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Yearb Med Inform 2014; 23(01): 167-169
DOI: 10.15265/IY-2014-0037
Original Article
Georg Thieme Verlag KG Stuttgart

Managing Free Text for Secondary Use of Health Data

Findings from the Yearbook 2014 Section on Knowledge Representation and Management
N. Griffon
1   CISMeF, Rouen University Hospital, Normandy & TIBS, LITIS EA 4108, Institute for Research and Innovation in Biomedicine, Rouen, France
2   INSERM, U1142, LIMICS, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1142, LIMICS, Paris, France; Université Paris 13, Sorbonne Paris Cité, LIMICS, (UMR_S 1142), Villetaneuse, France
,
J. Charlet
2   INSERM, U1142, LIMICS, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1142, LIMICS, Paris, France; Université Paris 13, Sorbonne Paris Cité, LIMICS, (UMR_S 1142), Villetaneuse, France
3   AP-HP, Dept. of Clinical Research and Development, Paris, France
,
S. J. Darmoni
1   CISMeF, Rouen University Hospital, Normandy & TIBS, LITIS EA 4108, Institute for Research and Innovation in Biomedicine, Rouen, France
2   INSERM, U1142, LIMICS, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1142, LIMICS, Paris, France; Université Paris 13, Sorbonne Paris Cité, LIMICS, (UMR_S 1142), Villetaneuse, France
,
Section Editors for the IMIA Yearbook Section on Knowledge Representation and Management › Author Affiliations
Further Information

Correspondence to:

Prof. SJ. Darmoni, MD, PhD
Rouen University Hospital
Department of BioMedical Informatics
1 rue de Gérmont
76031 Rouen Cedex, France
Phone: +33(0)232 8888 29   
Fax: +33(0)232 8889 09   

Publication History

15 August 2014

Publication Date:
05 March 2018 (online)

Also available at
 
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Summary

Objective: To summarize the best papers in the field of Knowledge Representation and Management (KRM).

Methods: A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM and natural language processing (NLP) published in 2013.

Results: Four articles were selected, one focuses on Electronic Health Record (EHR) interoperability for clinical pathway personalization based on structured data. The other three focus on NLP (corpus creation, de-identification, and co-reference resolution) and highlight the increase in NLP tools performances.

Conclusion: NLP tools are close to being seriously concurrent to humans in some annotation tasks. Their use could increase drastically the amount of data usable for meaningful use of EHR.


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Keywords

Medical informatics - knowledge representation - natural language processing - semantic web - ontology

 


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  • References

  • 1 Safran C, Bloomrosen M, Hammond WE, Labkoff S, Markel-Fox S, Tang PC, Detmer DE. Expert Panel.. Toward a national framework for the secondary use of health data: an American Medical Informatics Association White Paper. J Am Med Informatics Assoc 2007; 14 (01) 1-9.
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    PubMedSearch in Google Scholar
  • 2 Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q. et al. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc 2013; 20 (01) 84-94.
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  • 3 MacLean DL, Heer J. Identifying medical terms in patient-authored text: a crowdsourcing-based approach. J Am Med Inform Assoc 2013; 20 (06) 1120-7.
    CrossrefPubMedSearch in Google Scholar
  • 4 Chowdhury MFM, Zweigenbaum P. A controlled greedy supervised approach for co-reference resolution on clinical text. J Biomed Inform 2013; 46 (03) 506-15.
    CrossrefPubMedSearch in Google Scholar
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    PubMed
  • 6 Wang H-Q, Li J-S, Zhang Y-F, Suzuki M, Araki K. Creating personalised clinical pathways by semantic interoperability with electronic health records. Artif Intell Med 2013; 58 (02) 81-9.
    CrossrefPubMedSearch in Google Scholar
  • 7 Uzuner O, Bodnari A, Shen S, Forbush T, Pestian J, South BR. Evaluating the state of the art in coreference resolution for electronic medical records. J Am Med Inform Assoc 2012; SepOct 19 (05) 786-91.
    CrossrefPubMedSearch in Google Scholar
  • 8 Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Rubin DL. et al. Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards. Methods Inf Med 2013; 52 (04) 308-16.
    Thieme ConnectPubMedSearch in Google Scholar
  • 9 Tao C, Pathak J, Solbrig HR, Wei W-Q, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. J Biomed Inform 2013; 46 (01) 128-38.
    CrossrefPubMedSearch in Google Scholar
  • 10 Grosjean J, Soualmia L, Bouarech K, Jonquet C, Darmoni S. Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal?. In 2nd Int Work Bioinforma Biomed Eng. in press; 2014
    PubMedSearch in Google Scholar

Correspondence to:

Prof. SJ. Darmoni, MD, PhD
Rouen University Hospital
Department of BioMedical Informatics
1 rue de Gérmont
76031 Rouen Cedex, France
Phone: +33(0)232 8888 29   
Fax: +33(0)232 8889 09   

  • References

  • 1 Safran C, Bloomrosen M, Hammond WE, Labkoff S, Markel-Fox S, Tang PC, Detmer DE. Expert Panel.. Toward a national framework for the secondary use of health data: an American Medical Informatics Association White Paper. J Am Med Informatics Assoc 2007; 14 (01) 1-9.
    CrossrefPubMedSearch in Google Scholar
  • 2 Lamy J-B, Séroussi B, Griffon N, Kerdelhué G, Jaulent M-C, Bouaud J. Selection of the IMIA Yearbook best papers: reducing variability by formalizing the literature search strategy. Methods Inf Med: Submitted 2014
    PubMedSearch in Google Scholar
  • 2 Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q. et al. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc 2013; 20 (01) 84-94.
    CrossrefPubMedSearch in Google Scholar
  • 3 MacLean DL, Heer J. Identifying medical terms in patient-authored text: a crowdsourcing-based approach. J Am Med Inform Assoc 2013; 20 (06) 1120-7.
    CrossrefPubMedSearch in Google Scholar
  • 4 Chowdhury MFM, Zweigenbaum P. A controlled greedy supervised approach for co-reference resolution on clinical text. J Biomed Inform 2013; 46 (03) 506-15.
    CrossrefPubMedSearch in Google Scholar
  • 5 The Human Computer and the Birth of the Information Age. [ http://www.philsoc. org/2001Spring/2132transcript.html ]
    PubMed
  • 6 Wang H-Q, Li J-S, Zhang Y-F, Suzuki M, Araki K. Creating personalised clinical pathways by semantic interoperability with electronic health records. Artif Intell Med 2013; 58 (02) 81-9.
    CrossrefPubMedSearch in Google Scholar
  • 7 Uzuner O, Bodnari A, Shen S, Forbush T, Pestian J, South BR. Evaluating the state of the art in coreference resolution for electronic medical records. J Am Med Inform Assoc 2012; SepOct 19 (05) 786-91.
    CrossrefPubMedSearch in Google Scholar
  • 8 Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Rubin DL. et al. Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards. Methods Inf Med 2013; 52 (04) 308-16.
    Thieme ConnectPubMedSearch in Google Scholar
  • 9 Tao C, Pathak J, Solbrig HR, Wei W-Q, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. J Biomed Inform 2013; 46 (01) 128-38.
    CrossrefPubMedSearch in Google Scholar
  • 10 Grosjean J, Soualmia L, Bouarech K, Jonquet C, Darmoni S. Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal?. In 2nd Int Work Bioinforma Biomed Eng. in press; 2014
    PubMedSearch in Google Scholar

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