XTENS - A JSON-Based Digital Repository for Biomedical Data Management

详细信息    查看全文

• 作者：Massimiliano Izzo (20) (21)
  Gabriele Arnulfo (20) (22)
  Maria Carla Piastra (20)
  Valentina Tedone (20)
  Luigi Varesio (21)
  Marco Massimo Fato (20)
  
  20. Department of Computer Science Bioengineering Robotics and Systems Engineering ; University of Genoa ; Viale Causa 13 ; 16145 ; Genoa ; Italy
  21. Laboratory of Molecular Biology ; Giannina Gaslini Institute ; Largo Gaslini 5 ; 16147 ; Genoa ; Italy
  22. Neuroscience Center ; P.O. Box 56 ; FI-00014 ; University of Helsinki ; Finland
  
• 刊名：Lecture Notes in Computer Science
• 出版年：2015
• 出版时间：2015
• 年：2015
• 卷：9044
• 期：1
• 页码：123-130
• 全文大小：527 KB
• 参考文献：1. Krestyaninova, M., Zarins, A., Viksna, J., Kurbatova, N., Rucevskis, P., Neogi, S.G., Gostev, M., Perheentupa, T., Knuuttila, J., Barrett, A. (2009) A System for Information Management in BioMedical Studies鈥揝IMBioMS. Bioinformatics 25: pp. 2768-2769 CrossRef
  2. Bauch, A., Adamczyk, I., Buczek, P., Elmer, F.J., Enimanev, K., Glyzewski, P., Kohler, M., Pylak, T., Quandt, A., Ramakrishnan, C. (2012) openBIS: A flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 12: pp. 468 5-12-468" target="_blank" title="It opens in new window">CrossRef
  3. Herrick, R., McKay, M., Olsen, T. (2014) Data dictionary services in XNAT and the Human Connectome Project. Front. Neuroinform. 8: pp. 65 5" target="_blank" title="It opens in new window">CrossRef
  4. Scott, A., Courtney, W., Wood, D. (2011) COINS: An Innovative Informatics and Neuroimaging Tool Suite Built for Large Heterogeneous Datasets. Front. Neuroinform. 5: pp. 33 CrossRef
  5. Das, S., Zijdenbos, A.P., Harlap, J., Vins, D., Evans, A.C. (2011) LORIS: A web-based data management system for multi-center studies. Front. Neuroinform. 5: pp. 37
  6. Neu, S.C., Crawford, K.L., Toga, A.W. (2012) Practical management of heterogeneous neuroimaging metadata by global neuroimaging data repositories. Front. Neuroinform. 6: pp. 8 CrossRef
  7. Edwards, P.N., Mayernik, M.S., Batcheller, A.L., Bowker, G.C., Borgman, C.L. (2011) Science friction: data, metadata, and collaboration. Soc. Stud. Sci. 41: pp. 667-690 CrossRef
  8. JSON, http://www.json.org/
  9. Corradi, L., Porro, I., Schenone, A., Momeni, P., Ferrari, R., Nobili, F., Ferrara, M., Arnulfo, G., Fato, M.M. (2012) A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience. BMC Med. Inform. Decis. Mak. 12: pp. 115 5" target="_blank" title="It opens in new window">CrossRef
  10. Izzo, M., Mortola, F., Arnulfo, G., Fato, M., Varesio, L.: A digital repository with an extensible data model for biobanking and genomic analysis management. BMC Genomics聽15 (2014)
  11. Norlin, L., Fransson, M., Eriksson, M., Merino-Martinez, R., Anderberg, M., Kurtovic, S., Litton, J.: A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS. Biopreservation and Biobanking 10 (2012)
  12. XTENS source code, https://github.com/biolab-unige/xtens-app
  13. iRODS, http://irods.org/
  14. Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., Palva, J.M.: Phase and Amplitude correlations in resting state activity in human stereoEEG recordings. NeuroImage (submitted)
  15. Arnulfo, G., Narizzano, M., Cardinale, F., Fato, M.M., Palva, J.M.: Automatic Segmentation of Deeep intracerebral Electrodes in Computed Tomography Scans. BMC Bioinformatics (submitted)
  16. Cardinale, F., Cossu, M., Castana, L., Casaceli, G., Schiariti, M.P., Miserocchi, A. (2013) Stereoelectroencephalography: surgical methodology, safety, and stereotactic application accuracy in 500 procedures. Neurosurgery 72: pp. 353-366 CrossRef
  
• 作者单位：Bioinformatics and Biomedical Engineering
• 丛书名：978-3-319-16479-3
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349

文摘

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.