XML for Domain Viewpoints

Within research institutions like CERN (European Organization for Nuclear Research) there are often disparate databases (different in format, type and structure) that users need to access in a domain-specific manner. Users may want to access a simple unit of information without having to understand detail of the underlying schema or they may want to access the same information from several different sources. It is neither desirable nor feasible to require users to have knowledge of these schemas. Instead it would be advantageous if a user could query these sources using his or her own domain models and abstractions of the data. This paper describes the basis of an XML (eXtended Markup Language) framework that provides this functionality and is currently being developed at CERN. The goal of the first prototype was to explore the possibilities of XML for data integration and model management. It shows how XML can be used to integrate data sources. The framework is not only applicable to CERN data sources but other environments too.Comment: 9 pages, 6 figures, conference report from SCI'2001 Multiconference on Systemics & Informatics, Florid

Active Ontology: An Information Integration Approach for Dynamic Information Sources

In this paper we describe an ontology-based information integration approach that is suitable for highly dynamic distributed information sources, such as those available in Grid systems. The main challenges addressed are: 1) information changes frequently and information requests have to be answered quickly in order to provide up-to-date information; and 2) the most suitable information sources have to be selected from a set of different distributed ones that can provide the information needed. To deal with the first challenge we use an information cache that works with an update-on-demand policy. To deal with the second we add an information source selection step to the usual architecture used for ontology-based information integration. To illustrate our approach, we have developed an information service that aggregates metadata available in hundreds of information services of the EGEE Grid infrastructure

Toward Self-Organising Service Communities

This paper discusses a framework in which catalog service communities are built, linked for interaction, and constantly monitored and adapted over time. A catalog service community (represented as a peer node in a peer-to-peer network) in our system can be viewed as domain specific data integration mediators representing the domain knowledge and the registry information. The query routing among communities is performed to identify a set of data sources that are relevant to answering a given query. The system monitors the interactions between the communities to discover patterns that may lead to restructuring of the network (e.g., irrelevant peers removed, new relationships created, etc.)

Lion: Listen online. Using GraphQL as a mediator for data integration and ingestion

Data integration is the task of providing a unified view of multiple data sources. Thesesources can be, and are typically, heterogeneous in their data model, data query language (DQL), and data manipulation language (DML). In this thesis is described a system called”Listen Online”, or Lion for short. Lion utilizes the GraphQL specification to provide integration for querying of web services. Lion provides a general structure by which arbitrary mediators can be used within a query. Lastly, by building on top of open source libraries,Lion provides the open source community with components that enable it to function in the form of GraphQL servers, visual layout libraries, and query builders

Multimodal integration of disparate information sources with attribution

Cover title.Includes bibliographical references (p. [9]-[10]).Thomas Y. Lee & Stephane Bressan

Querying Web-Sources within a Data Federation

The Web is undoubtedly the largest and most diverse repository of data, but it was not designed to offer the capabilities of traditional data base management systems – which is unfortunate. In a true data federation, all types of data sources, such as relational databases and semi-structured Web sites, could be used together. IBM WebSphere uses the “request-reply-compensate” protocol to communicate with wrappers in a data federation. This protocol expects wrappers to reply to query requests by indicating the portion of the queries they can answer. While this provides a very generic approach to data federation, it also requires the wrapper developer to deal with some of the complexities of capability considerations through custom coding. Alternative approaches based on declarative capability restrictions have been proposed in the literature, but they have not found their way into commercial systems, perhaps due to their complexity. We offer a practical middle-ground solution to querying Web-sources, using IBM’s data federation system as an example. In lieu of a two-layered architecture consisting of wrapper and source layers, we propose to move the capability declaration from the wrapper layer to a single component between the wrapper and the native data source. The advantage of this three-layered architecture is that each new Web-source only needs to register its capability with the capability-declaration component once, which saves the work of writing a new wrapper each time. Thus the inclusion of Web-sources through this mechanism can be accelerated in a way that doesn\u27t require a change in existing data federation technology

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

AMMO-Prot: amine system project 3D-model finder

BACKGROUND: Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accumulated, which need to be integrated in order to be effective in the advance of biological knowledge in the field. For this purpose, a multidisciplinary group has started an ontology-based system named the Amine System Project (ASP) for which amine-related information is the validation bench. RESULTS: In this paper, we describe the Ontology-Based Mediator developed in the Amine System Project (http://asp.uma.es) using the infrastructure of Semantic Directories, and how this system has been used to solve a case related to amine metabolism-related protein structures. CONCLUSIONS: This infrastructure is used to publish and manage not only ontologies and their relationships, but also metadata relating to the resources committed with the ontologies. The system developed is available at http://asp.uma.es/WebMediator

Electronic Medical Records

Electronic Medical Record (EMR) relational database is considered to be a major component of any medical care information system. A major problem for researchers in medical informatics is finding the best way to use these databases to extract valued useful information to and about the patient’s diseases and treatments. Integrating different EMR databases is a great achievement that will improve health care systems. This paper presents an AI approach to extract generic EMR from different resources and transfer them to clinical cases. The utilized approach is based on retrieving different relationships between patients’ different data tables (files) and automatically generating EMRs in XML format, then building frame based medical cases to form a case repository that can be used in medical diagnostic systems