KnowBaSICS-M: An ontology-based system for semantic management of medical problems and computerised algorithmic solutions

Computer Methods and Programs in Biomedicine

Volumn 88, Issue 1, 2007, Pages 39-51

  Bratsas, Charalampos ^a   Koutkias, Vassilis ^a   Kaimakamis, Evangelos ^a   Bamidis, Panagiotis D ^a   Pangalos, George ^b   Maglaveras, Nicos ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b Faculty of Technology   (Greece)

Author keywords

Knowledge based system; Medical Computational Problems; Ontology based information retrieval; Semantic Description; UMLS; VSM based Semantic Similarity

Indexed keywords

INFORMATION MANAGEMENT; INFORMATION RETRIEVAL; KNOWLEDGE BASED SYSTEMS; MATHEMATICAL MODELS; ONTOLOGY; SEMANTICS;

MEDICAL COMPUTATIONAL PROBLEMS; SEMANTIC DESCRIPTION; SEMANTIC SIMILARITY; UNIFIED MEDICAL LANGUAGE SYSTEMS (UMLS);

MEDICAL COMPUTING;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; COMPUTER SYSTEM; HUMAN COMPUTER INTERACTION; INFORMATION RETRIEVAL; MEDICAL INFORMATICS; MEDICAL PRACTICE; SEMANTICS;

ACCESS TO INFORMATION; ALGORITHMS; ARTIFICIAL INTELLIGENCE; BIOMEDICAL RESEARCH; DECISION SUPPORT SYSTEMS, CLINICAL; GREECE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; KNOWLEDGE BASES; SEMANTICS; SOFTWARE;

EID: 34548205907     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cmpb.2007.06.005     Document Type: Article

References (34)

1. McGinn T.G., Guyatt G.H., Wyer P.C., Naylor C.D., Stiell I.G., and Richardson W.S. Users' guides to the medical literature. XXII: how to use articles about clinical decision rules. J. Am. Med. Assoc. 284 (2000) 79-84
2. Hartley D.S. In: Fawcett J., Stein D.J., and Jobson K.O. (Eds). The Language of Algorithms, In Textbook of Treatment Algorithms in Psychopharmacology (1999), John Wiley and Sons, New York 15-31
3. Arocha J.F., Wang D., and Patel V.L. Identifying reasoning strategies in medical decision making: a methodological guide. J. Biomed. Inform. 38 2 (2005) 154-171
4. Peleg M., et al. Comparing computer-interpretable guideline models: a case-study approach. J. Am. Med. Inform. Assoc. 10 1 (2003) 52-68
5. de Clercq P.A., Blom J.A., Korsten H.H., and Hasman A. Approaches for creating computer-interpretable guidelines that facilitate decision support. Artif. Intell. Med. 31 1 (2004) 1-27
6. Bratsas C., Quaresma P., Pangalos G., and Maglaveras N. Using ontologies to build a knowledge base of cardiology problems and algorithms. Proc. IEEE Comput. Cardiol. (2004) 609-612
7. Svirbely J.R., and Iyenga M.S. Issues in the implementation of computer-based medical algorithms. Technol. Health Care 13 5 (2005) 438-439
8. Henry I.C., Goldberger A.L., Moody G.B., and Mark R.G. PhysioNet: an NIH research resource for physiologic datasets and open-source software. Proceedings of the 14th IEEE Symposium on Computer-Based Medical Systems (2001) 245-250
9. Kantor G., Svirbely J., Johnson K., Sriram M., Rodriguez J.R., and Smith J. MedAl: the medical algorithm project. Proceedings of MEDINFO (2001) 298
10. Current UMLS Release-2007AA, available at: http://www.nlm.nih.gov/research/umls/documentation.html.
11. Castells P., Fernández M., and Vallet D. An adaptation of the vector-space model for ontology-based information retrieval. IEEE Trans. Knowl. Data Eng. 19 2 (2007) 261-272
12. Bratsas C., Hatzizisis I.S., Bamidis P., Quaresma P., and Maglaveras N. Similarity estimation among OWL descriptions of computational cardiology problems in a knowledge base. Proc. IEEE Comput. Cardiol. (2005) 243-246
13. Salton G., and McGill M. Introduction to Modern Information Retrieval (1983), McGraw-Hill, New York
14. Castells P., et al. Neptuno: semantic web technologies for a digital newspaper archive. In: Davies J., et al. (Ed). The Semantic Web: Research and Applications (2003), Springer Verlag, Berlin 445-458
15. Contreras J., et al. A semantic portal for the international affairs sector. In: Motta E., et al. (Ed). Engineering Knowledge in the Age of the Semantic Web (2004), Springer Verlag, Berlin 203-215
16. D.L. McGuinness, F. Harmelen, OWL Web Ontology Language overview, W3C recommendation, 2004, available at: http://www.w3.org/TR/owl-features.
17. Divita G., Tse T., and Roth L. Failure analysis of MetaMap Transfer (MMTx). Proceedings of Medinfo (2004) 763-767
18. Fung K.W., Hole W.T., and Srinivasan S. Who is using the UMLS and how-insights from the UMLS user annual reports. Proceedings of AMIA (2006) 274-278
19. Bodenreider O., and McCray A.T. Exploring semantic groups through visual approaches. J. Biomed. Inform. 36 6 (2003) 414-432
20. E. Prud'hommeaux, A. Seaborne, SPARQL Query Language for RDF, W3C working draft, 2006, available at: http://www.w3.org/TR/rdf-sparql-query.
21. Protégé an open source ontology editor, available at: http://protege.stanford.edu.
22. V. Haarslev, R. Moller, M. Wessel, RacerPro UserGuide, 2005, available at: http://www.racer-systems.com/products/racerpro/users-guide-1-9.pdf.
23. Jena semantic web framework for Java, available at: http://jena.sourceforge.net/.
24. Bangalore A., Thorn K.E., Tilley C., and Peters L. The UMLS knowledge source server: an object model for delivering UMLS data. Proceedings of AMIA (2003) 51-55
25. Lee D.T., Lee G.C., and Huang Y.W. Knowledge management for computational problem solving. J. Univ. Comput. Sci. 9 6 (2003) 563-570
26. Song J.-F., Zhang W.-M., Xiao W.-D., Li G.-H., and Xu Z.-N. Ontology-based information retrieval model for the semantic Web. Proceedings of the IEEE International Conference on e-Technology, e-Commerce, e-Services (2005) 152-155
27. Köhler J., Philippi S., Specht M., and Rüegg A. Ontology based text indexing and querying for the semantic web. Knowl. Based Syst. 19 8 (2006) 744-754
28. Müller H.M., Kenny E.E., and Sternberg P.W. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2 11 (2003) 1984-1998
29. Doms A., and Schroeder M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res. 33 (2005) 783-786
30. Friedman C., Shagina L., Lussier Y., and Hripcsak G. Automated encoding of clinical documents based on natural language. J. Am. Med. Inform. Assoc. 11 5 (2004) 392-402
31. Meystre S., and Haug P.J. Natural language processing to extract medical problems from electronic clinical documents: performance evaluation. J. Biomed. Inform. 39 6 (2006) 589-599
32. Chapman W.W., Bridewell W., Handury P., Cooper G.F., and Buchanan G.B. A simple algorithm for identifying negated findings and diseases in discharge summaries. J. Biomed. Inform. 34 5 (2001) 301-310
33. Charnock D., and Shepperd S. Learning to DISCERN online: applying an appraisal tool to health websites in a workshop setting. Health Educ. Res. 19 4 (2004) 440-446
34. Errico T.J. Syntegration: a "more complete" knowledge-based approach to the practice of medicine-North American Spine Society Presidential Address, Chicago, IL. Spine J. 5 1 (2005) 6-12