Paper presented at ISWC 2017 about the MedRed ontology

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
HES-SO:
University of Applied Sciences and Arts Western Switzerland
We are here,
surrounded by mountains!

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
Data Acquisition Instruments
Instruments:
• Questionnaires
• Forms
• Surveys
• Protocols

5. 5
Challenges
• Paper-based data acquisition
• Error prone
• Tedious
• Manual validation
• Missing data
• Slow acquisition tracking
• Manual transcription
• Slow data collection
• …

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
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
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
REDCap instrument edition

10. 10
REDCap instrument organization

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
MedRed: Design Principles

13. 13
Core model
Core model:
• Instruments
• Sections
• Questions
• Events
• Arms

14. 14
Composition & Derivation
compose with existing instruments
derive from existing forms/questions/studies

15. 15
Provenance

16. 16
http://w3id.org/medred/medred#
powered by:

17. 17
MedRed: Dependencies
steps
provenance
constraints

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
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
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
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
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
Evaluation with existing Instruments
From the
REDCap
shared library
Also our
pilot
projects

24. 24
We are in LOV

25. 25
Also in Zenodo

26. gracias! ¿tienes preguntas?
Jean-Paul Calbimonte
University of Applied Sciences and Arts Western Switzerland
HES-SO Valais-Wallis
@jpcik