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XML, Ontologies, and Their Clinical Applications

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Translational Biomedical Informatics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 939))

Abstract

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

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References

  1. Abidi SS, Manickam S. Leveraging XML-based electronic medical records to extract experiential clinical knowledge. An automated approach to generate cases for medical case-based reasoning systems. Int J Med Inform. 2002;68:187–203.

    Article  PubMed  Google Scholar 

  2. Abidi SR, et al. Ontology-based modeling of clinical practice guidelines: a clinical decision support system for breast cancer follow-up interventions at primary care settings. Stud Health Technol Inform. 2007;129:845–9.

    PubMed  Google Scholar 

  3. Adam TJ, Wang J. Adverse drug event ontology: gap analysis for clinical surveillance application. AMIA Jt Summits Transl Sci Proc. 2015;2015:16–20.

    PubMed  PubMed Central  Google Scholar 

  4. Bau CT, Chen RC, Huang CY. Construction of a clinical decision support system for undergoing surgery based on domain ontology and rules reasoning. Telemed J E Health. 2014;20:460–72.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Berman JJ, Bhatia K. Biomedical data integration: using XML to link clinical and research data sets. Expert Rev Mol Diagn. 2005;5:329–36.

    Article  PubMed  Google Scholar 

  6. Drozd DR, et al. Developing a relational XML schema for sharing HIV clinical data. AMIA Annu Symp Proc. 2005;2005:943.

    PubMed Central  Google Scholar 

  7. Eminaga O, et al. Clinical map document based on XML (cMDX): document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens. BMC Med Inform Decis Mak. 2010;10:71.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Galopin A, et al. Using an ontological modeling to evaluate the consistency of clinical practice guidelines: application to the comparison of three guidelines on the management of adult hypertension. Stud Health Technol Inform. 2014;205:38–42.

    PubMed  Google Scholar 

  9. Galopin A, et al. An ontology-based clinical decision support system for the management of patients with multiple chronic disorders. Stud Health Technol Inform. 2015;216:275–9.

    PubMed  Google Scholar 

  10. Gordon CL, et al. Design and evaluation of a bacterial clinical infectious diseases ontology. AMIA Annu Symp Proc. 2013;2013:502–11.

    PubMed  PubMed Central  Google Scholar 

  11. Guo J, et al. CLAIM (CLinical Accounting InforMation)—an XML-based data exchange standard for connecting electronic medical record systems to patient accounting systems. J Med Syst. 2005;29:413–23.

    Article  PubMed  Google Scholar 

  12. Haghighi M, et al. Development of clinical ontology for mood disorder with combination of psychomedical information. J Med Dent Sci. 2009;56:1–15.

    PubMed  Google Scholar 

  13. Heller B, et al. Standardized terminology for clinical trial protocols based on top-level ontological categories. Stud Health Technol Inform. 2004;101:46–60.

    CAS  PubMed  Google Scholar 

  14. Hirose Y, Yamamoto R, Ueda S. The nodes focusing tool for clinical course data of hypergraph structure in the ontological framework CSX output from POMR-based EMR system. Stud Health Technol Inform. 2007;129:741–5.

    PubMed  Google Scholar 

  15. Hoelzer S, et al. Value of XML in the implementation of clinical practice guidelines—the issue of content retrieval and presentation. Med Inform Internet Med. 2001;26:131–46.

    Article  CAS  PubMed  Google Scholar 

  16. Hoffman M, Arnoldi C, Chuang I. The clinical bioinformatics ontology: a curated semantic network utilizing RefSeq information. Pac Symp Biocomput. 2005;2005:139–50.

    Google Scholar 

  17. http://www.who.int/ictrp/en/WHO International clinical trials registry platform

  18. Hulse NC, et al. Application of an XML-based document framework to knowledge content authoring and clinical information system development. AMIA Annu Symp Proc. 2003;2003:870.

    PubMed Central  Google Scholar 

  19. Jeong S, et al. Clinical data element ontology for unified indexing and retrieval of data elements across multiple metadata registries. Healthc Inform Res. 2014;20:295–303.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Johnson SB, et al. A native XML database design for clinical document research. AMIA Annu Symp Proc. 2003;2003:883.

    PubMed Central  Google Scholar 

  21. Lozano-Rubi R, Pastor X. OWLing clinical data repositories with the ontology web language. JMIR Med Inform. 2014;2:e14.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Manickam S, Abidi SS. Extracting clinical cases from XML-based electronic patient records for use in web-based medical case based reasoning systems. Stud Health Technol Inform. 2001;84:643–7.

    CAS  PubMed  Google Scholar 

  23. Min H, et al. Integration of prostate cancer clinical data using an ontology. J Biomed Inform. 2009;42:1035–45.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Mludek V, et al. Integration of clinical practice guidelines into a distributed regional electronic patient record for tumour-patients using XML: a means for standardization of the treatment processes. Stud Health Technol Inform. 2001;84:658–62.

    CAS  PubMed  Google Scholar 

  25. Mludek V, et al. Supporting clinical practice guidelines: lifecycle of guidelines for oncology within an XML-based guideline framework. Stud Health Technol Inform. 2002;90:466–70.

    PubMed  Google Scholar 

  26. Moskovitch R, et al. A comparative evaluation of full-text, concept-based, and context-sensitive search. J Am Med Inform Assoc. 2007;14:164–74.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Moskovitch R, Shahar Y. Vaidurya: a multiple-ontology, concept-based, context-sensitive clinical-guideline search engine. J Biomed Inform. 2009;42:11–21.

    Article  PubMed  Google Scholar 

  28. Okada O, Ohboshi N, Yoshihara H. Clinical path modeling in XML for a web-based benchmark test system for medication. J Med Syst. 2005;29:539–53.

    Article  PubMed  Google Scholar 

  29. Omaish M, Abidi S, Abidi SS. Ontology-based computerization of acute coronary syndrome clinical guideline for decision support in the emergency department. Stud Health Technol Inform. 2012;180:437–41.

    PubMed  Google Scholar 

  30. Patrao DF, et al. Recruit—an ontology based information retrieval system for clinical trials recruitment. Stud Health Technol Inform. 2015;216:534–8.

    PubMed  Google Scholar 

  31. Perez-Rey D, et al. ONTOFUSION: ontology-based integration of genomic and clinical databases. Comput Biol Med. 2006;36:712–30.

    Article  CAS  PubMed  Google Scholar 

  32. Philipp F, et al. Introducing DoT-U2—an XML-based knowledge supported checklist software for documentation of a newborn clinical screening examination. Comput Methods Prog Biomed. 2005;77:115–20.

    Article  CAS  Google Scholar 

  33. Roth C, et al. DEDUCE clinical text: an ontology-based module to support self-service clinical notes exploration and cohort development. AMIA Jt Summits Transl Sci Proc. 2013;2013:227.

    PubMed  Google Scholar 

  34. Saadawi GM, Harrison Jr JH. Definition of an XML markup language for clinical laboratory procedures and comparison with generic XML markup. Clin Chem. 2006;52:1943–51.

    Article  CAS  PubMed  Google Scholar 

  35. Sahoo SS, et al. Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care. J Am Med Inform Assoc. 2014;21:82–9.

    Article  PubMed  Google Scholar 

  36. Schriml LM, Mitraka E. The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. Mamm Genome. 2015;26:584–9.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Schweiger R, et al. XML structured clinical information: a practical example. Stud Health Technol Inform. 2000;77:822–6.

    CAS  PubMed  Google Scholar 

  38. Schweiger R, et al. Linking clinical data using XML topic maps. Artif Intell Med. 2003;28:105–15.

    Article  PubMed  Google Scholar 

  39. Shankar RD, et al. An ontology-based architecture for integration of clinical trials management applications. AMIA Annu Symp Proc. 2007;2007:661–5.

    PubMed Central  Google Scholar 

  40. Slaughter L, et al. The core clinical protocol ontology (C2PO): a realist ontology for representing the recommendations within clinical guidelines. Stud Health Technol Inform. 2013;192:997.

    PubMed  Google Scholar 

  41. Smith JR, et al. The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. J Biomed Semantics. 2013;4:26.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Song D, Chute CG, Tao C. Semantator: annotating clinical narratives with semantic web ontologies. AMIA Jt Summits Transl Sci Proc. 2012;2012:20–9.

    PubMed  PubMed Central  Google Scholar 

  43. Sousa AM, Pereira MO, Lourenco A. MorphoCol: an ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies. J Biomed Inform. 2015;55:55–63.

    Article  PubMed  Google Scholar 

  44. Stenzhorn H, et al. The ObTiMA system—ontology-based managing of clinical trials. Stud Health Technol Inform. 2010;160:1090–4.

    PubMed  Google Scholar 

  45. Tao C, Solbrig HR, Chute CG. CNTRO 2.0: a harmonized semantic web ontology for temporal relation inferencing in clinical narratives. AMIA Jt Summits Transl Sci Proc. 2011;2011:64–8.

    PubMed  PubMed Central  Google Scholar 

  46. Tarczy-Hornoch P, et al. GeneClinics: a hybrid text/data electronic publishing model using XML applied to clinical genetic testing. J Am Med Inform Assoc. 2000;7:267–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Tenenbaum JD, et al. The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform. 2011;44:137–45.

    Article  PubMed  Google Scholar 

  48. Tran VA, et al. OnWARD: ontology-driven web-based framework for multi-center clinical studies. J Biomed Inform. 2011;44 Suppl 1:S48–53.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Uciteli A, Herre H. OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research. J Biomed Semantics. 2015;6:41.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Zhang YF, et al. Integrating HL7 RIM and ontology for unified knowledge and data representation in clinical decision support systems. Comput Methods Prog Biomed. 2016;123:94–108.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Suzhou Industrial Park Institute of Services Outsourcing, No. 99 Ruoshui Road, Suzhou Industrial Park, Suzhou, 215123, Jiangsu, China

    Chunjiang Yu

  2. Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China

    Bairong Shen

Authors
  1. Chunjiang Yu
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  2. Bairong Shen
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Corresponding author

Correspondence to Bairong Shen .

Editor information

Editors and Affiliations

  1. Center for Systems Biology, Soochow University, Jiangsu, China

    Bairong Shen

  2. School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA

    Haixu Tang

  3. Department of Biomedical Informatics, University of California San Diego, La Jolla, California, USA

    Xiaoqian Jiang

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© 2016 Springer Science+Business Media Singapore

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Yu, C., Shen, B. (2016). XML, Ontologies, and Their Clinical Applications. In: Shen, B., Tang, H., Jiang, X. (eds) Translational Biomedical Informatics. Advances in Experimental Medicine and Biology, vol 939. Springer, Singapore. https://doi.org/10.1007/978-981-10-1503-8_11

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