put data semantics in the foundation of an integration process. We present and correlate means of integration as components of the mediation level of an interoperable system. For our domain of interest we present MADS domain ontologies and MADS conceptual data model dedicated to modeling of spatio-temporal data. Using as example two MADSschemas we outline an integration methodology based on semantic interschema correspondence assertions and integration goals

LinkEHR-Ed: A multi-reference model archetype editor based on formal semantics

Purpose To develop a powerful archetype editing framework capable of handling multiple reference models and oriented towards the semantic description and standardization of legacy data. Methods The main prerequisite for implementing tools providing enhanced support for archetypes is the clear specification of archetype semantics. We propose a formalization of the definition section of archetypes based on types over tree-structured data. It covers the specialization of archetypes, the relationship between reference models and archetypes and conformance of data instances to archetypes. Results LinkEHR-Ed, a visual archetype editor based on the former formalization with advanced processing capabilities that supports multiple reference models, the editing and semantic validation of archetypes, the specification of mappings to data sources, and the automatic generation of data transformation scripts, is developed. Conclusions LinkEHR-Ed is a useful tool for building, processing and validating archetypes based on any reference model.This work was supported in part by the Spanish Ministry of Education and Science under grant TS12007-66S7S-C02; by the Generalitat Valenciana under grant APOSTD/2007/055 and by the program PAID-06-07 de la Universidad Politecnica de Valencia.Maldonado Segura, JA.; Moner Cano, D.; Boscá Tomás, D.; Fernandez Breis, JT.; Angulo Fernández, C.; Robles Viejo, M. (2009). LinkEHR-Ed: A multi-reference model archetype editor based on formal semantics. International Journal of Medical Informatics. 78(8):559-570. https://doi.org/10.1016/j.ijmedinf.2009.03.006S55957078

SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases

Köhler J. SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases. Bielefeld (Germany): Bielefeld University; 2003.The work presented in this thesis is outlined in the following. The state of the art in the relevant disciplines is introduced and reviewed in chapter 2. This includes on the one hand the current state of molecular biological databases, their heterogeneity and the integration of molecular biological databases. On the other hand the current usage of ontologies in general and with special regard to database integration is described. The principles of semantic database integration as introduced in this thesis are new and suitable to be used also in other database integration systems, which have to deal with a high number of semantically heterogeneous databases. Therefore in Chapter 3 the newly introduced principles for ontology based semantic database integration are presented independent of their implementation. Chapter 4 introduces the requirements for the implementation of a semantic database integration system (SEMEDA). Several general requirements for the integration of molecular biological systems from the scientific literature are discussed with regard to the feasibility of their implementation in general and in SEMEDA. In addition, the requirements specific to semantic database integration are introduced. In addition how the BioDataServer is used to overcome "technical" heterogeneity, so that SEMEDA only has to deal with semantic heterogeneity is analysed. In chapter 5, an appropriate data structure for storing ontologies, database metadata and the semantic definitions as described in Chapter 3 is developed. Subsequently, it is discussed how this data structure can be edited and queried. In Chapter 6, SEMEDAs software design, implementation and system architecture is given. Chapter 7 describes the use of SEMEDA and its interfaces. The user interface SEMEDA-edit is used to collaboratively edit ontologies and to semantically define databases using ontologies. SEMEDA-query is the query interface that provides uniform access to heterogeneous databases. In addition, a set of procedures exists which can be used by external applications. In order to use SEMEDA to semantically define databases, an appropriate ontology is needed. Although SEMEDA allows building ontologies from the scratch, due to the fact that generating ontologies is a labour intensive time-consuming task, it would be preferable to use an existing ontology. Therefore, in chapter 8 several ontologies were evaluated for their usability in SEMEDA. The intention was to find out if a suitable ontology can be found and imported or whether it is more appropriate to build a custom ontology for SEMEDA. It turned out that the existing ontologies were not well suited for semantic database integration. In chapter 9 general and SEMEDA specific ontology design principles are introduced which were then followed to build a custom ontology for database integration. The structure of this custom ontology and some issues concerning its use for semantic database integration are explained. In chapter 10, the practical use of SEMEDA is described by two examples. The first section of this chapter shows how SEMEDA supports the building of user schemata for the BioDataServer. The second section describes how the clone database of the RZPD Berlin (Deutsches Ressourcenzentrum für Genomforschung GmbH) is connected to SEMEDA and thus linked to the other databases. In the discussion (chapter 11) SEMEDA is compared to existing database integration systems, especially other ontology based integration systems. It is further discussed how principles for semantic database integration apply to other database integration systems and how they might be implemented there. A database mirror is proposed to improve the overall performance of SEMEDA and the BioDataServer

Semantic validation in spatio-temporal schema integration

This thesis proposes to address the well-know database integration problem with a new method that combines functionality from database conceptual modeling techniques with functionality from logic-based reasoners. We elaborate on a hybrid - modeling+validation - integration approach for spatio-temporal information integration on the schema level. The modeling part of our methodology is supported by the spatio-temporal conceptual model MADS, whereas the validation part of the integration process is delegated to the description logics validation services. We therefore adhere to the principle that, rather than extending either formalism to try to cover all desirable functionality, a hybrid system, where the database component and the logic component would cooperate, each one performing the tasks for which it is best suited, is a viable solution for semantically rich information management. First, we develop a MADS-based flexible integration approach where the integrated schema designer has several viable ways to construct a final integrated schema. For different related schema elements we provide the designer with four general policies and with a set of structural solutions or structural patterns within each policy. To always guarantee an integrated solution, we provide for a preservation policy with multi-representation structural pattern. To state the inter-schema mappings, we elaborate on a correspondence language with explicit spatial and temporal operators. Thus, our correspondence language has three facets: structural, spatial, and temporal, allowing to relate the thematic representation as well as the spatial and temporal features. With the inter-schema mappings, the designer can state correspondences between related populations, and define the conditions that rule the matching at the instance level. These matching rules can then be used in query rewriting procedures or to match the instances within the data integration process. We associate a set of putative structural patterns to each type of population correspondence, providing a designer with a patterns' selection for flexible integrated schema construction. Second, we enhance our integration method by employing validation services of the description logic formalism. It is not guaranteed that the designer can state all the inter-schema mappings manually, and that they are all correct. We add the validation phase to ensure validity and completeness of the inter-schema mappings set. Inter-schema mappings cannot be validated autonomously, i.e., they are validated against the data model and the schemas they link. Thus, to implement our validation approach, we translate the data model, the source schemas and the inter-schema mappings into a description logic formalism, preserving the spatial and temporal semantics of the MADS data model. Thus, our modeling approach in description logic insures that the model designer will correctly define spatial and temporal schema elements and inter-schema mappings. The added value of the complete translation (i.e., including the data model and the source schemas) is that we validate not only the inter-schema mappings, but also the compliance of the source schemas to the data model, and infer implicit relationships within them. As the result of the validation procedure, the schema designer obtains the complete and valid set of inter-schema mappings and a set of valid (flexible) schematic patterns to apply to construct an integrated schema that meets application requirements. To further our work, we model a framework in which a schema designer is able to follow our integration method and realize the schema integration task in an assisted way. We design two models, UML and SEAM models, of a system that provides for integration functionalities. The models describe a framework where several tools are employed together, each involved in the service it is best suited for. We define the functionalities and the cooperation between the composing elements of the framework and detail the logics of the integration process in an UML activity diagram and in a SEAM operation model