A model-driven approach for representing clinical archetypes for Semantic Web environments

Journal of Biomedical Informatics

Volumn 42, Issue 1, 2009, Pages 150-164

  Martínez Costa, Catalina ^a   Menárguez Tortosa, Marcos ^a   Fernández Breis, Jesualdo Tomás ^a   Maldonado, José Alberto ^b  

^a UNIVERSITY OF MURCIA   (Spain)

^b UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

Author keywords

Archetypes; Biomedical informatics; Electronic Healthcare Records; Model driven Engineering; Ontology; Semantic Web

Indexed keywords

ARCHETYPES; BIOMEDICAL INFORMATICS; CLINICAL ARCHETYPES; CLINICAL INFORMATIONS; ELECTRONIC HEALTH RECORDS; ELECTRONIC HEALTHCARE RECORDS; HETEROGENEOUS SYSTEMS; MODEL-DRIVEN APPROACHES; MODEL-DRIVEN ENGINEERING; ONTOLOGY WEB LANGUAGES; SEMANTIC WEB TECHNOLOGIES; WEB ENVIRONMENTS;

BIOINFORMATICS; FOURIER TRANSFORMS; INFORMATION THEORY; LINGUISTICS; ONTOLOGY; RECORDS MANAGEMENT; SEMANTICS; SYSTEMS ANALYSIS;

SEMANTIC WEB;

ARTICLE; COMPUTER PROGRAM; ELECTRONIC MEDICAL RECORD; INFORMATION TECHNOLOGY; MEDICAL DECISION MAKING; MEDICAL INFORMATION SYSTEM; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; HUMANS; MEDICAL INFORMATICS; MEDICAL RECORDS SYSTEMS, COMPUTERIZED; PROGRAMMING LANGUAGES; SEMANTICS; SYSTEMS INTEGRATION; VOCABULARY, CONTROLLED;

EID: 60049087516     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.05.005     Document Type: Article

References (62)

1. Ashburner M.C.A., Ball J.A., Blake D., Botstein H., Butler J.M., Cherry A.P., et al. Gene ontology: tool for the unification of biology. Nature Genetics 25 (2000) 25-29
2. Beale T. Archetypes, Constraint-based Domain Models for Future-proof Information Systems. Available from: http://www.deepthought.com.au/it/archetypes/archetypes.pdf; 2001.
3. Berners-Lee T, Hendler J, Lassila O. The Semantic Web. The Scientific American; May 2001.
4. Blobel B.G. Advanced EHR architectures-promises or reality. Methods of Information in Medicine 45 1 (2006) 95-101
5. Boxwala A.A., Peleg M., Tu S., Ogunyemi O., Zeng Q.T., Wang D., et al. GLIF3: a representation format for shareable computer-interpretable clinical practice guidelines. Journal of Biomedical Informatics 37 (2004) 147-161
6. Brewster C., O'Hara K., Fuller S., Wilks Y., Franconi E., Musen M.A., et al. Knowledge representation with ontologies: the present and future. IEEE Intelligent Systems 19 1 (2004) 72-81
7. Della Valle E., Cerizza D., Celino I., Estublier J., Vega G., Kerrigan M., et al. SEEMP: a semantic interoperability infrastructure for e-government services in the employment sector. Lecture Notes in Computer Science 4519 (2007) 220-234
8. Dogac A., Laleci G., Kirbas S., Kabak Y., Sinir S., Yildiz A., et al. Artemis: deploying semantically enriched web services in the healthcare domain. Information Systems Journal 31 4-5 (2006) 321-339
9. Eichelberg M, Aden T, Riesmeier J, Dogac A, Laleci GB. Electronic health record standards-a brief overview. In: 4th international conference on information and communications technology, Cairo, Egypt; December 2006.
10. Euzenat J., and Shvaiko P. Ontology matching (2007), Springer-Verlag, Berlin Heidelberg
11. Fernández-Breis J.T., and Martínez-Béjar R. A cooperative framework for integrating ontologies. International Journal of Human-Computer Studies 56 6 (2002) 662-717
12. Garde S., Knaup P., Hovenga E.J.S., and Heard S. Towards semantic interoperability for electronic health records. Methods of Information in Medicine 46 2 (2007) 332-343
13. Gasevic D, Djuric D, Devedzic V, Damjanovic V. Approaching OWL and MDA through technological spaces, Third Workshop in Software Model Engineering-WiSME2004; 2004.
14. In: Gonçalves R.J., Müller J.P., Mertins K., and Zelm M. (Eds). Enterprise interoperability II: new challenges and approaches (2007), Springer
15. Gruber T.R. A translation approach to portable ontology specifications. Knowledge Acquisition 5 (1993) 199-220
16. Kilic O, Bicer V, Dogac A. Mapping Archetypes to OWL. Technical Report; 2005.
17. Kurtev I, Bézivin J, Aksit M. Technological Spaces: an Initial Appraisal, CoopIS, DOA'2002.
18. Linthicum D. Leveraging Ontologies: The Intersection of Data Integration and Business Intelligence Part I. DMR Review Magazine; June 2004.
19. Moner D, Maldonado JA, Bosca D, Fernández-Breis JT, Angulo C, Crespo P, et al. Archetype-based semantic integration and standardization of clinical data. In: 28th annual international conference ieee engineering in medicine and biology, New York: EEUU; 2006.
20. Nardon F.B., and Moura L.A. Knowledge sharing and information integration in healthcare using ontologies and deductive databases. Medinfo 11 Pt. 1 (2004) 62-66
21. Object Management Group: MOF QVT Final Adopted Specification. Available from: http://www.omg.org/docs/ptc/05-11-01.pdf; 2005.
22. OMG, Meta Object Facility (MOF) 2.0 Core Specification, OMG Document formal/2006-01-01. Available from: http://www.omg.org/cgi-bin/doc?formal/2006-01-01; 2006.
23. Ontology Metamodel Definition Specification. OMG Documentformal/2006-05-01. Available from: http://www.omg.org/cgi-bin/doc?ad/2006-05-01.pdf; 2006.
24. Partridge C. The Role of Ontology in Semantic Integration; 2002.
25. Paterson GI. Semantic Interoperability for Decision Support Using Case Formalism and Controlled Vocabulary. Health'04; 2004.
26. Rector A.L. Clinical terminology: why is it so hard?. Methods of Information in Medicine 6 (1999) 245-251
27. Rector A.L., Bechhofer S., Goble C.A., Horrocks I., Nowlan W.A., and Solomon W.D. The GRAIL concept modelling language for medical terminology. Artificial Intelligence in Medicine 9 2 (1997) 139-171
28. Resnik P. Semantic similarity in a taxonomy: an information based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 11 (1999) 95-130
29. Rodríguez M.A., and Egenhofer M.J. Determining semantic similarity among entity classes from different ontologies. IEEE Transactions on Knowledge and Data Engineering 15 2 (2003) 442-456
30. Rose JS, Fisch BJ, Hogan WR, Levy B, Marshal P, Thomas DR, et al. Common medical terminology comes of age, Part One: standard language improves healthcare quality. Journal of Healthcare Information Management 2001(Fall);15(3):307-318.
31. Sánchez-Cuadrado J, García-Molina J, Menárguez-Tortosa M. RubyTL: A Practical, Extensible Transformation Language. ECMDA-FA. Available from: http://rubytl.rubyforge.org/; 2006.
32. Schulz S., and Hahn U. Part-whole representation and reasoning in formal biomedical ontologies. Artificial Intelligence in Medicine 34 3 (2005) 179-200
33. Semantic Health. Semantic Health Final Report. Available from: http://www.semantichealth.org/DELIVERABLES/SemanticHEALTH_D1_1_finalC.pdf; 2006.
34. Semantic Interoperability Community of Practice. White Paper Series Module 1: Introducing Semantic Technologies and the Vision of the Semantic Web; 2005.
35. Smith B., and Ceusters W. An ontology-based methodology for the migration of biomedical terminologies to electronic health records. AMIA Annual Symposium Proceedings (2005) 704-708
36. Smith B. From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies. Journal of Biomedical Informatics 39 3 (2006) 288-298
37. Stuckenschmidt H., Wache H., Visser U., and Schuster G. Methodologies for ontology-based semantic translation. ECIMF (2001)
38. Van Heijst G., Schreiber A.T., and Wielinga B.J. Using explicit ontologies in KBS development. International Journal of Human-Computer Studies 45 (1997) 183-292
39. Available from: http://colab.cim3.net/cgi-bin/wiki.pl?SICoP.
40. Available from: http://jena.sourceforge.net/.
41. Available from: http://obo.sourceforge.net.
42. Available from: http://ontolog.cim3.net/.
43. Available from: http://owl.man.ac.uk/factplusplus/.
44. Available from: http://pellet.owldl.com/.
45. Available from: http://protege.stanford.edu/.
46. Available from: http://svn.openehr.org/ref_impl_java/TRUNK/project_page.htm.
47. Available from: http://trajano.us.es/~isabel/.
48. Available from: http://www.centc251.org.
49. Available from: http://www.eclipse.org/emf/.
50. Available from: http://www.eclipse.org/gmt/mofscript/.
51. Available from: http://www.eclipse.org/gmt/oaw.
52. Available from: http://www.eclipse.org/gmt/tcs/.
53. Available from: http://www.hl7.org.
54. Available from: http://www.medicomp.com.
55. Available from: http://www.nlm.nih.gov/research/umls/.
56. Available from: http://www.omg.org.
57. Available from: http://www.openehr.org.
58. Available from: http://www.opengalen.org/.
59. Available from: http://www.regenstrief.org/medinformatics/loinc/.
60. Available from: http://www.snomed.org/.
61. Available from: http://www.w3.org/TR/owl-ref/.
62. Available from: http://www.webont.org/owl/1.1/.