Dynamic integration of biological data sources using the data concierge

Peng Gong

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Scientific Computing and Data Management Semantic Web and Ontologies Biomedical Text Mining and Ontologies

Abstract

BACKGROUND: The ever-changing landscape of large-scale network environments and innovative biology technologies require dynamic mechanisms to rapidly integrate previously unknown bioinformatics sources at runtime. However, existing integration technologies lack sufficient flexibility to adapt to these changes, because the techniques used for integration are static, and sensitive to new or changing bioinformatics source implementations and evolutionary biologist requirements. METHODS: To address this challenge, in this paper we propose a new semantics-based adaptive middleware, the Data Concierge, which is able to dynamically integrate heterogeneous biological data sources without the need for wrappers. Along with the architecture necessary to facilitate dynamic integration, API description mechanism is proposed to dynamically classify, recognize, locate, and invoke newly added biological data source functionalities. Based on the unified semantic metadata, XML-based state machines are able to provide flexible configurations to execute biologist's abstract and complex operations. RESULTS AND DISCUSSION: Experimental results demonstrate that for obtaining dynamic features, the Data Concierge sacrifices reasonable performance on reasoning knowledge models and dynamically doing data source API invocations. The overall costs to integrate new biological data sources are significantly lower when using the Data Concierge. CONCLUSIONS: The Data Concierge facilitates the rapid integration of new biological data sources in existing applications with no repetitive software development required, and hence, this mechanism would provide a cost-effective solution to the labor-intensive software engineering tasks.

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