XTENS - A JSON-based digital repository for biomedical data management

Massimiliano Izzo*, Gabriele Arnulfo, Maria Carla Piastra, Valentina Tedone, Luigi Varesio, Marco Massimo Fato

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

3 Citations (Scopus)

Abstract

Biomedical Science poses unique challenges in data management. Heterogeneous information - such as clinical records, biological specimens, imaging and genomic data, different technology-associated formats - must be collected and integrated to provide a unified overview of each patient. International scale research collaborations involve different disciplines (Medicine/ Biology, Engineering/IT, Physics,…). Extensive metadata is required to maximize information sharing among the partners. To properly tackle these issues, we have developed XTENS, a data repository built on a flexible and extensible JSON-based data model. The JSON data model is conceived to achieve maximal flexibility, to allow adaptive metadata management, and to perceive metadata as a dynamical process of scientific communication rather than an enduring product fixed in time. XTENS is integrated with iRODS, a data grid software that allows distributed storage, metadata file annotation and advanced policies for data curation. We have adopted the platform for a functional connectomics multicentric project where heterogeneous data sources (radiological images, electroencephalography signals) must be integrated and analysed to compute connectivity maps of the brain. To this end, we have tested the repository prototype allowing the external programs to interact with XTENS using a service-oriented REST interface. We demonstrated XTENS usefulness because we could input heterogeneous data, run the required processing tool and store the process output.

Original languageEnglish
Title of host publicationBioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings
EditorsFrancisco Ortuño, Ignacio Rojas
PublisherSpringer
Pages123-130
Number of pages8
ISBN (Electronic)9783319164793
DOIs
Publication statusPublished - 2015
Externally publishedYes
Event3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 - Granada, Spain
Duration: 15 Apr 201517 Apr 2015
Conference number: 3

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9044
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015
Abbreviated titleIWBBIO 2015
CountrySpain
CityGranada
Period15/04/1517/04/15

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