SD-Core: Generic Semantic Middleware Components for the Semantic Web

Navas‐Delgado, Ismael; Aldana‐Montes, José F.

doi:10.1007/978-3-540-85565-1_76

Cited by 4 publications

(3 citation statements)

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“…KOMF is a generic infrastructure to register and manage ontologies, their relationships and also information relating to the resources. This infrastructure is based on a resource directory, called Semantic Directory [ 40 ], with information about web resource semantics. KOMF has been successfully instantiated in the context of molecular biology for integrating biological data sources [ 41 - 43 ].…”

Section: Methodsmentioning

confidence: 99%

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

et al. 2012

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BackgroundSaccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data.ResultsTo provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface.ConclusionsYeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/.

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Section: Methodsmentioning

confidence: 99%

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

et al. 2012

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“…KOMF is a generic infrastructure to register and manage ontologies, their relationships and also information relating to the resources. This infrastructure is based on a resource directory, called Semantic Directory [14], with information about web resource semantics. KOMF has been successfully instantiated in the context of molecular biology for integrating biological data sources which are accessible via internet pages.…”

Section: Sb-kommentioning

confidence: 99%

YeastMed: An XML-Based System for Biological Data Integration of Yeast

et al. 2010

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A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of biological data. SGD, Yeastract, CYGD-MIPS, BioGrid and PhosphoGrid are five of the most visited databases by the yeast community. These sources provide complementary data on biological entities. Biologists are brought systematically to query these data sources in order to analyse the results of their experiments. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned result is a complex and laborious task. To provide transparent and simultaneous access to these sources, we have developed a mediator-based system called YeastMed. In this paper, we present YeastMed focusing on its architecture. merge the results obtained from different sources. This places a burden on biologists, most of whom are not bioinformatics experts, and limits the use that can be made of the available information.The challenges of modern bioinformatics research is not only storing data in repositories, but also processing and integrating them. Multiple solutions to biological data integration have been developed. Researchers have come up with some approaches that integrate diverse biological data sources. There are mainly two integration approaches being used in addressing the issue of the interoperability between biological databases: data warehousing approach [1] and mediator-based approach [3].The data warehousing approach is adopted by numerous integration systems like GUS [2] and DiscoveryLink [4]. This approach uses a data warehouse repository that provides a single access point to a collection of data, obtained from a set of distributed, heterogeneous sources. Data from the remote heterogeneous databases are copied on a local server and the user will use a unique interface within the system to allow multi-database queries to be issued to this single interface.A mediator does not store any data, but it provides a virtual view of the integrated sources. The mediator approach basically translates the user query, into queries that are understood by the integrated sources. It maps the relationship between source descriptions and the mediator and thus allows queries on the mediator to be translated to queries on the data source.The mediator-based approach has several strengths compared to data warehouse. It does not have the updating problem as the query goes directly to the original source. Mediators can be seen as a cheaper and more effective approach since they use schema or view integration, rather than having to have huge storage capacity to store copied data from all the data sources involved.This paper presents a mediator-based system called YeastMed that aims to provide transparent access to disparate biological databases of yeast. It provides a unique interface between the user who submits a query, and a set of five data sources accessible via ...

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“…In this section, we briefly describe an ontology-based mediator framework (KOMF) which uses a Semantic Directory (SD-Core [ 19 ]), a generic infrastructure to register and manage ontologies, their relationships and also information relating to the resources. In the proposed framework (Figure 1 ) our goal is to provide access to the data using a common data model, and a common query language.…”

Section: Introductionmentioning

confidence: 99%