OWL-based reasoning methods for validating archetypes

Journal of Biomedical Informatics

Volumn 46, Issue 2, 2013, Pages 304-317

  Menárguez Tortosa, Marcos ^a   Fernández Breis, Jesualdo Tomás ^a  

^a UNIVERSITY OF MURCIA   (Spain)

Author keywords

Archetypes; Electronic healthcare records; Ontologies; OWL

Indexed keywords

ARCHETYPES; CONCEPTUAL LEVELS; ELECTRONIC HEALTHCARE RECORDS; MODELING FRAMEWORKS; OWL; REASONING METHODS; SEMANTIC INTEROPERABILITY; SEMANTIC WEB TECHNOLOGY;

ARCHITECTURE; ERRORS; HEALTH CARE; MODELS; ONTOLOGY;

TERMINOLOGY;

ANALYTICAL ERROR; ARTICLE; CLINICAL DATA REPOSITORY; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; ELECTRONIC MEDICAL RECORD; HEALTH CARE; HEALTH PROGRAM; HUMAN; MEDICAL INFORMATICS; MEDICAL INFORMATION; MEDICAL TERMINOLOGY; NATIONAL HEALTH SERVICE; PRIORITY JOURNAL; SEMANTICS; VALIDATION PROCESS; WEB BROWSER; WEB ONTOLOGY LANGUAGE;

ELECTRONIC HEALTH RECORDS; HUMANS; MEDICAL INFORMATICS; MODELS, THEORETICAL; REPRODUCIBILITY OF RESULTS; SEMANTICS; VOCABULARY, CONTROLLED;

EID: 84875622122     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2012.11.009     Document Type: Article

References (54)

1. Beale T. Archetypes: constraint-based domain models for futureproof information systems. Eleventh OOPSLA workshop on behavioral semantics: serving the customer; 2002.
2. openEHR Foundation, OpenEHR. [accessed 10.12]. http://www.openehr.org.
3. European Committee for Standardization, Health informatics - electronic health record communication standard (ISO/EN 13606). [accessed 10.12]. http://www.iso.org/iso/.
4. HL7. [accessed 10.12]. http://www.hl7.org.
5. Coyle J, Heras Y, Oniki T, Huff S. Clinical element model. [accessed 10.12]. http://informatics.mayo.edu/sharp/images/e/e2/CEM_Reference20081114.pdf.
6. European Commission. Semantic interoperability for better health and safer healthcare. Deployment and research roadmap for europe. ISBN-13: 978-92-79-11139-6; 2009.
7. Dogac A, Namli T, Okcan A, Laleci G, Kabak Y, Eichelberg M. Key issues of technical interoperability solutions in ehealth and the ride project. Software R&D Center, Dept. of Computer Eng., Middle East Technical University, Ankara 6531; 2007.
8. Kalra D., Tapuria A., Freriks G., Mennerat F., Devlies J. Management and maintenance policies for ehr interoperability resources. Q-REC Project IST 2008, 27370.
9. Clinical Information Modeling Initiative. CIMI London meeting; 2011.http://informatics.mayo.edu/CIMI/index.php/London_2011.
10. openEHR Foundation. Archetype Definition Language 1.4 (ADL); 2008.http://www.openehr.org/releases/1.0.2/architecture/am/adl.pdf.
11. Kalra D, Tapuria A. The EHR and clinical archetypes: time for clinical engagement. eHealth planning and management symposium; 2008.
12. Kalra D., Tapuria A., Austin T., De Moor G. Quality requirements for EHR archetypes. Stud Health Technol Inform 2012, 48-52.
13. Maldonado J.A., Moner D., Boscá D., Fernández-Breis J.T., Angulo C., Robles M. Linkehr-ed: a multi-reference model archetype editor based on formal semantics. Int J Med Inform 2009, 78:559-570.
14. Schulz S., Schober D., Daniel C., Jaulent M.-C. Bridging the semantics gap between terminologies, ontologies, and information models. Stud Health Technol Inform 2010, 160:1000-1004.
15. Marti{dotless}́nez-Costa C., Menárguez-Tortosa M., Fernández-Breis J. A model-driven approach for representing clinical archetypes for Semantic Web environments. J Biomed Inform 2009, 42(1):150-164.
16. Marti{dotless}́nez-Costa C., Menárguez-Tortosa M., Fernández-Breis J.T. An approach for the semantic interoperability of ISO EN 13606 and OpenEHR archetypes. J Biomed Inform 2010, 43:736-746.
17. Marti{dotless}́nez-Costa C., Menárguez-Tortosa M., Fernández-Breis J. Clinical data interoperability based on archetype transformation. J Biomed Inform 2011, 44:869-880.
18. Kilic O, Bicer V, Dogac A. Mapping archetypes to OWL. Technical Report. Software Research and Development Center, Middle East Technical University, Turkey; 2005.
19. Lezcano L., Sicilia M.-A., Rodri{dotless}́guez-Solano C. Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. J Biomed Inform 2011, 44:343-353.
20. Baader F., Horrocks I., Sattler U. Description logics as ontology languages for the semantic web. Mech Math Reason 2005, 228-248.
21. Rector A., Qamar R., Marley T. Binding ontologies and coding systems to electronic health records and messages. Appl Ontol 2009, 4:51-69.
22. Object Management Group. Ontology definition metamodel.[accessed 10.12]. http://www.omg.org/docs/formal/09-05-01.pdf.
23. Oemig F., Blobel B. An ontology architecture for HL7 v3: pitfalls and outcomes. World congress on medical physics and biomedical engineering 2009, 408-410. Springer, Munich, Germany.
24. Iqbal A. An OWL-DL ontology for the HL7 reference information model. Toward Useful Services for Elderly and People with Disabilities 2011, 168-175.
25. Heymans S., McKennirey M., Phillips J. Semantic validation of the use of SNOMED CT in HL7 clinical documents. J Biomed Semantics 2011, 2:2.
26. Tao C, Parker C, Oniki T, Pathak J, Huff S, Chute C. An OWL meta-ontology for representing the Clinical Element Model. In: AMIA annual symposium proceedings, vol. 2011. American Medical Informatics Association; 2011. p. 1372.
27. Sahay R., Fox R., Zimmermann A., Polleres A., Hauswrith M. A methodological approach for ontologising and aligning health level seven (HL7) applications, availability, reliability and security for business. Enterprise Health Inform Syst 2011, 102-117.
28. OpenEHR, OpenEHR clinical knowledge manager. <> [accessed 10.12]. http://www.openehr.org/knowledge/.
29. NHS connecting for health. Archetype repository from NHS connection for health. <> [accessed 10.12]. http://https://svn.connectingforhealth.nhs.uk/svn/public/nhscontentmodels/TRUNK/cm/archetypes/.
30. openEHR Foundation. Archetype definition and principles; 2007.http://www.openehr.org/releases/1.0.2/architecture/am/archetype_principles.pdf.
31. IHTSDO, SNOMED-CT. <> [accessd 10.12]. http://www.ihtsdo.org/snomed-ct/.
32. McDonald C., Huff S., Suico J., Hill G., Leavelle D., Aller R., et al. a universal standard for identifying laboratory observations: a 5-year update. Clin Chem 2003, 49:624-633.
33. openEHR foundation. OpenEHR specifications. [accessed 10.12]. http://www.openehr.org/releases/1.0.2.
34. W3C, OWL web ontology language. <> [accessed 10.12]. http://www.w3.org/TR/owl-ref/.
35. Tsarkov D., Horrocks I. Fact++ description logic reasoner: system description. Autom Reason 2006, 292-297.
36. Shearer R, Motik B, Horrocks I. HermiT: a highly-efficient OWL reasoner. In: Proceedings of the 5th international workshop on OWL: experiences and directions (OWLED 2008); 2008. p. 26-7.
37. Sirin E., Parsia B., Grau B., Kalyanpur A., Katz Y. Pellet: a practical OWL-DL reasoner. Web Semantics: science, services and agents on the World Wide Web 2007, 5:51-53.
38. openEHR foundation. EHR information model; 2008.http://www.openehr.org/releases/1.0.2/architecture/rm/ehr_im.pdf.
39. W3C, OWL web ontology language manchester syntax. [accessed 10.12]. http://www.w3.org/TR/owl2-manchester-syntax/.
40. Rector A., Brandt S., Drummond N., Horridge M., Pulestin C., Stevens R. Engineering use cases for modular development of ontologies in OWL. Appl Ontol 2012, 7:113-132.
41. openEHR foundation. openEHR archetype profile. [accessed 10.12]. http://www.openehr.org/releases/1.0.1/architecture/am/openehr_archetype_profile.pdf.
42. Chen R., Klein G. The openEHR Java reference implementation project. Stud Health Technol Inform 2007, 129:58-62.
43. Horridge M, Bechhofer S. The OWL API: a Java API for working with OWL 2 ontologies. In: Proc. of OWL experiences and directions; 2009.
44. National E-Health transitition authority. NEHTA clinical knowledge manager. [accessed 10.12]. http://dcm.nehta.org.au/ckm/.
45. Menárguez-Tortosa M., Fernández-Breis J.T. Validation of the openEHR archetype library by using OWL reasoning. Stud Health Technol Inform 2011, 169:789-793.
46. Kazakov Y, Krötzsch M, Simanči{dotless}́k F. ELK: a reasoner for OWL EL ontologies. Technical Report, Tech. rep., University of Oxford; 2012.
47. Coenen A., Kim T.Y. Development of terminology subsets using ICNP®. Int J Med Inform 2010, 79:530-538.
48. Lee D., Cornet R., Lau F. Implications of SNOMED CT versioning. Int J Med Inform 2011, 80:442-453.
49. Matney S.A., Warren J.J., Evans J.L., Kim T.Y., Coenen A., Auld V.A. Development of the nursing problem list subset of SNOMED CT. J Biomed Inform 2012, 45:683-688.
50. SemanticHealthNet. Semantic interoperability for health network.[accessed 10.12]. http://www.semantichealthnet.eu/.
51. Clinical information modeling initiative. CIMI wiki. [accessed 10.12]. http://informatics.mayo.edu/CIMI/index.php/Main_Page.
52. Drummond N, Rector A, Stevens R, Moulton G, Horridge M, Wang H, et al. Putting OWL in order: patterns for sequences in OWL. In: Proc. 2nd workshop on OWL: experiences and directions; 2006.
53. Horridge M., Parsia B., Sattler U. Laconic and precise justifications in OWL. Lecture notes in computer science 2008, vol. 5318:323-338. Springer. A.P. Sheth, S. Staab, M. Dean, M. Paolucci, D. Maynard, T.W. Finin (Eds.).
54. Legaz-Garci{dotless}́a MC, Marti{dotless}́nez-Costa C, Menárguez-Tortosa M, Fernández-Breis JT. Exploitation of ontologies for the management of clinical archetypes in ArchMS. In: Third international conference on biomedical ontology; 2012.