Skip to main content
SpringerLink
Log in

Results: XTENS 2, A JSON-Compliant Repository

  • Chapter
  • First Online:
Biomedical Research and Integrated Biobanking: An Innovative Paradigm for Heterogeneous Data Management

Part of the book series: Springer Theses ((Springer Theses))

  • 393 Accesses

Abstract

In this chapter I will present the efforts done to develop a novel, fully JSON-compliant environment for the JSON data model outlined in Chap. 3. The original XTENS repository and XTENS 1.5—from now on collectively named “old XTENS”—were developed using a Java-based software stack and a MySQL database backend. As illustrated in Chap. 4, it proved to be successful in managing the workflow of a medium-sized integrated biobank.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Here I speak of interface in the Software Engineering sense: a common set of public methods and properties.

  2. 2.

    An event loop is “an entity that handles and processes external events and converts them into callback invocations” [3].

  3. 3.

    At the time I started developing the system MySQL had no native JSON support. Binary JSON support in MySQL was first introduced in 5.7.8 (July 2015).

  4. 4.

    Here and afterwards, “schemaless” means that no fixed (tabular) schema is enforced or constrained by the RDBMS on write. The schema may be provided or enforced by an external application (in our case XTENS 2).

  5. 5.

    I know, this is an unfortunate naming choice, because it may create ambiguity with the JSON metadata model. But I found all the other possible candidate names, namely template, classTemplate, or class even more inappropriate. Every time I refer to the JSON data model I call it explicitly the JSON data model.

  6. 6.

    To futher decouple the Postgres database from the XTENS application, the xtens-query together with all the transactional CRUD operations handled in the xtens-transact module have been merged at a later time (November 2015) in a single “Postgres” module, named xtens-pg [11].

  7. 7.

    As defined in statistics, “a data sample is a set of data collected and/or selected from a statistical population by a defined procedure” [20].

  8. 8.

    The cost is an arbitrary unit used by the RDBMS to estimate the best query plan.

References

  1. Mahmoud, Q.:. Servlets and JSP Pages Best Practices. Sun Developer Network (2003)

    Google Scholar 

  2. Tilkov, Stefan, Vinoski, Steve: Node.js: using JavaScript to build high-performance network programs. IEEE Int. Comput. 14(6), 0080–83 (2010)

    Article  Google Scholar 

  3. Understanding the Node.js Event Loop. http://blog.mixu.net/2011/02/01/understanding-the-node-js-event-loop/ (2011). Accessed 27 Mar 2015

  4. Sails.js - Realtime MVC Framework for Node.js. http://sailsjs.org/ (2015). Accessed 09 Feb 2015

  5. Express - Node.js Web Application Framework. http://expressjs.com/ (2015). Accessed 09 Feb 2015

  6. Peter Lubbers and Frank Greco. HTML5 Web Sockets: A Quantum Leap in Scalability for the Web. SOA World Magazine (2010)

    Google Scholar 

  7. Lerner, RM.: At the forge: PostgreSQL, the NoSQL database. Linux J. 2014(247), 5 (2014)

    Google Scholar 

  8. Postgresql 9.4 Documentation: JSON Functions and Operators. http://www.postgresql.org/docs/9.4/static/functions-json.html (2014). Accessed 10 Feb 2015

  9. Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design Patterns: Elements of Reusable Object-oriented Software. Pearson Education, Upper Saddle River (1994)

    Google Scholar 

  10. Norlin, L., Fransson, M.N., Eriksson, M., Merino-Martinez, R., Anderberg, M., Kurtovic, S., Litton, J.-E.: A minimum data set for sharing biobank samples, information, and data: MIABIS. Biopreservation Biobanking 10(4), 343–348 (2012)

    Google Scholar 

  11. XTENS-pg: A Query Module for the XTENS Repository. https://github.com/biolab-unige/xtens-pg (2015). Accessed 08 Dec 2015

  12. XTENS-Query: A Query Module for the XTENS Repository. https://github.com/biolab-unige/xtens-query (2015). Accessed 17 Feb 2015

  13. Exome Variant Server, NHLBI GO Exome Sequencing Project, Seattle. http://evs.gs.washington.edu/EVS/ (2013). Accessed 20 Mar 2015

  14. Forbes, S.A., Tang, G., Bindal, N., Bamford, S., Dawson, E., Cole, C., Yin Kok, C., Jia, M., Ewing, R., Menzies, A., et al.: COSMIC (the catalogue of somatic mutations in cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 38(1), D652–D657 (2009) (gkp995)

    Google Scholar 

  15. Vogelstein, B., Nickolas, P., Velculescu, V.E., Zhou, S., Diaz, L.A., Kinzler, K.W.: Cancer genome landscapes. Science 339(6127), 1546–1558 (2013)

    Google Scholar 

  16. Nadkarni, P.M.: Metadata-driven Software Systems in Biomedicine: Designing Systems that Can Adapt to Changing Knowledge. Springer, Berlin (2011)

    Google Scholar 

  17. Smith, G.: PostgreSQL 9.0: High Performance. Packt Publishing Ltd, Birmingham (2010)

    Google Scholar 

  18. Chen, R.S., Nadkarni, P., Marenco, L., Levin, F., Erdos, J., Miller, P.L.: Exploring performance issues for a clinical database organized using an entity-attribute-value representation. J. Am. Med. Inf. Assoc. 7(5), 475–487 (2000)

    Google Scholar 

  19. Schema-less PostgreSQL. http://www.slideshare.net/yandex/jsonb-jsquery (2014). Accessed 29 Mar 2015

  20. Peck, R., Olsen, C., Devore, J.: Introduction to Statistics and Data Analysis. Cengage Learning, Stamford (2008)

    Google Scholar 

  21. Arnulfo, G., Narizzano, M., Cardinale, F., Fato, M.M., Palva J.M.: Automatic segmentation of deeep intracerebral electrodes in computed tomography scans. BMC Bioinformatics (2015). (to appear)

    Google Scholar 

  22. Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., Palva, J.M.: Phase and amplitude correlations in resting-state activity in human stereotactical EEG recordings. NeuroImage 12, 114–127 (2015)

    Google Scholar 

  23. McGonigal, Aileen, Bartolomei, Fabrice, Régis, Jean, Guye, Maxime, Gavaret, Martine, Fonseca, Agnès Trébuchon-Da, Dufour, Henry, Figarella-Branger, Dominique, Girard, Nadine, Péragut, Jean-Claude, et al.: Stereoelectroencephalography in presurgical assessment of MRI-negative epilepsy. Brain 130(12), 3169–3183 (2007)

    Article  Google Scholar 

  24. Cossu, M., Cardinale, F., Castana, L., Citterio, A., Francione, S., Tassi, L., Benabid, A.L., Russo, G.L.: Stereoelectroencephalography in the presurgical evaluation of focal epilepsy: a retrospective analysis of 215 procedures. Neurosurgery 57(4), 706–718 (2005)

    Google Scholar 

  25. Fischl, Bruce, van der Kouwe, André, Destrieux, Christophe, Halgren, Eric, Ségonne, Florent, Salat, David H., Busa, Evelina, Seidman, Larry J., Goldstein, Jill, Kennedy, David, et al.: Automatically parcellating the human cerebral cortex. Cereb. Cortex 14(1), 11–22 (2004)

    Article  Google Scholar 

  26. Destrieux, Christophe, Fischl, Bruce, Dale, Anders, Halgren, Eric: Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage 53(1), 1–15 (2010)

    Article  Google Scholar 

  27. xpr-seeg: a query module for the XTENS 2 repository. https://github.com/biolab-unige/xpr-seeg (2015). Accessed 22 Mar 2015

  28. Izzo, M., Arnulfo, G., Piastra, M.C., Tedone, V., Varesio, L., Fato, M.M.: XTENS-a JSON-based digital repository for biomedical data management. Bioinformatics and Biomedical Engineering, pp. 123–130. Springer, Berlin (2015)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford, UK

    Massimiliano Izzo

Authors
  1. Massimiliano Izzo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Massimiliano Izzo .

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Izzo, M. (2016). Results: XTENS 2, A JSON-Compliant Repository. In: Biomedical Research and Integrated Biobanking: An Innovative Paradigm for Heterogeneous Data Management. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-31241-5_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-31241-5_5

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-31240-8

  • Online ISBN: 978-3-319-31241-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation