Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules

Journal of Biomedical Informatics

Volumn 44, Issue 2, 2011, Pages 343-353

  Lezcano, Leonardo ^a   Sicilia, Miguel Angel ^a   Rodríguez Solano, Carlos ^a  

^a UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

Clinical archetypes; Electronic healthcare record; Ontologies; OWL; Semantic interoperability; SWRL

Indexed keywords

CLINICAL ARCHETYPES; ELECTRONIC HEALTHCARE RECORD; OWL; SEMANTIC INTEROPERABILITY; SWRL;

DATA STRUCTURES; HEALTH CARE; INTEROPERABILITY; QUERY LANGUAGES; RECORDS MANAGEMENT; SEMANTIC WEB; SEMANTICS; TRANSLATION (LANGUAGES); WORK SIMPLIFICATION;

ONTOLOGY;

ANTIBIOTIC THERAPY; ARCHETYPE DEFINITION LANGUAGE; ARTICLE; BIOINFORMATICS; CLINICAL DATA REPOSITORY; CLINICAL PRACTICE; ELECTRONIC DATA INTERCHANGE; INFORMATION SCIENCE; INTERDISCIPLINARY COMMUNICATION; INTERNATIONAL COOPERATION; INTERNET; MEDICAL INFORMATICS; ONTOLOGY WEB LANGUAGE; PATIENT SAFETY; PRESCRIPTION; PRIORITY JOURNAL; SEMANTIC INTEROPERABILITY; SEMANTIC WEB RULE LANGUAGE; SEMANTICS; SYSTEMATIZED NOMENCLATURE OF MEDICINE; THINKING;

DATABASES, FACTUAL; ELECTRONIC HEALTH RECORDS; MEDICAL ORDER ENTRY SYSTEMS; PROGRAMMING LANGUAGES; SEMANTICS;

EID: 79952748773     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2010.11.005     Document Type: Article

References (37)

1. Stroetmann VN, Kalra D, Lewalle P, Rodrigues JM, Stroetmann KA, Surjan G, et al. Semantic interoperability for better health and safer healthcare. Project report. European Commission, Luxembourg: Office for Official Publications of the European Communities; 2009.
2. Beale T. Archetypes, constraint-based domain models for future-proof information systems. In: Proceedings of the OOPSLA 2002 conference, Northeastern University, Boston, Seattle, Washington, USA; 2002. p. 16-32.
3. Gruber T.R., Gruber T.R. A translation approach to portable ontology specifications. Knowl Acquis 1993, 5:199-220.
4. Rosse C., Mejino J.L.V. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 2003, 36(6):478-500.
5. Golbreich C., Zhang S., Bodenreider O. Science, services and agents on the world wide web: the foundational model of anatomy in OWL: experience and perspectives. Web Semantics 2006, 4(3):181-195.
6. Rector AL, Rogers JE. Ontological & practical issues in using a description logic to represent medical concepts: experience from GALEN, Tech rep CSPP-35:1-35, School of Computer Science PrePrint, University of Manchester; December 2005.
7. Sicilia J.-J., Sicilia M.-A., Sánchez-Alonso S., García-Barriocanal E., Pontikaki M. Knowledge representation issues in ontology-based clinical knowledge management systems. Int J Technol Manage 2009, 47(1-3):191-206.
8. Argüello M., Des J.J. Clinical practice guidelines: a case study of combining OWL-S, OWL, and SWRL. Knowl-Based Syst 2008, 21(3):247-255.
9. Djedidi R, Aufaure M. Medical domain ontology construction approach: a basis for medical decision support. In: Computer-based medical systems (CBMS'07); 2007. p. 509-11.
10. Lezcano L, Sicilia MA. Serrano-Balazote P. Combining OpenEHR archetype definitions with SWRL rules-a translation approach. In: Emerging technologies and information systems for the knowledge society; 2008. p. 79-87. http://dx.doi.org/10.1007/978-3-540-87781-3_9.
11. Schloeffel P., Beale T., Hayworth G., Heard S., Leslie H. The relationship between CEN 13606, HL7, and openEHR. Proc HIC 2006 bridging the digital divide: clinician, consumer and computer 2006, Seattle, Washington, USA.
12. O'Connor M, Knublauch H, Tu S, Grosof B, Dean M, Grosso W, et al. Supporting rule system interoperability on the semantic web with SWRL. In: The semantic web ISWC 2005; 2005. p. 974-86. http://dx.doi.org/10.1007/11574620_69.
13. Baader F., Calvanese D., McGuinness D., Nardi D., Patel-Schneider P. The description logic handbook: theory, implementation, and applications 2003, Cambridge University Press, New York (NY).
14. Sánchez-Macián A, Pastor E, de López Vergara J, López D. Extending SWRL to enhance mathematical support. In: Web reasoning and rule systems; 2007. p. 358-60. http://dx.doi.org/10.1007/978-3-540-72982-2_30.
15. Schulz S., Suntisrivaraporn B., Baader F., Boeker M. SNOMED reaching its adolescence: ontologists and logicians health check. Int J Med Inform 2009, 78:S86-S94.
16. Jiang G., Chute C.G. Auditing the semantic completeness of SNOMED CT using formal concept analysis. J Am Med Inform Assoc 2009, 16(1):89-102.
17. Rector A, Brandt S. Why do it the hard way? The case for an expressive description logic for SNOMED. J Am Med Inform Assoc 2008;15(6);744-51. http://jamia.bmj.com/content/15/6/744.abstract.
18. Spackman KA. An examination of owl and the requirements of a large health care terminology. In: OWLED; 2007.
19. Wroe C. Is semantic web technology ready for healthcare? In: 3rd European semantic web conference (ESWC'06), Budva, Montenegro; 2006. http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-194/paper2.pdf.
20. Martínez-Costa C., Menárguez-Tortosa M., Fernández-Breis J.T., Maldonado J.A. A model-driven approach for representing clinical archetypes for semantic web environments. J Biomed Inform 2009, 42(1):150-164.
21. Kilic O, Bicer V, Dogac A. Mapping archetypes to OWL. Technical report; 2005.
22. Bicer V., Kilic O., Dogac A., Laleci G.B. Archetype-based semantic interoperability of web service messages in the health care domain. Int J Semantic Web Inform Syst 2005, 1(4):1-23.
23. Pan JZ, Horrocks I. OWL-Eu: adding customised datatypes into OWL. In: The semantic web: research and applications; 2005. p. 153-66. http://dx.doi.org/10.1007/11431053_11.
24. Chen C, Chen K, Hsu C, Li Y. Developing guideline-based decision support systems using protégé and jess. Comput Method Program Biomed. doi:10.1016/j.cmpb.2010.05.010.
25. Rector A., Qamar R., Marley T. Binding ontologies and coding systems to electronic health records and messages. Appl Ontol 2009, 4(1):51-69.
26. Cormen T.H., Leiserson C.E., Rivest R.L., Stein C. Introduction to algorithms 1990, McGraw-Hill Companies.
27. Román I., Roa L.M., Reina-Tosina J., Madinabeitia G. Demographic management in a federated healthcare environment. Int J Med Inform 2006, 75(9):671-682.
28. Horridge M. A practical guide to building OWL ontologies using Protégé 4 and CO-ODE tools, The University Of Manchester; 2009. http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/resources/ProtegeOWLTutorialP4_v1_2.pdf.
29. Knublauch H. User-defined datatypes in protégé-owl; 2005. http://protege.stanford.edu/plugins/owl/xsp.html.
30. Rector A, Schreiber G. Qualified cardinality restrictions: constraining the number of values of a particular type for a property; 2005. http://www.w3.org/2001/sw/BestPractices/OEP/QCR/.
31. Horrocks I., Patel-schneider P.F., Bechhofer S., Tsarkov D. OWL rules: a proposal and prototype implementation. J Web Semantics 2005, 3:23-40.
32. Lezcano L, Sánchez-Alonso S, Sicilia MA. Associating clinical archetypes through UMLS metathesaurus term clusters. J Med Syst 2010. http://dx.doi.org/10.1007/s10916-010-9586-9.
33. Lezcano L. A model for integrating disease and diagnosis semantics in clinical archetypes. In: Signs, symptoms and findings: towards an ontology for clinical phenotypes (SSFW09), Milan, Italy; 2009. http://bimib.disco.unimib.it/index.php/SSFW09_Presentations.
34. Tzitzikas YT. Collaborative ontology-based information indexing and retrieval, PhD thesis, Department of Computer Science, University of Crete; September 2002.
35. Kalra D. Terminologies and EHR systems. In: Toward semantic interoperability of EHR systems: a joint effort for Europe. Expert Workshop, Brussels; 2008.
36. Rector A, Johnson P, Tu S, Wroe C, Rogers J. Interface of inference models with concept and medical record models. In: Artificial intelligence in medicine; 2001. p. 314-23. http://dx.doi.org/10.1007/3-540-48229-6_43.
37. Qamar R., Kola J., Rector A. Unambiguous data modeling to ensure higher accuracy term binding to clinical terminologies. AMIA Ann Symp Proc 2007, 2007:608-613. [PMC2655827].