Semantic normalization and query abstraction based on SNOMED-CT and HL7: Supporting multicentric clinical trials

IEEE Journal of Biomedical and Health Informatics

Volumn 19, Issue 3, 2015, Pages 1061-1067

  Paraiso Medina, Sergio ^a   Perez Rey, David ^a   Bucur, Anca ^b   Claerhout, Brecht ^c   Alonso Calvo, Raul ^a  

^a UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^b PHILIPS RESEARCH LABORATORIES   (Netherlands)

^c NONE   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; BIOINFORMATICS; BIOMARKERS; CLINICAL RESEARCH; MEDICAL APPLICATIONS; POPULATION STATISTICS; QUERY PROCESSING;

ABSTRACTION MECHANISM; BIOMEDICAL INFORMATION; BIOMEDICAL VOCABULARIES; DATA REPRESENTATIONS; NORMALIZATION PROCESS; SEMANTIC INTEROPERABILITY; SEMANTIC KNOWLEDGE; SEMANTIC WEB TECHNOLOGY;

DATA INTEGRATION;

CLINICAL TRIAL (TOPIC); DOCUMENTATION; ELECTRONIC MEDICAL RECORD; HUMAN; STANDARDS; SYSTEMATIZED NOMENCLATURE OF MEDICINE;

ABSTRACTING AND INDEXING AS TOPIC; CLINICAL TRIALS AS TOPIC; ELECTRONIC HEALTH RECORDS; HUMANS; SYSTEMATIZED NOMENCLATURE OF MEDICINE;

EID: 84929327432     PISSN: 21682194     EISSN: 21682208     Source Type: Journal    
DOI: 10.1109/JBHI.2014.2357025     Document Type: Article

References (31)

1. L. M. McShane, M. M. Cavenagh, T. G. Lively, D. A. Eberhard, W. L. Bigbee, P. M. Williams, and B. A. Conley, "Criteria for the use of omics-based predictors in clinical trials," Nature, vol. 502, no. 7471, pp. 317-320, 2013.
2. J. G. Hodge Jr., L. O. Gostin, and P. D. Jacobson, "Legal issues concerning electronic health information," J. Amer. Med. Assoc., vol. 282, no. 15, pp. 1466-1471, 1999.
3. A. Anguita, L. Martin, D. Pérez-Rey, and V. Maojo, "A review of methods and tools for database integration in biomedicine," Curr. Bioinformat., vol. 5, pp. 253-269, 2010.
4. B. Claerhout, N. Forgó, T. Krügel, M. Arning, and G. De Moor, "A data protection framework for trans-European genetic research projects," Stud. Health Technol. Informat., vol. 141, pp. 67-72, 2008.
5. K. C. Oeffinger, J. S. Ford, C. S. Moskowitz, L. R. Diller, M. M. Hudson, J. F. Chou, and L. L. Robison, "Breast cancer surveillance practices among women previously treated with chest radiation for a childhood cancer," J. Amer. Med. Assoc., vol. 301, no. 4, pp. 404-414, 2009.
6. S. Pakhomov, S. A. Weston, S. J. Jacobsen, C. G. Chute, R. Meverden, and V. L. Roger, "Electronic medical records for clinical research: Application to the identification of heart failure," Amer. J. Managed Care, vol. 13, no. 6 Part 1, pp. 281-288, 2007.
7. W. R. Hersh, "Adding value to the electronic health record through secondary use of data for quality assurance, research, and surveillance," Clin. Pharmacol. Therapeutics, vol. 81, pp. 126-128, 2007.
8. P. E. Stang, P. B. Ryan, J. A. Racoosin, J. M. Overhage, A. G. Hartzema, C. Reich, and J. Woodcock, "Advancing the science for active surveillance: Rationale and design for the observational medical outcomes partnership," Ann. Internal Med., vol. 153, no. 9, pp. 600-606, 2010.
9. S. N. Murphy, G. Weber, M. Mendis, V. Gainer, H. C. Chueh, S. Churchill, and I. Kohane, "Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)," J. Amer. Med. Informat. Assoc., vol. 17, no. 2, pp. 124-130, 2010.
10. S. Oster, S. Langella, S. Hastings, D. Ervin, R. Madduri, J. Phillips, and J. Saltz, "Cagrid 1.0: An enterprise grid infrastructure for biomedical research," J. Amer. Med. Informat. Assoc., vol. 15, no. 2, pp. 138-149, 2008.
11. Fp7-integrate.eu. (Dec. 31, 2013). Driving Excellence in In-tegrative Cancer Research [Online]. Available: http://www.fp7-integrate.eu/index.php/project
12. eurecaproject.eu. (Dec. 31, 2013). Enabling Information Re-Use by Linking Clinical Research and Care [Online]. Available from: http://eurecaproject.eu/
13. M. Antonioletti, M. Atkinson, R. Baxter, A. Borley, N. P. Chue Hong, B. Collins, and M. Westhead, "The design and implementation of grid database services in OGSA-DAI," Concurrency Comput.: Practice Experience, vol. 17, nos. 2-4, pp. 357-376, 2005.
14. J. M. Moratilla, R. Alonso-Calvo, G. Molina-Vaquero, S. Paraiso-Medina, D. Perez-Rey, and V. Maojo, "A data model based on semantically enhanced HL7 RIM for sharing patient data of breast cancer clinical trials," Stud. Health Technol. Informat., vol. 192, pp. 971-971, 2012.
15. D. Kalra, T. Beale, and S. Heard, "The openEHR foundation, "Stud. Health Technol. Informat., vol. 115, pp. 153-173, 2005.
16. D. B. Fridsma, J. Evans, S. Hastak, and C. N. Mead, "The BRIDG project: A technical report," J. Amer. Med. Informat. Assoc., vol. 15, no. 2, pp. 130-137, 2008.
17. W. Kuchinke, J. Aerts, S. C. Semler, and C. Ohmann, "CDISC standard-based electronic archiving of clinical trials," Methods Inf. Med., vol. 48, no. 5, pp. 408-413, 2009.
18. T. Benson, Principles of Health Interoperability HL7 and SNOMED. New York, NY, USA: Springer, 2012.
19. G. W. Beeler, "HL7 Version 3-An object-oriented methodology for collaborative standards development," Int. J. Med. Informat., vol. 48, no. 1, pp. 151-161, 1998.
20. S. Aso, D. Perez-Rey, R. Alonso-Calvo, A. Rico-Diez, A. Bucur, B. Claerhout, and V. Maojo, "Analyzing SNOMED CT and HL7 terminology binding for semantic interoperability on post-genomic clinical trials," Stud. Health Technol. Informat., vol. 192, pp. 980-980, 2012.
21. L. Bos, "SNOMED-CT: The advanced terminology and coding system for eHealth," Stud. Health Technol. Informat., vol. 121, pp. 279-290, 2006.
22. R. L. Seal, S. M. Gordon, M. J. Lush, M. W. Wright, and E. A. Bruford, "Genenames.org: The HGNC resources in 2011," Nucleic Acids Res., vol. 39, suppl 1, pp. D514-D519, 2011.
23. C. J. McDonald, S. M. Huff, J. G. Suico, G. Hill, D. Leavelle, R. Aller, and P. Maloney, "LOINC, a universal standard for identifying laboratory observations: A 5-year update," Clin. Chem., vol. 49, no. 4, pp. 624-633, 2003.
24. S. Paraiso-Medina, D. Perez-Rey, R. Alonso-Calvo, B. Claerhout, K. de Schepper, P. Hennebert, J. Lhaut, J. Van Leeuwen, and A. Bucur, "Semantic interoperability solution for multicentric breast cancer trials at the integrate EU project," in Proc. Int. Conf. Health Informat., 2013, no. 1, pp. 34-41.
25. A. Bucur, J. van Leeuwen, D. Perez-Rey, R. A. Calvo, B. Claerhout, and K. de Schepper, "Identifying the semantics of eligibility criteria of clinical trials based on relevant medical ontologies," in Proc. IEEE 12th Int. Conf. Bioinformat. Bioeng., Nov. 2012, pp. 413-421.
26. The ICD-10 Classification of Mental and Behavioural Disorders: Clinical Descriptions and Diagnostic Guidelines, World Health Organization, Geneva, Switzerland, vol. 1, 1992.
27. N. Sioutos, S. D. Coronado, M. W. Haber, F. W. Hartel, W. L. Shaiu, and L. W. Wright, "NCI thesaurus: A semantic model integrating cancer-related clinical and molecular information," J. Biomed. Informat., vol. 40, no. 1, pp. 30-43, 2007.
28. N. F. Noy, N. H. Shah, P. L. Whetzel, B. Dai, M. Dorf, N. Griffith, and M. A. Musen, "BioPortal: Ontologies and integrated data resources at the click of a mouse," Nucleic Acids Res., vol. 37, suppl 2, pp. W170-W173, 2009.
29. E. H. Cheetham, R. Dolin, D. Markwell, J. Curry, D. Gabriel, R. Hausam, B. Knight, A. Rector, K. Spackman, and I. Townend, Using SNOMED CT in HL7 v3 Implementation Guide, Release 1.5, 2008.
30. TOP, Jules Bordet Institute. (Dec. 31, 2013). Topoisomerase II Alpha Gene Amplification and Protein Overexpression Predicting Efficacy of Epirubicin (TOP) [Online]. Available: http://clinicaltrials. gov/ct2/show/NCT00162812
31. A. Goldhirsch, W. C. Wood, A. S. Coates, R. D. Gelber, B. Thürlimann, and H. J. Senn, "Strategies for subtypes-Dealing with the diversity of breast cancer: Highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011," Ann. Oncol., vol. 22, no. 8, pp. 1736-1747, 2011.