Download PDF
Appl Clin Inform 2011; 02(01): 116-117
DOI: 10.4338/ACI-2010-09-CR-0051
Case Report
Schattauer GmbH

Unlocking Data for Clinical Research – The German i2b2 Experience

T. Ganslandt
1   Center for Medical Information and Communication, Erlangen University Hospital, Erlangen, Germany
,
S. Mate
2   Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
,
K Helbing
3   Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
,
U. Sax
3   Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
4   Division of Information Technology, University Medical Center Göttingen, Göttingen, Germany
,
H.U. Prokosch
1   Center for Medical Information and Communication, Erlangen University Hospital, Erlangen, Germany
2   Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
› Author Affiliations
Further Information

Correspondence to:

Dr. med. Thomas Ganslandt
Center for Medical Information and Communication
Erlangen University Hospital
Krankenhausstr. 12, DE-91054 Erlangen
Germany

Publication History

received: 10 September 2010

accepted: 19 January 2011

Publication Date:
16 December 2017 (online)

Also available at
 
 PDF Download Permissions and Reprints

Summary

Objective: Data from clinical care is increasingly being used for research purposes. The i2b2 platform has been introduced in some US research communities as a tool for data integration and querying by clinical users. The purpose of this project was to assess the applicability of i2b2 in Germany regarding use cases, functionality and integration with privacy enhancing tools.

Methods: A set of four research usage scenarios was chosen, including the transformation and import of ontology and fact data from existing clinical data collections into i2b2 v1.4 instances. Query performance was measured in comparison to native SQL queries. A setup and administration tool for i2b2 was developed. An extraction tool for CDISC ODM data was programmed. Interfaces for the TMF privacy enhancing tools (PID Generator, Pseudonymization Service) were implemented.

Results: Data could be imported in all tested scenarios from various source systems, including the generation of i2b2 ontology definitions. The integration of TMF privacy enhancing tools was possible without modification of the platform. Limitations were found regarding query performance in comparison to native SQL and certain temporal queries.

Conclusions: i2b2 is a viable platform for data query tasks in use cases typical for networked medical research in Germany. The integration of privacy enhancing tools facilitates the use of i2b2 within established data protection concepts. Entry barriers should be lowered by providing tools for simplified setup and import of medical standard formats like CDISC ODM.


#

Keywords

Medical Record Systems - Information Storage and Retrieval - Single-Source

 


#

Conflict of Interest

The authors have established in 08/2009 a memorandum of understanding with the i2b2 National Center for Biomedical Computing to collaborate on the further development, evaluation and dissemination of i2b2 in Germany.

  • References

  • 1 Prokosch HU, Ganslandt T. Perspectives for medical informatics. Reusing the electronic medical record for clinical research. Methods Inf Med 2009; 48 (01) 38-44. PMid:19151882.
    Thieme ConnectPubMedSearch in Google Scholar
  • 2 Ohmann C, Kuchinke W. Future developments of medical informatics from the viewpoint of networked clinical research. Interoperability and integration. Methods Inf Med 2009; 48 (01) 45-54. PMid:19151883.
    Thieme ConnectPubMedSearch in Google Scholar
  • 3 Kush R, Alschuler L, Ruggeri R, Cassells S, Gupta N, Bain L. et al. Implementing Single Source: the STARBRITE proof-of-concept study. J Am Med InformAssoc 2007; 14 (05) 662-673. doi:10.1197/jamia. M2157 PMid:17600107 PMCid:1975790.
    PubMedSearch in Google Scholar
  • 4 Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh HC. Integration of clinical and genetic data in the i2b2 architecture. AMIA Annu Symp Proc 2006; 1040. PMid:17238659 PMCid:1839291.
    PubMedSearch in Google Scholar
  • 5 Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S. et al. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med InformAssoc 2010; 17 (02) 124-130. doi:10.1136/jamia.2009.000893 PMid:20190053.
    PubMedSearch in Google Scholar
  • 6 Mendis M, Wattanasin N, Kuttan R, Pan W, Philips L, Hackett K. et al. Integration of Hive and cell software in the i2b2 architecture. AMIA Annu Symp Proc 2007; 1048. PMid:18694146.
    PubMedSearch in Google Scholar
  • 7 Mendis M, Phillips LC, Kuttan R, Pan W, Gainer V, Kohane I. et al. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc 2008; 1054. PMid:18999021.
    PubMedSearch in Google Scholar
  • 8 Goryachev S, Sordo M, Zeng QT. A suite of natural language processing tools developed for the I2B2 project. AMIA Annu Symp Proc 2006; 931. PMid:17238550 PMCid:1839726.
    PubMedSearch in Google Scholar
  • 9 Gainer V, Hackett K, Mendis M, Kuttan R, Pan W, Phillips LC. et al. Using the i2b2 hive for clinical discovery: an example. AMIA Annu Symp Proc 2007; 959. PMid:18694059.
    PubMedSearch in Google Scholar
  • 10 Uzuner O. Second i2b2 workshop on natural language processing challenges for clinical records. AMIA Annu Symp Proc 2008: 1252-1253.
    PubMed
  • 11 Heinze DT, Morsch ML, Potter BC, Sheffer Jr. RE. Medical i2b2 NLP smoking challenge: the A-Life system architecture and methodology. J Am Med Inform Assoc 2008; 15 (01) 40-43. doi:10.1197/jamia. M2438 PMid:17947621 PMCid:2274871.
    CrossrefPubMedSearch in Google Scholar
  • 12 Childs LC, Enelow R, Simonsen L, Heintzelman NH, Kowalski KM, Taylor RJ. Description of a rule-based system for the i2b2 challenge in natural language processing for clinical data. J Am Med Inform Assoc 2009; 16 (04) 571-575. doi:10.1197/jamia. M3083 PMid:19390103 PMCid:2705261.
    CrossrefPubMedSearch in Google Scholar
  • 13 Szalma S, Koka V, Khasanova T, Perakslis ED. Effective knowledge management in translational medicine. J Transl Med 2010; 8 (01) 68. doi:10.1186/1479-5876-8-68 PMid:20642836 PMCid:2914663.
    CrossrefPubMedSearch in Google Scholar
  • 14 Nadkarni PM, Brandt C. Data extraction and ad hoc query of an entity-attribute-value database. J Am Med InformAssoc 1998; 5 (06) 511-527. PMid:9824799 PMCid:61332.
    PubMedSearch in Google Scholar
  • 15 Deshmukh VG, Meystre SM, Mitchell JA. Evaluating the informatics for integrating biology and the bedside system for clinical research. BMC Med Res Methodol 2009; 9: 70. doi:10.1186/1471-2288-9-70 PMid:19863809 PMCid:2779809.
    CrossrefPubMedSearch in Google Scholar
  • 16 Meystre SM, Deshmukh VG, Mitchell J. A clinical use case to evaluate the i2b2 Hive: predicting asthma exacerbations. AMIA Annu Symp Proc 2009; 2009: 442-446.
    PubMedSearch in Google Scholar
  • 17 TMF e.. V. TMF Homepage. [Internet] Berlin (Germany)2010 [updated 11/19/2010; cited 11/28/2010]; Available from: http://www.tmf-ev.de.
    PubMed
  • 18 i2b2 NCBC.. i2b2 Software Download. [Internet] Boston (MA): Partners Healthcare; 2010 [updated 11/10/2010; cited 11/28/2010]; Available from: https://www.i2b2.org/software.
    PubMed
  • 19 Kimball R, Ross M. The Data Warehouse Toolkit. John Wiley & Sons; 2002
    Search in Google Scholar
  • 20 Faldum A, Pommerening K. An optimal code for patient identifiers. Comput Methods Programs Biomed 2005; 79 (01) 81-88. doi:10.1016/j.cmpb.2005.03.004 PMid:15888350.
    CrossrefPubMedSearch in Google Scholar
  • 21 Pommerening K, Reng M. Secondary use of the EHR via pseudonymisation. Studies in Health Technology and Informatics 2004; 103: 441-446. PMid:15747953.
    PubMedSearch in Google Scholar
  • 22 Helbing K, Demiroglu SY, Rakebrandt F, Pommerening K, Rienhoff O, Sax U. A Data Protection Scheme for Medical Research Networks. Review after Five Years of Operation. Methods Inf Med. 2010 49. 5 PMid:20644898
    PubMedSearch in Google Scholar
  • 23 DIMDI.. International Classification of Diseases (ICD10) with German Modifications. [Internet] Cologne (Germany): German Institute of Medical Documentation and Information (DIMDI); 2010 [updated 09/27/2010; cited 11/28/2010]; Available from: http://www.dimdi.de/static/de/klassi/diagnosen/icd10.
    PubMed
  • 24 DIMDI.. German Procedure Codes (OPS). [Internet] Cologne (Germany): German Institute of Medical Documentation and Information (DIMDI); 2010 [updated 09/27/2010; cited 11/28/2010]; Available from: http://www.dimdi.de/static/de/klassi/prozeduren/ops301.
    PubMed
  • 25 Klein A, Prokosch HU, Muller M, Ganslandt T. Experiences with an interoperable data acquisition platform for multi-centric research networks based on HL7 CDA. Methods Inf Med 2007; 46 (05) 580-585. PMid:17938783.
    Thieme ConnectPubMedSearch in Google Scholar
  • 26 Kuchinke W, Wiegelmann S, Verplancke P, Ohmann C. Extended cooperation in clinical studies through exchange of CDISC metadata between different study software solutions. Methods Inf Med 2006; 45 (04) 441-446. PMid:16964363.
    Thieme ConnectPubMedSearch in Google Scholar
  • 27 CDISC.. Operational Data Model (ODM). [Internet] Austin, TX: Clinical Data Interchange Standards Consortium;. 2010 [cited 11/28/2010]; Available from: http://www.cdisc.org/odm.
    PubMedSearch in Google Scholar
  • 28 TMF e.. V. TMF Forum (registration required). [Internet] Berlin (Germany)2010 [updated 11/19/2010; cited 11/28/2010]; Available from: http://www.tmf-ev.de/Forum.aspx.
    PubMed
  • 29 i2b2 NCBC.. i2b2 Academic Users Group. [Internet] Boston (MA)2010 [cited 11/28/2010]; Available from: http://www.i2b2aug.org.
    PubMed
  • 30 i2b2 NCBC.. i2b2 Roadmap Release 1.6. [Internet] Boston (MA)2010 [updated 10/05/2010; cited 11/28/2010]; Available from: https://community.i2b2.org/wiki/display/roadmap/Release+1.6.
    PubMed
  • 31 Tokyo Medical and Dental University.. Japanese i2b2 database development project in TMDU. [Internet] Tokyo (Japan)2010 [updated 10/27/2010; cited 11/28/2010]; Available from: http://bioomix.tmd.ac.jp/disease/i2b2.
    PubMed
  • 32 Wynden RW MG, Sim I, Gabriel D, Casale M, Carini S, Hastings S, Ervin D, Tu S, Gennari JH, Anderson N, Mobed K, Lakshminarayanan P, Massary M, Cucina RJ. Ontology Mapping and Data Discovery for the Translational Investigator. AMIA Summit on Clinical Research Informatics. San Francisco: 2010
    PubMedSearch in Google Scholar
  • 33 i2b2 NCBC.. Optimizing Query Performance with the Ontology Total_Num field. [Internet] Boston (MA)2010 [updated 10/12/2010; cited 11/28/2010]; Available from: https://community.i2b2.org/wiki/x/h4AW.
    PubMed

Correspondence to:

Dr. med. Thomas Ganslandt
Center for Medical Information and Communication
Erlangen University Hospital
Krankenhausstr. 12, DE-91054 Erlangen
Germany

  • References

  • 1 Prokosch HU, Ganslandt T. Perspectives for medical informatics. Reusing the electronic medical record for clinical research. Methods Inf Med 2009; 48 (01) 38-44. PMid:19151882.
    Thieme ConnectPubMedSearch in Google Scholar
  • 2 Ohmann C, Kuchinke W. Future developments of medical informatics from the viewpoint of networked clinical research. Interoperability and integration. Methods Inf Med 2009; 48 (01) 45-54. PMid:19151883.
    Thieme ConnectPubMedSearch in Google Scholar
  • 3 Kush R, Alschuler L, Ruggeri R, Cassells S, Gupta N, Bain L. et al. Implementing Single Source: the STARBRITE proof-of-concept study. J Am Med InformAssoc 2007; 14 (05) 662-673. doi:10.1197/jamia. M2157 PMid:17600107 PMCid:1975790.
    PubMedSearch in Google Scholar
  • 4 Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh HC. Integration of clinical and genetic data in the i2b2 architecture. AMIA Annu Symp Proc 2006; 1040. PMid:17238659 PMCid:1839291.
    PubMedSearch in Google Scholar
  • 5 Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S. et al. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med InformAssoc 2010; 17 (02) 124-130. doi:10.1136/jamia.2009.000893 PMid:20190053.
    PubMedSearch in Google Scholar
  • 6 Mendis M, Wattanasin N, Kuttan R, Pan W, Philips L, Hackett K. et al. Integration of Hive and cell software in the i2b2 architecture. AMIA Annu Symp Proc 2007; 1048. PMid:18694146.
    PubMedSearch in Google Scholar
  • 7 Mendis M, Phillips LC, Kuttan R, Pan W, Gainer V, Kohane I. et al. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc 2008; 1054. PMid:18999021.
    PubMedSearch in Google Scholar
  • 8 Goryachev S, Sordo M, Zeng QT. A suite of natural language processing tools developed for the I2B2 project. AMIA Annu Symp Proc 2006; 931. PMid:17238550 PMCid:1839726.
    PubMedSearch in Google Scholar
  • 9 Gainer V, Hackett K, Mendis M, Kuttan R, Pan W, Phillips LC. et al. Using the i2b2 hive for clinical discovery: an example. AMIA Annu Symp Proc 2007; 959. PMid:18694059.
    PubMedSearch in Google Scholar
  • 10 Uzuner O. Second i2b2 workshop on natural language processing challenges for clinical records. AMIA Annu Symp Proc 2008: 1252-1253.
    PubMed
  • 11 Heinze DT, Morsch ML, Potter BC, Sheffer Jr. RE. Medical i2b2 NLP smoking challenge: the A-Life system architecture and methodology. J Am Med Inform Assoc 2008; 15 (01) 40-43. doi:10.1197/jamia. M2438 PMid:17947621 PMCid:2274871.
    CrossrefPubMedSearch in Google Scholar
  • 12 Childs LC, Enelow R, Simonsen L, Heintzelman NH, Kowalski KM, Taylor RJ. Description of a rule-based system for the i2b2 challenge in natural language processing for clinical data. J Am Med Inform Assoc 2009; 16 (04) 571-575. doi:10.1197/jamia. M3083 PMid:19390103 PMCid:2705261.
    CrossrefPubMedSearch in Google Scholar
  • 13 Szalma S, Koka V, Khasanova T, Perakslis ED. Effective knowledge management in translational medicine. J Transl Med 2010; 8 (01) 68. doi:10.1186/1479-5876-8-68 PMid:20642836 PMCid:2914663.
    CrossrefPubMedSearch in Google Scholar
  • 14 Nadkarni PM, Brandt C. Data extraction and ad hoc query of an entity-attribute-value database. J Am Med InformAssoc 1998; 5 (06) 511-527. PMid:9824799 PMCid:61332.
    PubMedSearch in Google Scholar
  • 15 Deshmukh VG, Meystre SM, Mitchell JA. Evaluating the informatics for integrating biology and the bedside system for clinical research. BMC Med Res Methodol 2009; 9: 70. doi:10.1186/1471-2288-9-70 PMid:19863809 PMCid:2779809.
    CrossrefPubMedSearch in Google Scholar
  • 16 Meystre SM, Deshmukh VG, Mitchell J. A clinical use case to evaluate the i2b2 Hive: predicting asthma exacerbations. AMIA Annu Symp Proc 2009; 2009: 442-446.
    PubMedSearch in Google Scholar
  • 17 TMF e.. V. TMF Homepage. [Internet] Berlin (Germany)2010 [updated 11/19/2010; cited 11/28/2010]; Available from: http://www.tmf-ev.de.
    PubMed
  • 18 i2b2 NCBC.. i2b2 Software Download. [Internet] Boston (MA): Partners Healthcare; 2010 [updated 11/10/2010; cited 11/28/2010]; Available from: https://www.i2b2.org/software.
    PubMed
  • 19 Kimball R, Ross M. The Data Warehouse Toolkit. John Wiley & Sons; 2002
    Search in Google Scholar
  • 20 Faldum A, Pommerening K. An optimal code for patient identifiers. Comput Methods Programs Biomed 2005; 79 (01) 81-88. doi:10.1016/j.cmpb.2005.03.004 PMid:15888350.
    CrossrefPubMedSearch in Google Scholar
  • 21 Pommerening K, Reng M. Secondary use of the EHR via pseudonymisation. Studies in Health Technology and Informatics 2004; 103: 441-446. PMid:15747953.
    PubMedSearch in Google Scholar
  • 22 Helbing K, Demiroglu SY, Rakebrandt F, Pommerening K, Rienhoff O, Sax U. A Data Protection Scheme for Medical Research Networks. Review after Five Years of Operation. Methods Inf Med. 2010 49. 5 PMid:20644898
    PubMedSearch in Google Scholar
  • 23 DIMDI.. International Classification of Diseases (ICD10) with German Modifications. [Internet] Cologne (Germany): German Institute of Medical Documentation and Information (DIMDI); 2010 [updated 09/27/2010; cited 11/28/2010]; Available from: http://www.dimdi.de/static/de/klassi/diagnosen/icd10.
    PubMed
  • 24 DIMDI.. German Procedure Codes (OPS). [Internet] Cologne (Germany): German Institute of Medical Documentation and Information (DIMDI); 2010 [updated 09/27/2010; cited 11/28/2010]; Available from: http://www.dimdi.de/static/de/klassi/prozeduren/ops301.
    PubMed
  • 25 Klein A, Prokosch HU, Muller M, Ganslandt T. Experiences with an interoperable data acquisition platform for multi-centric research networks based on HL7 CDA. Methods Inf Med 2007; 46 (05) 580-585. PMid:17938783.
    Thieme ConnectPubMedSearch in Google Scholar
  • 26 Kuchinke W, Wiegelmann S, Verplancke P, Ohmann C. Extended cooperation in clinical studies through exchange of CDISC metadata between different study software solutions. Methods Inf Med 2006; 45 (04) 441-446. PMid:16964363.
    Thieme ConnectPubMedSearch in Google Scholar
  • 27 CDISC.. Operational Data Model (ODM). [Internet] Austin, TX: Clinical Data Interchange Standards Consortium;. 2010 [cited 11/28/2010]; Available from: http://www.cdisc.org/odm.
    PubMedSearch in Google Scholar
  • 28 TMF e.. V. TMF Forum (registration required). [Internet] Berlin (Germany)2010 [updated 11/19/2010; cited 11/28/2010]; Available from: http://www.tmf-ev.de/Forum.aspx.
    PubMed
  • 29 i2b2 NCBC.. i2b2 Academic Users Group. [Internet] Boston (MA)2010 [cited 11/28/2010]; Available from: http://www.i2b2aug.org.
    PubMed
  • 30 i2b2 NCBC.. i2b2 Roadmap Release 1.6. [Internet] Boston (MA)2010 [updated 10/05/2010; cited 11/28/2010]; Available from: https://community.i2b2.org/wiki/display/roadmap/Release+1.6.
    PubMed
  • 31 Tokyo Medical and Dental University.. Japanese i2b2 database development project in TMDU. [Internet] Tokyo (Japan)2010 [updated 10/27/2010; cited 11/28/2010]; Available from: http://bioomix.tmd.ac.jp/disease/i2b2.
    PubMed
  • 32 Wynden RW MG, Sim I, Gabriel D, Casale M, Carini S, Hastings S, Ervin D, Tu S, Gennari JH, Anderson N, Mobed K, Lakshminarayanan P, Massary M, Cucina RJ. Ontology Mapping and Data Discovery for the Translational Investigator. AMIA Summit on Clinical Research Informatics. San Francisco: 2010
    PubMedSearch in Google Scholar
  • 33 i2b2 NCBC.. Optimizing Query Performance with the Ontology Total_Num field. [Internet] Boston (MA)2010 [updated 10/12/2010; cited 11/28/2010]; Available from: https://community.i2b2.org/wiki/x/h4AW.
    PubMed

   Permissions and Reprints