Abstract
The increasing capability and sophistication of biomedical instruments has led to rapid generation of large volumes of disparate data that is often characterized as biomedical “big data”. Effective analysis of biomedical big data is providing new insights to advance healthcare research, but it is difficult to efficiently manage big data without a conceptual model, such as ontology, to support storage, query, and analytical functions. In this paper, we describe the Cloudwave platform that uses a domain ontology to support optimal data partitioning, efficient network transfer, visualization, and querying of big data in the neurology disease domain. The domain ontology is used to define a new JSON-based Cloudwave Signal Format (CSF) for neurology signal data. A comparative evaluation of the ontology-based CSF with existing data format demonstrates that it significantly reduces the data access time for query and visualization of large scale signal data.
Keywords
- Domain Ontology
- Biomedical Big Data
- Cloud-based Data Management
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References
Madden, S.: From databases to big data. IEEE Internet Computing 16, 4–6 (2012)
Embley, D.W., Liddle, S.W.: Big Data - Conceptual Modeling to the Rescue. In: Ng, W., Storey, V.C., Trujillo, J.C. (eds.) ER 2013. LNCS, vol. 8217, pp. 1–8. Springer, Heidelberg (2013)
Hitzler, P., Krötzsch, M., Parsia, B., Patel-Schneider, P.F., Rudolph, S.: OWL 2 Web Ontology Language Primer. World Wide Web Consortium W3C (2009)
Ashburner, M., et al.: Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000)
Rosse, C., Mejino Jr., J.L.: A reference ontology for biomedical informatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics 36, 478–500 (2003)
Motik, B., Patel-Schneider, P.F., Grau, B.C.: OWL 2 Web Ontology Language Direct Semantics, World Wide Web Consortium W3C December 11 (2012)
Ferrucci, D., et al.: Building Watson: An Overview of the DeepQA Project. AI Magazine 31, 59–79 (2010)
Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., Schneider, L.: Sweetening Ontologies with DOLCE. In: 13th International Conference on Knowledge Engineering and Knowledge Management. Ontologies and the Semantic Web, Siguenza, Spain, pp. 166–181 (2002)
Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biol. 6, R46 (2005)
Brain Research through Advancing Innovative Neurotechnologies (BRAIN), The White House, Washington, D.C. (2013)
Schwartzkroin, P.A.: Cellular electrophysiology of human epilepsy. Epilepsy Research 17, 185–192 (1994)
Koden, N.: Nihon Koden Neurology, http://www.nkusa.com/neurology_cardiology/
Shvachko, K., Kuang, H., Radia, S., Chansler, R.: The Hadoop Distributed File System. Presented at the IEEE 26th Symposium on Mass Storage Systems and Technologies (MSST), NV (2010)
Kemp, B., Olivan, J.: European data format ‘plus’ (EDF+), an EDF alike standard format for the exchange of physiological data. Clinical Neurophysiology 114, 1755–1761 (2003)
Henson, C.A., Thirunarayan, K., Sheth, A.P.: An Efficient Bit Vector Approach to Semantics-Based Machine Perception in Resource-Constrained Devices. In: International Semantic Web Conference, Washington D.C, pp. 149–164 (2012)
Stonebraker, M., Abadi, D.J., Batkin, A., Chen, X., Cherniack, M., Ferreira, M., Lau, E., Lin, A., Madden, S., O’Neil, E., O’Neil, P., Rasin, A., Tran, N., Zdonik, S.: C-store: A column-oriented DBMS. In: 31st International Conference on Very Large Data Bases (VLDB 2005), Trondheim, Norway, pp. 553–564 (2005)
Sekhavat, Y.A., Parsons, J.: Sliced column-store (SCS): ontological foundations and practical implications. In: Atzeni, P., Cheung, D., Ram, S. (eds.) ER 2012. LNCS, vol. 7532, pp. 102–115. Springer, Heidelberg (2012)
Dean, J., Ghemawat, S.: MapReduce: Simplified Data Processing on Large Clusters. In: OSDI 2004, San Francisco (2004)
Hamer, H.M., Lüders, H.O.: Electrode montages and localization of potentials in clinical electroencephalography. In: Levin, K., Luders, H.O. (eds.) Comprehensive Clinical Neurophysiology, pp. 358–386. WB Saunders Company (2000)
Sahoo, S.S., Lhatoo, S.D., Gupta, D.K., Cui, L., Zhao, M., Jayapandian, C., Bozorgi, A., Zhang, G.Q.: Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care. Journal of American Medical Association 21, 82–89 (2014)
Sahoo, S.S., Zhao, M., Luo, L., Bozorgi, A., Gupta, A., Lhatoo, S.D., Zhang, G.Q.: OPIC: Ontology-driven Patient Information Capturing System for Epilepsy. In: The American Medical Informatics Association (AMIA) Annual Symposium, Chicago, pp. 799–808 (2012)
Cui, L., Bozorgi, A., Lhatoo, S.D., Zhang, G.Q., Sahoo, S.S.: EpiDEA: Extracting Structured Epilepsy and Seizure Information from Patient Discharge Summaries for Cohort Identification. In: The American Medical Informatics Association (AMIA) Annual Symposium, Chicago, pp. 1191–1200 (2012)
Loddenkemper, T., Kellinghaus, C., Wyllie, E., Najm, I.M., Gupta, A., Rosenow, F., Luders, H.O.: A proposal for a five-dimensional patient oriented epilepsy classification. Epileptic Disord 7, 308–316 (2005)
Kellinghaus, C., et al.: Suggestion for a new, patient-oriented epilepsy classification. Nervenarzt 77, 961–969 (2006)
Nelson, S.J., et al.: Normalized names for clinical drugs: RxNorm at 6 years. J. Am. Med. Inform. Assoc. 18, 441–448 (2011)
Crockford, D.: Introducing JSON (1999), http://www.json.org/
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Jayapandian, C., Chen, CH., Dabir, A., Lhatoo, S., Zhang, GQ., Sahoo, S.S. (2014). Domain Ontology As Conceptual Model for Big Data Management: Application in Biomedical Informatics. In: Yu, E., Dobbie, G., Jarke, M., Purao, S. (eds) Conceptual Modeling. ER 2014. Lecture Notes in Computer Science, vol 8824. Springer, Cham. https://doi.org/10.1007/978-3-319-12206-9_12
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DOI: https://doi.org/10.1007/978-3-319-12206-9_12
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