Biomedical Research and Integrated Biobanking: An Innovative by Massimiliano Izzo

By Massimiliano Izzo

This doctoral thesis experiences on an leading edge facts repository delivering adaptive metadata administration to maximize details sharing and comprehension in multidisciplinary and geographically dispensed collaborations.  It techniques metadata as a fluid, loosely based and dynamical approach instead of a hard and fast product, and describes the advance of a unique information administration platform in line with a schemaless JSON information version, which represents the 1st totally JSON-based metadata repository designed for the biomedical sciences. Results obtained in a number of software eventualities (e.g. built-in biobanking, sensible genomics and computational neuroscience) and corresponding functionality assessments are mentioned on intimately. final yet no longer least, the booklet deals a scientific review of information structures common within the biomedical sciences, including a clean point of view at the position of and instruments for info sharing and heterogeneous information integration in modern biomedical research.

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Metadata are managed separately from bulk data to ease scalability issue. Metadata are stored within the relational database located on the so-called Application Server, while the bulk data is stored in one or more file systems managed by Data Store Servers. In this way, bandwidth consuming operations like file uploads are not performed on the system that provides metadata management, and that might be used frequently for searches and retrieval. In openBIS, datasets are immutable: once uploaded, they cannot be modified any more.

With the latter I mean that the format should be fast to search and that speed performances should scale-up well with the database dimensions. Both of these statements are not true for XML. Firstly, it was not conceived to be object-oriented and requires some 32 2 Motivation and State of the Art level of manipulation and mapping, named data binding, to obtain a business object from an XML document tree. Many binding tools have been developed for Java, which is the language adopted by many of the biomedical repositories: the most popular are JAXB, JiBX, and XMLBeans; C++ offers CodeSynthesis XSD.

Clin. Chem. 55(4), 611–622 (2009) 18. : Guidelines for reporting an fMRI study. Neuroimage 40(2), 409–414 (2008) 19.

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