A unified structural/terminological interoperability framework based on lexEVS: Application to TRANSFoRm

Journal of the American Medical Informatics Association

Volumn 20, Issue 5, 2013, Pages 986-994

  Ethier, Jean François ^a   Dameron, Olivier ^a   Curcin, Vasa ^b   McGilchrist, Mark M ^c   Verheij, Robert A ^d   Arvanitis, Theodoros N ^e   Taweel, Adel ^f   Delaney, Brendan C ^f   Burgun, Anita ^a  

^a UNIVERSITÉ DE RENNES 1   (France)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

^d NETHERLANDS INSTITUTE FOR HEALTH SERVICES RESEARCH   (Netherlands)

^e UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^f KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLINICAL RESEARCH; DATA BASE; EVALUATION; INFORMATION RETRIEVAL; MEDICAL INFORMATICS; NOMENCLATURE; PRIMARY MEDICAL CARE;

INTEROPERABILITY; LEXEVS; ONTOLOGY; SEMANTICS; TERMINOLOGY; TRANSLATIONAL MEDICAL RESEARCH;

BIOMEDICAL RESEARCH; DATABASES AS TOPIC; SOFTWARE; SYSTEMS INTEGRATION; TERMINOLOGY AS TOPIC;

EID: 84882790566     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1136/amiajnl-2012-001312     Document Type: Article

References (75)

1. Cimino J J. Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inf Med 1998;37:394-403.
2. Cimino JJ. In defense of the Desiderata. J Biomed Inform 2006;39:299-306.
3. Sujansky W. Heterogeneous database integration in biomedicine. J Biomed Inform 2001;34:285-98.
4. Rector AL, Qamar R, Marley T. Binding ontologies and coding systems to electronic health records and messages. Appl Ontol 2009;4:51-69.
5. Eichelberg M, Aden T, Riesmeier J, et al. A survey and analysis of electronic healthcare record standards. ACM Comput Surv 2005;37:277-315.
6. Haux R, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2006. Methods Inf Med 2006;45(Suppl 1):S136-44.
7. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008;47(Suppl 1):67-79.
8. Rector AL. Clinical terminology: why is it so hard?. Methods Inf Med 1999;38:239-52.
9. Qamar R, Kola JS, Rector AL. Unambiguous data modeling to ensure higher accuracy term binding to clinical terminologies. AMIA Annu Symp Proc 2007;2007:608-13.
10. Delaney B. TRANSFoRm: translational medicine and patient safety in Europe. In: Grossman C, Powers B, McGinnis JM, eds. Digital infrastructure for the learning health system: the foundation for continuous improvement in health and health care: workshop series summary. Washington, DC: National Academies Press, 2011: 198-202.
11. TRANSFoRm Project. http://www.transformproject.eu (accessed 11 Apr 2012).
12. Beale T, Heard S, Kalra D, et al. The openEHR reference model-EHR information model-Release 1.0.2. http://www.openehr.org/releases/1.0.2 (accessed 29 Jun 2012)
13. Murphy SN, Mendis M, Hackett K, et al. Architecture of the open-source clinical research chart from informatics for integrating biology and the bedside. AMIA Annu Symp Proc 2007;2007:548-52.
14. Schadow G, Mead CN, Walker DM. The HL7 reference information model under scrutiny. Stud Health Technol Inform 2006;124:151-6.
15. CDASH-Basic Recommended Data Collection Fields for Medical Research. http://www.cdisc.org/cdash (accessed 8 Dec 2012).
16. Clinical Information Modelling Initiative. http://www.openehr.org/326-OE.html?branch=1&language=1 (accessed 8 Dec 2012).
17. Fridsma DB, Evans J, Hastak S, et al. The BRIDG Project: a technical report. J Am Med Inform Assoc 2008;15:130-7.
18. Weber GM, Murphy SN, McMurry AJ, et al. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc 2009;16:624-30.
19. Murphy SN, Weber G, Mendis M, et al. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc 2010;17:124-30.
20. Szalma S, Koka V, Khasanova T, et al. Effective knowledge management in translational medicine. J Transl Med 2010;8:68.
21. Lowe HJ, Ferris TA, Hernandez PM, et al. STRIDE-an integrated standards-based translational research informatics platform. AMIA Annu Symp Proc 2009;2009:391-5.
22. Avillach P, Dufour J-C, Diallo G, et al. Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. J Am Med Inform Assoc 2013;20:446-52.
23. Delaney BC, Peterson KA, Speedie S, et al. Envisioning a learning health care system: the electronic primary care research network, a case study. Ann Fam Med 2012;10:54-9.
24. Peterson KA, Fontaine P, Speedie S. The electronic primary care Research Network (ePCRN): a new era in practice-based research. J Am Board Fam Med 2006;19:93-7.
25. Wiederhold G. Mediators in the architecture of future information systems. Comput J 1992;25:38-49.
26. Martin L, Anguita A, Graf N, et al. ACGT: advancing clinico-genomic trials on cancer-four years of experience. Stud Health Technol Inform 2011;169:734-8.
27. Gupta A, Ludascher B, Martone ME. Knowledge-based integration of neuroscience data sources. In: Scientific and Statistical Database Management, 2000. Proceedings. 12th International Conference, 2000: 39-52.
28. Astakhov V, Gupta A, Grethe JS, et al. Semantically based data integration environment for biomedical research. In: Proc of the 19th IEEE Symp Comput Based Med Syst; 22-23 June 2006, Washington, DC: IEEE Computer Society, 2006:171-6.
29. Ashish N, Ambite JL, Muslea M, et al. Neuroscience data integration through mediation: an (F)BIRN case study. Front Neuroinform 2010;4:118.
30. Stanford J, Mikula R. A model for online collaborative cancer research: report of the NCI caBIG project. Int J Healthc Technol Manag 2008;9:231-46.
31. González-Beltrán A, Tagger B, Finkelstein A. Federated ontology-based queries over cancer data. BMC Bioinformatics 2011;13(Suppl. 1):S9.
32. Saltz J, Oster S, Hastings S, et al. caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics 2006;22:1910-16.
33. Livne O, Schultz N, Narus S. Federated querying architecture with clinical & translational health IT application. J Med Syst 2011;35:1211-24.
34. Ouagne D, Hussain S, Sadou E, et al. The Electronic Healthcare Record for Clinical Research (EHR4CR) information model and terminology. Stud Health Technol Inform 2012;180:534-8.
35. Core Ontology-SHRINE. https://open.med.harvard.edu/display/SHRINE/Core+Ontology (accessed 18 Apr 2012).
36. Bug W, Ascoli G, Grethe J, et al. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 2008;6:175-94.
37. D3.5.2_Appendix_E_Ontology_Specifications_01.pdf. http://www.epsos.eu/uploads/tx_epsosfileshare/D3.5.2_Appendix_E_Ontology_Specifications_01.pdf (accessed 8 Dec 2012).
38. epSOS: About epSOS. http://www.epsos.eu/home/about-epsos.html (accessed 11 Apr 2012).
39. Matney S, Bradshaw R, Livne O, et al. Developing a semantic framework for clinical and translational research. In: AMIA Summit on Translational Bioinformatics; 7-9 March 2011, Bethesda, MD: AMIA, 2011:24.
40. Segagni D, Tibollo V, Dagliati A, et al. An ICT infrastructure to integrate clinical and molecular data in oncology research. BMC Bioinformatics 2012;13(Suppl. 4):S5.
41. NCI Thesaurus Browser. https://cabig-stage.nci.nih.gov/community/tools/NCI_Thesaurus (accessed 8 Dec 2012).
42. LexEVS 6.0 Architecture. https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_6.0_Architecture (accessed 30 May 2011).
43. Noy NF, Shah NH, Whetzel PL, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009;37(web server issue): W170-3.
44. Pathak J, Solbrig HR, Buntrock JD, et al. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime. J Am Med Inform Assoc 2009;16:305-15.
45. CTS2. http://informatics.mayo.edu/cts2/index.php/Main_Page (accessed 14 Jun 2011).
46. LexEVS 6.0 CTS2 Guide-EVS-LexEVS-National Cancer Institute-Confluence Wiki. https://wiki.nci.nih.gov/display/LexEVS/LexEVS+6.0+CTS2+Guide (accessed 2 Jul 2012).
47. caDSR and ISO 11179-caDSR-National Cancer Institute-Confluence Wiki. https://wiki.nci.nih.gov/display/caDSR/caDSR+and+ISO+11179 (accessed 8 Dec 2012).
48. Warzel DB, Andonyadis C, McCurry B, et al. Common Data Element (CDE) management and deployment in clinical trials. AMIA Annu Symp Proc 2003;2003:1048.
49. Terminfo Project-Overview. http://www.hl7.org/Special/committees/terminfo/overview.cfm (accessed 9 Dec 2012).
50. NIVEL|LINH. http://www.nivel.nl/en/netherlands-information-network-generalpractice-jlinh (accessed 28 Jul 2012).
51. NIVEL|Netherlands institute for health services research. http://www.nivel.nl/en (accessed 11 Apr 2012).
52. Clinical Practice Research Datalink-CPRD. http://www.cprd.com/intro.asp (accessed 28 Jul 2012).
53. Medicines and Healthcare products Regulatory Agency. http://www.mhra.gov.uk/#page=DynamicListMedicines (accessed 28 Jul 2012).
54. Lenzerini M. Data integration: a theoretical perspective. In: Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems; 3-6 June 2002, New York, NY: ACM, 2002:233-46.
55. Smith B, Ceusters W. Ontological realism: a methodology for coordinated evolution of scientific ontologies. Appl Ontol 2010;5:139-88.
56. Grenon P, Smith B. SNAP and SPAN: Towards dynamic spatial ontology. Spat Cogn Comput 2004;4:69-104.
57. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 2004;32(database issue):D267-70.
58. Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. AMIA Summit on Translational Bioinformatics 2009;2009: 116-20.
59. Goldfain A, Smith B, Arabandi S, et al. Vital sign ontology. In: Proceedings of the Workshop on Bio-Ontologies, Vienna, ISMB, 2011:71-4.
60. information-artifact-ontology-The Information Artifact Ontology (IAO) is an ontology of information entities based on the BFO-Google Project Hosting. http://code.google.com/p/information-artifact-ontology/(accessed 9 Dec 2012).
61. Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics 2010;1(Suppl. 1):S7.
62. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
63. Luciano JS, Andersson B, Batchelor C, et al. The translational medicine ontology and knowledge base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2011;2(Suppl. 2):S1.
64. Leysen P, Bastiaens H, Van Royen P. TRANSFoRm : development of use cases. http://transformproject.eu/Deliverable_List_files/D1.1%20Detailed%20Use%20Cases_V2.1-2.pdf (accessed 28 Feb 2013).
65. Qamar R, Rector A. Semantic issues in integrating data from different models to achieve data interoperability. Stud Health Technol Inform 2007;129:674-8.
66. Park J, Ram S. Information systems interoperability: what lies beneath?. ACM Transactions on Information Systems 2004;22:595-632.
67. Pathak J, Wang J, Kashyap S, et al. Mapping clinical phenotype data elements to standardized metadata repositories and controlled sterminologies: the eMERGE network experience. J Am Med Inform Assoc 2011;18:376-86.
68. Shvaiko P, Euzenat J. Ontology matching: state of the art and future challenges. IEEE Trans Knowl Data Eng 2013;25:158-76.
69. Choi N, Song I-Y, Han H. A survey on ontology mapping. ACM SIGMOD Rec 2006;35:34-41.
70. Shvaiko P, Euzenat J. A survey of schema-based matching approaches. In: Spaccapietra S (ed) Journal on data semantics IV. Berlin/Heidelberg: Springer, 2005: 146-71.
71. CTS2-HL7Wiki. http://wiki.hl7.org/index.php?title=CTS2 (accessed 28 Jul 2012).
72. Cimino JJ, Clayton PD, Hripcsak G, et al. Knowledge-based approaches to the maintenance of a large controlled medical terminology. J Am Med Inform Assoc 1994;1:35-50.
73. Cimino JJ. Terminology tools: state of the art and practical lessons. Methods Inf Med 2001;40:298-306.
74. Miller GC, Britt H. A new drug classification for computer systems: the ATC extension code. Int J Biomed Comput 1995;40:121-4.
75. BNF.org. http://www.bnf.org/bnf/index.htm (accessed 10 Dec 2012). 994