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The MedRed Ontology for Representing Clinical Data Acquisition Metadata

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Paper presented at ISWC 2017 about the MedRed ontology

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The MedRed Ontology for Representing Clinical Data Acquisition Metadata

  1. 1. The MedRed Ontology for Representing Clinical Data Acquisition Metadata Jean-Paul Calbimonte, Fabien Dubosson, Roger Hilfiker, Alexandre Cotting, Michael Schumacher University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) International Semantic Web Conference ISWC Vienna, October 2017 @jpcik
  2. 2. 2 HES-SO: University of Applied Sciences and Arts Western Switzerland We are here, surrounded by mountains!
  3. 3. 3 The MedRed Ontology for Representing Clinical Data Acquisition Metadata This paper is about an ontology Find it here: http://w3id.org/medred/medred#
  4. 4. 4 Data Acquisition Instruments Instruments: • Questionnaires • Forms • Surveys • Protocols
  5. 5. 5 Challenges • Paper-based data acquisition • Error prone • Tedious • Manual validation • Missing data • Slow acquisition tracking • Manual transcription • Slow data collection • …
  6. 6. 6 MedRed: A Platform for Medical Research Data Acquisition • Data lifecycle solution for research medical data instruments. Based on the REDCap platform. • Design, adapt and implement surveys and questionnaires for selected pilot projects led by HES-SO Valais Institut Santé. • Validation and evaluation: effectiveness and usability. • Formulate a middle and long-term strategy for a research lifecycle data service facility. Mandated by:
  7. 7. 7 REDCap • essentially no cost for academic purposes • not an open-sourced software. • active and well-established community of users • large number of partner institutions. • none belong to a Swiss University of Applied Sciences. • need to support for data research in professional health sciences (e.g. nursing, physiotherapy, ergotherapy, etc.) • HUG, Geneva • CHUV, Lausanne • Swiss THP, Basel • Cantonal Hospital of Basel Landschaft • University of Bern, Institut d'éducation médicale • ARTOG, biomédical engineering research center • CTU Bern, clinic studies unit • INSELSPITAL University Hospital • Cantonal Hospital of Luzern • Rehabilitation center of Davos • University Children’s Hospital Basel • University Hospital of Basel • Schulthess Clinic, Zurich • University Hospital, Zurich
  8. 8. 8 MedRed approach • Paperless research data input • Computer-supported acquisition design • Mobile-device electronic acquisition • Distributed data acquisition • Support for instrument designers and administrators • Training for acquisition assistants • Deployment of an inter-institutional service • Data security and privacy management
  9. 9. 9 REDCap instrument edition
  10. 10. 10 REDCap instrument organization
  11. 11. 11 Challenges • Standardized forms/questionnaires/surveys • Strict definition • Reuse of instruments/parts of instruments • Authoring • Provenance of changes • Variable definition • Validation rules • Scoring rules • Longitudinal studies, study events • Multi-arm studies
  12. 12. 12 MedRed: Design Principles
  13. 13. 13 Core model Core model: • Instruments • Sections • Questions • Events • Arms
  14. 14. 14 Composition & Derivation compose with existing instruments derive from existing forms/questions/studies
  15. 15. 15 Provenance
  16. 16. 16 http://w3id.org/medred/medred# powered by:
  17. 17. 17 MedRed: Dependencies steps provenance constraints
  18. 18. 18 MedRed: overview medred:Questionnaire medred:Information medred:Question medred:Operation prov:Plan medred:Section medred:Instrumentmedred:Item p-plan:Step p-plan:Plan p-plan:MultiStep medred:Study disco:Study medred:CaseReportForm medred: includedInStudy medred: isItemOfInstrument medred: isItemOfSection p-plan: isPrecededBy p-plan: isStepOfPlan p-plan:Variable medred:ChoiceList medred: hasChoices p-plan: isOutputVarOf medred:LongitudinalStudy medred:Arm medred:StudyEvent medred: includedInStudy medred: isEventOfArm medred: includesInstrument sh:PropertyShape medred: validationShape
  19. 19. 19 MedRed: a study ex:3MonthFollowUpStudy a medred:Study ; dcterms:description "General health conditions of a patient study ..." ; dcterms:identifier "3MonthFollowUpStudy" ; dcterms:title "3-Month follow up study" ; medred:hasInstruments ( ex:demographics ex:baseline_data ex:month_1_data ex:month_2_data ex:month_3_data ex:completion_data). instruments
  20. 20. 20 MedRed: an instrument ex:expanded_prostate_cancer_index_composite_epic_v2 a medred:Instrument ; medred:items ( ex:epic2200_section1 ex:epic2200_section2 ex:epic2200_section3 ex:epic2200_section4 ex:epic2200_section5 ex:epic2200_section6) ; dcterms:identifier "expanded_prostate_cancer_index_composite_epic_2200" ; prov:wasAttributedTo ex:wei, ex:dunn, ex:litwin, ex:sandler; prov:generatedAtTime "2011-07-16T01:52:02Z"ˆˆxsd:dateTime; prov:hadPrimarySource ex:epic_article_Urology_56_2000; prov:wasRevisionOf :ex:expanded_prostate_cancer_index_composite_epic_v1; sections authors provenance
  21. 21. 21 MedRed: a question ex:epic_q48 a medred:Question ; medred:isItemofSection ex:section3 ; dcterms:identifier "epic_q48" ; dcterms:title "14. How often have you had crampy pain in your abdomen, pelvis or rectum?" ; medred:choices ( ex:Morethanonceaday_1 ex:Aboutonceaday_2 ex:Morethanonceaweek_3 ex:Aboutonceaweek_4 ex:Rarelyornever_5 ) ; pplan:hasOutputVar ex:epic_q48_var . multi-choice question variable
  22. 22. 22 MedRed: another question ex:chol_3 a medred:Question ; dcterms:identifier "chol_3" ; dcterms:title "Cholesterol (mg/dL)" ; pplan:hasOutputVar ex:chol_3_var ; medred:isItemOfSection ex:month_3_datasection1 ; medred:validationShape ex:chol_3_shape . ex:chol_3_shape a sh:PropertyShape ; sh:path medred:dataValue ; sh:maxInclusive "300.0" ; sh:minInclusive "100.0" . ex:chol_3_var a pplan:Variable ; medred:dataType xsd:double ; medred:varName "chol_3" . variable validation
  23. 23. 23 Evaluation with existing Instruments From the REDCap shared library Also our pilot projects
  24. 24. 24 We are in LOV
  25. 25. 25 Also in Zenodo
  26. 26. gracias! ¿tienes preguntas? Jean-Paul Calbimonte University of Applied Sciences and Arts Western Switzerland HES-SO Valais-Wallis @jpcik

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