Rule-based information extraction from patients' clinical data

Journal of Biomedical Informatics

Volumn 42, Issue 5, 2009, Pages 923-936

  Mykowiecka, Agnieszka ^a   Marciniak, Małgorzata ^a   Kupść, Anna ^a  

^a INSTITUTE OF COMPUTER SCIENCE   (Poland)

Author keywords

Linguistic analysis; Polish clinical data; Rule based information extraction

Indexed keywords

CLINICAL DATA; DIABETIC PATIENT; FEATURE STRUCTURE; INFORMATION EXTRACTION; INFORMATION EXTRACTION SYSTEMS; LINGUISTIC ANALYSIS; MEDICAL DOCUMENTATION; POLISH CLINICAL DATA; POST PROCESSING; PRECISION AND RECALL; RULE BASED; RULE-BASED INFORMATION EXTRACTION; SAMPLE DATA;

COORDINATION REACTIONS; INFORMATION ANALYSIS; LINGUISTICS; ONTOLOGY; SUGAR (SUCROSE);

HEURISTIC ALGORITHMS;

INSULIN; ORAL ANTIDIABETIC AGENT;

ACCURACY; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DATA EXTRACTION; DIABETES MELLITUS; GRAMMAR; INFORMATION RETRIEVAL; INFORMATION SYSTEM; LANGUAGE ABILITY; LANGUAGE PROCESSING; MAMMOGRAPHY; MEDICAL DOCUMENTATION; MEDICAL RECORD; POLAND; PRIORITY JOURNAL;

ALGORITHMS; AUTOMATIC DATA PROCESSING; DATABASES, FACTUAL; FEMALE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MAMMOGRAPHY; MEDICAL INFORMATICS; MEDICAL RECORDS; MODELS, THEORETICAL; NATURAL LANGUAGE PROCESSING; TERMINOLOGY AS TOPIC;

EID: 70349440815     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2009.07.007     Document Type: Article

References (47)

1. In: Agirre E., and Edmonds P. (Eds). Word sense disambiguation. Algorithms and applications. Text, speech and language technology (2007), Springer-Verlag
2. Bontcheva K, Dimitrov M, Maynard D, Tablan V, Cunningham H. Shallow methods for named entity coreference resolution. In: Proceedings of traitement automatique des langues naturelles. TALN Nancy; 2002.
3. Boytcheva S, Strupchanska A, Paskaleva E, Tcharaktchiev D. Some aspects of negation processing in electronic health records. In: Proceedings of international workshop language and speech infrastructure for information access in the Balkan countries; 2005. p. 1-8.
4. Bunescu R, Ge R, Kate RJ, Mooney RJ, Wong YW. Learning to extract proteins and their interactions from medline abstracts. In: Proceedings of ICML-2003 workshop on machine learning in bioinformatics; 2003. p. 46-53.
5. Burnside E, Rubin D, Shachter R. A Bayesian network for mammography. In: Proceedings of the American medical informatics association symposium; 2000. p. 16-110.
6. Burnside E, Strasberg H, Rabin D. Automated indexing of mammography using linear least squares fit. In: CARS 2000 international conference on computer assisted radiology and surgery, San Francisco, CA; 2000.
7. Buyko E, Tomanek K, Hahn U. Resolution of coordination ellipses in biological named entities using conditional random field. In: Proceedings of the 10th conference of the Pacific association for computational linguistics; 2007.
8. Carpenter B. The logic of typed feature structures. Cambridge tracts in theoretical computer science (1992), Cambridge University Press
9. Chapman W.W., Hanbury B., Cooper P., and Buchanan G. A simple algorithm for identifying negated findings and diseases in discharge summaries. J Biomed Inform 34 (2001) 204-230
10. Chapman WW, Dowling JN, Chu D. Context: an algorithm for identifying contextual features from clinical text. In: ACL 2007. Proceedings of the workshop on BioNLP 2007; 2007.
11. Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying respiratory findings in emergency department reports for biosurveillance using metamap. In: Medinfo; 2004. p. 487-91.
12. Chapman WW, Dowling JN, Ivanov O, Gesteland P, Olszewski R, Espino J, et al. Evaluating natural language processing applications applied to outbreak and disease surveillance. In: Proceedings of 36th symposium on the interface: computing science and statistics, Baltimore, MD; 2004.
13. In: Chen H., Fuller S., Friedman C., and Hersh W. (Eds). Medical informatics: knowledge management and data mining in biomedicine (2005), Springer
14. Christensen LM, Haug PJ, Fiszman M. MPLUS: a probabilistic medical language understanding. In: Proceedings of ACL workshop on natural language processing in the biomedical domain; 2002.
15. Drożdżyñski W, Krieger H-U, Piskorski J, Schäfer U, Xu F. Shallow processing with unification and typed feature structures - foundations and applications. German AI J KI-Zeitschrift 2004;01/04.
16. Elkin P.L., Brown S.H., Bauer B.A., Husser C.S., Carruth W., Bergstrom L.R., et al. A controlled trial of automated classification of negation from clinical notes. BMC Med Inform Decision Making 5 (2005)
17. Fiszman M., Chapman W., Aronsky D., Evans S., and Haug P. Automatic detection of acute bacterial pneumonia from chest X-ray reports. J Am Med Inform Assoc 7 (2000)
18. Friedman C., Alderson P., Austin J., Cimino J., and Johnson S. A general natural language text processor for clinical radiology. J Am Med Inform Assoc 1 (1994)
19. Friedman C., and Hripcsak G. Natural language processing and its future in medicine. Acad Med 74 8 (1999) 890-895
20. Gasperin C, Briscoe T. Statistical anaphora resolution in biomedical texts. In: Proceedings of the 22nd international conference on computational linguistics (Coling 2008), Manchester, UK, August 2008. Coling 2008 Organizing Committee; 2008. p. 257-64.
21. Hahn U., Romacker M., and Schultz S. medsynDikate - a natural language system for the extraction of medical information from findings reports. Int J Med Inform 67 (2002) 63-74
22. Hahn U, Romacker M, Schulz S. Creating knowledge repositories from biomedical reports: the MEDSYNDIKATE text mining system. Pac Symp Biocomput 2002;338-49.
23. Harkema H, Gaizauskas R, Hepple M, Roberts A, Roberts I, Davis N, et al. A large scale terminology resource for biomedical text processing. In: HLT-NAACL 2004 workshop: BioLINK 2004 linking biological literature. Ontologies and databases; 2004.
24. Harkema H, Roberts I, Gaizauskas R, Hepple M. Information extraction from clinical records. In: Proceedings of the 4th UK e-Science all hands meeting, Nottingham, UK; 2005.
25. Hripcsak G., Austin J., Anderson P., and Friedman C. Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reports. Radiology 224 (2002) 157-163
26. Hripcsak G., Friedman C., Alderson P.O., DuMouchel W., Johnson S.B., and Clayton P.D. Unlocking clinical data from narrative reports: a study of natural language processing. Ann Intern Med 122 9 (1995) 681-688
27. Jain NL, Friedman C. Identification of findings suspicious for breast cancer based on natural language processing of mammogram reports. In: Proceedings of the American medical informatics association annual fall symposium; 1997. p. 829-33.
28. Kopans DB, D'Orsi C, Adler D, Bassett LW, Brenner RJ, Dodd GD, et al. Breast imaging reporting and data system (BI-RADS). In: American College of Radiology, Reston, Va; 1993.
29. Marciniak M., Mykowiecka A., Kupść A., and Piskorski J. Intelligent content extraction from Polish medical reports. International workshop on intelligent media technology for communicative intelligence. LNCS 3490 (2005), Springer-Verlag
30. Mykowiecka A, Kupść A, Marciniak M. Rule-based medical content extraction and classification. In: Proceedings of ISMIS 2005, Gdańsk. Springer-Verlag; 2005.
31. Mykowiecka A., and Marciniak M. Domain-driven automatic spelling correction for mammography reports. Proceedings of intelligent information systems 2006 (2006) Springer
32. Mykowiecka A, Marciniak M. Domain model for medical information extraction - LightMedOnt ontology. In: Aspects of natural language processing, Festschrift in Honor of L. Bolc, LNAI 5070. Springer-Verlag. p. 341-67.
33. Mykowiecka A, Marciniak M, Podsiadły-Marczynkowska T. A data-driven ontology for an information extraction system from mammography reports. In: Proceedings of 10th International Protégé conference, Budapest; 2007.
34. No JC, Zhang J, Pustejovsky J. Anaphora resolution in biomedical literature. In: Proceedings of international symposium on reference resolution for NLP, Alicante, Spain; 2002.
35. Piskorski J., Homola P., Marciniak M., Mykowiecka A., Przepiórkowski A., and Woliński M. Information extraction for Polish using the SProUT platform. Intelligent information processing and web mining. Proceedings of the IIS: IIPWM'04 (2004), Springer-Verlag
36. Sager N., Friedman C., and Lyman M. Medical language processing: computer management of narrative data (1987), Addison-Wesley Publishing Company
37. Sager N., Lyman M., Bucknall C., Nhan N., and Tick L.J. Natural language processing and the representation of clinical data. J Am Med Inform Assoc 1 2 (1994) 142-160
38. Sanchez-Graillet O, Poesio M, Kabadjov M, Tesar R. What kind of problems do protein interactions raise for anaphora resolution? - a preliminary analysis. In: Proceedings of the second international symposium on semantic mining in biomedicine, Jena, April 9-12, 2006.
39. Savova G., Coden A., Sominsky I., Johnson R., Ogren P., Groen P., et al. Word sense disambiguation across two domains: biomedical literature and clinical notes. J Biomed Inform 41 6 (2008) 1088-1100
40. Soderland SG. Building a machine learning based text understanding system. In: Proceedings of IJCAI-2001 workshop on adaptive text extraction and mining; 2001.
41. Spyns P. Natural language processing in medicine: an overview. Methods Inform Med 35 (1996) 285-301
42. Spyns P, Nhan TN, Baert E, Sager N, Moor GD. Medical language processing applied to extract clinical information from Dutch medical documents. In: Proceedings of the 9th world congress on medical informatics (MEDINFO98); 1998. p. 685-9.
43. Taira R.K., Soderland S.G., and Jakobovits R.M. Automatic structuring of radiology free-text reports. Radiographics 21 (2001) 237-245
44. Tveit A, Saetre R. Protchew: automatic extraction of protein names from biomedical literature. In: Proceedings of the 21st international conference on data engineering workshops; 2005.
45. Uzuner O., Sibanda T.C., Luo Y., and Szolovits P. A de-identifier for medical discharge summaries. Artif Intell Med 42 (2007) 13-35
46. Yang X, Su J, Zhou G, Tan CL. An np-cluster based approach to coreference resolution. In: Proceedings of Coling 2004, Geneva, Switzerland, August 23-27, 2004; COLING. p. 226-32.
47. Yangarber R. Acquisition of domain knowledge. In: Pazienza T. (editor). Information extraction: in the Web Era. Natural language communication for knowledge acquisition and intelligent information agents, LNAI 2700. Springer-Verlag; 2003. p. 1-28.