PDF herunterladen
Yearb Med Inform 2017; 26(01): 53-58
DOI: 10.15265/IY-2017-006
Special Section: Learning from Experience: Secondary Use of Patient Data
Working Group Contributions
Georg Thieme Verlag KG Stuttgart

The Role of Free/Libre and Open Source Software in Learning Health Systems

C. Paton
1   Group Head for Global Health Informatics, Centre for Tropical Medicine and Global Health, University of Oxford, UK
,
T. Karopka
2   Chair of IMIA OS WG, Chair of EFMI LIFOSS WG, Project Manager, BioCon Valley GmbH, Greifswald, Germany
› Institutsangaben Funding Statement CP is funded by the Health Systems Research Initiative grant (MR/N005600/1) jointly supported by the Department for International Development (DFID), the Economic and Social Research Council (ESRC), the Medical Research Council (MRC) and the Wellcome Trust (WT).
Weitere Informationen

Publikationsverlauf

Publikationsdatum:
11. September 2017 (online)

   Lizenzen und Reprints

Summary

Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs).

Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement.

Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed.

Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS.

Keywords

FLOSS - Open Source - Learning Health Systems - Secondary Use
 

  • References

  • 1 About PCORnet - PCORnet [Internet]. PCORnet. [cited 2017 Mar 24]. Available from: http://www.pcornet.org/about-pcornet/.
    PubMed
  • 2 Delaney BC, Curcin V, Andreasson A, Arvanitis TN, Bastiaens H, Corrigan D. et al. Translational Medicine and Patient Safety in Europe: TRANSFoRm—Architecture for the Learning Health System in Europe. Biomed Res Int [Internet]. 2015 Oct 11 [cited 2017 Mar 24];2015. Available from: https://www.hindawi.com/journals/ bmri/2015/961526/.
    PubMedGoogle Scholar
  • 3 Friedman C, Rubin J, Brown J, Buntin M, Corn M, Etheredge L. et al. Toward a science of learning systems: a research agenda for the high-functioning Learning Health System. J Am Med Inform Assoc 2015; Jan; 22 (01) 43-50.
    PubMedGoogle Scholar
  • 4 Roundtable on Value & Science-Driven Health Care, The Learning Health, Institute of Medicine. Digital Infrastructure for the Learning Health System: The Foundation for Continuous Improvement in Health and Health Care: Workshop Series Summary. Grossmann C, Powers B, McGinnis JM. editors. Washington (DC): National Academies Press; 2011: 320.
    Google Scholar
  • 5 English M, Irimu G, Agweyu A, Gathara D, Oliwa J, Ayieko P. et al. Building Learning Health Systems to Accelerate Research and Improve Outcomes of Clinical Care in Low- and Middle-Income Countries. PLoS Med 2016; Apr; 13 (04) e1001991.
    PubMedGoogle Scholar
  • 6 Medical Free/Libre and Open Source Software | Structured project database, service providers, publications, events, [Internet]. [cited 2017 Mar 24]. Available from: http://medfloss.org.
    PubMedGoogle Scholar
  • 7 Brown SH, Lincoln MJ, Groen PJ, Kolodner RM. VistA—U.S. Department of Veterans Affairs national-scale HIS. Int J Med Inform 2003/3; 69 (2– 3): 135-56.
    PubMedGoogle Scholar
  • 8 Todd R. Spine2 built on Riak database | Digital Health [Internet]. Digital Health. 2013 [cited 2017 Mar 24]. Available from: https://www.digitalhealth.net/2013/10/spine2-built-on-riak-database/.
    PubMedGoogle Scholar
  • 9 Hackl WO, Rauchegger F, Ammenwerth E. A Nursing Intelligence System to Support Secondary Use of Nursing Routine Data. Appl Clin Inform 2015; Jun 24; 06 (02) 418-28.
    PubMedGoogle Scholar
  • 10 i2b2: Informatics for Integrating Biology & the Bedside [Internet]. [cited 2017 Mar 24]. Available from: https://www.i2b2.org/.
    PubMedGoogle Scholar
  • 11 Endel F, Duftschmid G. Secondary Use of Claims Data from the Austrian Health Insurance System with i2b2: A Pilot Study. Stud Health Technol Inform 2016; 223: 245-52.
    PubMedGoogle Scholar
  • 12 Ganslandt T, Mate S, Helbing K, Sax U, Prokosch HU. Unlocking Data for Clinical Research – The German i2b2 Experience. Appl Clin Inform 2011; Mar 30; 02 (01) 116-27.
    PubMedGoogle Scholar
  • 13 Bauer CRKD, Ganslandt T, Baum B, Christoph J, Engel I, Löbe M. et al. Integrated Data Repository Toolkit (IDRT). A Suite of Programs to Facilitate Health Analytics on Heterogeneous Medical Data. Methods Inf Med 2016; 55 (02) 125-35.
    PubMedGoogle Scholar
  • 14 Gabetta M, Malovini A, Bucalo M, Zini E, Tibollo V, Priori SG. et al. Beyond Cohort Selection: An Analytics-Enabled i2b2. Stud Health Technol Inform 2016; 228: 572-6.
    PubMedGoogle Scholar
  • 15 Gabetta M, Limongelli I, Rizzo E, Riva A, Segagni D, Bellazzi R. BigQ: a NoSQL based framework to handle genomic variants in i2b2. BMC Bioinformatics 2015; Dec 29; 16: 415.
    PubMedGoogle Scholar
  • 16 Westra BL, Christie B, Johnson SG, Pruinelli L, LaFlamme A, Park JI. et al. Expanding Interprofessional EHR Data in i2b2. AMIA Jt Summits Transl Sci Proc 2016; Jul 20; 2016: 260-8.
    PubMedGoogle Scholar
  • 17 Rance B, Canuel V, Countouris H, Laurent-Puig P, Burgun A. Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure. Appl Clin Inform 2016; May 4; 07 (02) 260-74.
    PubMedGoogle Scholar
  • 18 Dunn Jr W, Burgun A, Krebs M-O, Rance B. Exploring and visualizing multidimensional data in translational research platforms. Brief Bioinform [Internet]. 2016 Sep 1; Available from: http://dx.doi.org/10.1093/bib/bbw080.
    CrossrefPubMedGoogle Scholar
  • 19 Haarbrandt B, Tute E, Marschollek M. Automated population of an i2b2 clinical data warehouse from an openEHR-based data repository. J Biomed Inform 2016; Oct; 63: 277-94.
    PubMedGoogle Scholar
  • 20 Cavelaars M, Rousseau J, Parlayan C, de Ridder S, Verburg A, Ross R. et al. OpenClinica. J Clin Bioinforma 2015; 05 (Suppl 1) S2.
    PubMedGoogle Scholar
  • 21 Tuti T, Bitok M, Paton C, Makone B, Malla L, Muinga N. et al. Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya. J Am Med Inform Assoc 2016; Jan; 23 (01) 184-92.
    PubMedGoogle Scholar
  • 22 Athey BD, Braxenthaler M, Haas M, Guo Y. tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research. AMIA Jt Summits Transl Sci Proc 2013; Mar 18; 2013: 6-8.
    PubMedGoogle Scholar
  • 23 Camacho JCRodriguez, Stäubert S, Löbe M. Automated Import of Clinical Data from HL7 Messages into OpenClinica and tranSMART Using Mirth Connect. Stud Health Technol Inform 2016; 228: 317-21.
    PubMedGoogle Scholar
  • 24 Firnkorn D, Merker S, Ganzinger M, Muley T, Knaup P. Unlocking Data for Statistical Analyses and Data Mining: Generic Case Extraction of Clinical Items from i2b2 and tranSMART. Stud Health Technol Inform 2016; 228: 567-71.
    PubMedGoogle Scholar
  • 25 Satagopam V, Gu W, Eifes S, Gawron P, Ostaszewski M, Gebel S. et al. Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. Big Data 2016; Jun; 04 (02) 97-108.
    PubMedGoogle Scholar
  • 26 Gawron P, Ostaszewski M, Satagopam V, Gebel S, Mazein A, Kuzma M. et al. MINERVA—a platform for visualization and curation of molecular interaction networks. NPJ Syst Biol Appl 2016; Sep 22; 02: 16020.
    PubMedGoogle Scholar
  • 27 Goecks J, Nekrutenko A, Taylor J. Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010; Aug 25; 11 (08) R86.
    PubMedGoogle Scholar
  • 28 Home - Weasis - dcm4che.org Wiki [Internet]. [cited 2017 Mar 24]. Available from: https://dcm4che.atlassian.net/wiki/display/WEA/Home.
    PubMed
  • 29 Haak D, Page C-E, Reinartz S, Krüger T, Deserno TM. DICOM for Clinical Research: PACS-Integrated Electronic Data Capture in Multi-Center Trials. J Digit Imaging 2015; Oct; 28 (05) 558-66.
    PubMedGoogle Scholar
  • 30 Dixit A, Dobson RJB. CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas. JMIR Med Inform 2014; Dec 1; 02 (02) e32.
    PubMedGoogle Scholar
  • 31 Klann JG, McCoy AB, Wright A, Wattanasin N, Sittig DF, Murphy SN. Health care transformation through collaboration on open-source informatics projects: integrating a medical applications platform, research data repository, and patient summarization. Interact J Med Res 2013; May 30 02 (01) e11.
    PubMedGoogle Scholar
  • 32 Klann JG, Abend A, Raghavan VA, Mandl KD, Murphy SN. Data interchange using i2b2. J Am Med Inform Assoc 2016; Sep 23 (05) 909-15.
    PubMedGoogle Scholar
  • 33 Rea S, Pathak J, Savova G, Oniki TA, Westberg L, Beebe CE. et al. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project. J Biomed Inform 2012; Aug 45 (04) 763-71.
    PubMedGoogle Scholar
  • 34 Oniki TA, Zhuo N, Beebe CE, Liu H, Coyle JF, Parker CG. et al. Clinical element models in the SHARPn consortium. J Am Med Inform Assoc 2016; Mar; 23 (02) 248-56.
    PubMedGoogle Scholar
  • 35 Index - FHIR v3.0.0 [Internet]. [cited 2017 Mar 24]. Available from: http://hl7.org/fhir/index.html.
    PubMed
  • 36 Mandel JC, Kreda DA, Mandl KD, Kohane IS, Ramoni RB. SMART on FHIR: a stan- dards-based, interoperable apps platform for electronic health records. J Am Med Inform Assoc 2016; Sep; 23 (05) 899-908.
    CrossrefPubMedGoogle Scholar
  • 37 Wagholikar KB, Mandel JC, Klann JG, Wattanasin N, Mendis M, Chute CG. et al. SMART-on-FHIR implemented over i2b2. J Am Med Inform Assoc [Internet]. 2016. Jun 6; Available from: http://dx.doi.org/10.1093/jamia/ocw079.
    CrossrefPubMedGoogle Scholar
  • 38 Pfiffner PB, Pinyol I, Natter MD, Mandl KD. C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR. PLoS One 2016; Mar 31; 11 (03) e0152722.
    CrossrefPubMedGoogle Scholar
  • 39 Stang PE, Ryan PB, Racoosin JA, Overhage JM, Hartzema AG, Reich C. et al. Advancing the science for active surveillance: rationale and design for the Observational Medical Outcomes Partnership. Ann Intern Med 2010; Nov 2; 153 (09) 600-6.
    CrossrefPubMedGoogle Scholar
  • 40 Wolfe BA, Mamlin BW, Biondich PG, Fraser HSF, Jazayeri D, Allen C. et al. The OpenMRS system: collaborating toward an open source EMR for developing countries. AMIA Annu Symp Proc. 2006: 1146.
    PubMedGoogle Scholar
  • 41 Carter P, Laurie GT, Dixon-Woods M. The social licence for research: why care.data ran into trouble. J Med Ethics 2015; May; 41 (05) 404-9.
    PubMedGoogle Scholar
  • 42 Review of data security, consent and opt-outs - GOV.UK [Internet]. [cited 2017 Mar 24]. Available from: https://www.gov.uk/government/publications/review-of-data-security-consent-and-opt-outs.
    PubMedGoogle Scholar