Abstract
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent 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.
Highlights
In the last few decades the intersection of computer science and biology has evolved to the point at which answers to fundamental biological questions have emerged [1]
It is currently evident that fields such as computational biology and bioinformatics are practically fueled by the increasing computational resources available and the development of software encapsulation and abstraction layers [3]
Ezra Tsur BioData Mining (2017) 10:11 regarding biological entities is stored in databases, which have become the most important corner stone for research in computational biology and bioinformatics
Summary
In the last few decades the intersection of computer science and biology has evolved to the point at which answers to fundamental biological questions have emerged [1]. Biological database designers currently face two main challenges: data heterogeneity and the emergence of new relational connections between data entities. One of the main alternatives to relational data model is object-based representation of information, in which entities are defined with a set of properties and connected as attributes.
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