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Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces

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BIODATA MINING 2017年第1期10卷 11-11页

作者： Tsur, Elishai Ezra Jerusalem Coll Technol Fac Engn Neuro Biomorph Engn Lab Jerusalem Israel

databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and contextdependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever- growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open- source framework for the curation of specialized databases is proposed. The framework supports user- designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c. dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3- dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http:// nbel- lab. com.

关键词： Specialized databases object relational databases EclipseLink Apache Derby object oriented programming

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Reasoning about uniqueness constraints in object relational databases

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IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2003年第5期15卷 1295-1306页

作者： Khizder, VL Weddell, GE Oracle Corp Nashua NH 03062 USA Univ Waterloo Dept Comp Sci Waterloo ON N2L 3G1 Canada

Uniqueness constraints such as keys and functional dependencies in the relational model are a core concept in information systems technology. In this paper, we consider uniqueness constraints suitable for object relational data models and identify a boundary between tractable and intractable varieties. The subclass that is tractable is still a strict generalization of both keys and relational functional dependencies. We present an efficient decision procedure for the logical implication problem of this subclass. The problem itself is formulated as an implication problem for a simple dialect of description logic (DL). DLs are a family of languages for knowledge representation that have many applications in information systems technology and for which model building procedures have been developed that can decide implication problems for dialects that are very expressive. Our own procedure complements this approach and can be integrated with these earlier procedures. Finally, to motivate our results, we review some applications of our procedure in query optimization.

关键词： complex objects uniqueness constraints object relational databases semantic query optimization description logics subsumption algorithms

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