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

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

doi:10.1007/978-3-319-16480-9_13

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 proceeding › Conference contribution › Academic › peer-review

4 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 language	English
Title of host publication	Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings
Editors	Francisco Ortuño, Ignacio Rojas
Publisher	Springer
Pages	123-130
Number of pages	8
ISBN (Electronic)	9783319164793
DOIs	https://doi.org/10.1007/978-3-319-16480-9_13
Publication status	Published - 2015
Externally published	Yes
Event	3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 - Granada, Spain Duration: 15 Apr 2015 → 17 Apr 2015 Conference number: 3

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9044
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015
Abbreviated title	IWBBIO 2015
Country/Territory	Spain
City	Granada
Period	15/04/15 → 17/04/15

Access to Document

10.1007/978-3-319-16480-9_13

Cite this

Izzo, M., Arnulfo, G., Piastra, M. C., Tedone, V., Varesio, L., & Fato, M. M. (2015). XTENS - A JSON-based digital repository for biomedical data management. In F. Ortuño, & I. Rojas (Eds.), Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings (pp. 123-130). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044). Springer. https://doi.org/10.1007/978-3-319-16480-9_13

Izzo, Massimiliano ; Arnulfo, Gabriele ; Piastra, Maria Carla et al. / XTENS - A JSON-based digital repository for biomedical data management. Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. editor / Francisco Ortuño ; Ignacio Rojas. Springer, 2015. pp. 123-130 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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.",

author = "Massimiliano Izzo and Gabriele Arnulfo and Piastra, {Maria Carla} and Valentina Tedone and Luigi Varesio and Fato, {Marco Massimo}",

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Izzo, M, Arnulfo, G, Piastra, MC, Tedone, V, Varesio, L & Fato, MM 2015, XTENS - A JSON-based digital repository for biomedical data management. in F Ortuño & I Rojas (eds), Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9044, Springer, pp. 123-130, 3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, Granada, Spain, 15/04/15. https://doi.org/10.1007/978-3-319-16480-9_13

XTENS - A JSON-based digital repository for biomedical data management. / Izzo, Massimiliano; Arnulfo, Gabriele; Piastra, Maria Carla et al.
Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. ed. / Francisco Ortuño; Ignacio Rojas. Springer, 2015. p. 123-130 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

T1 - XTENS - A JSON-based digital repository for biomedical data management

AU - Izzo, Massimiliano

AU - Arnulfo, Gabriele

AU - Piastra, Maria Carla

AU - Tedone, Valentina

AU - Varesio, Luigi

AU - Fato, Marco Massimo

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DO - 10.1007/978-3-319-16480-9_13

M3 - Conference contribution

AN - SCOPUS:84925251497

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings

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Izzo M, Arnulfo G, Piastra MC, Tedone V, Varesio L, Fato MM. XTENS - A JSON-based digital repository for biomedical data management. In Ortuño F, Rojas I, editors, Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Springer. 2015. p. 123-130. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-16480-9_13

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

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