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

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

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The MedRed Ontology for Representing
Clinical Data Acquisition Metadata
This paper is about an ontology
Find it here:
http://w3id.org/medred/medred#

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

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

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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:

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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

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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

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REDCap instrument edition

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REDCap instrument organization

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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

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MedRed: Design Principles

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

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

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Provenance

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

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MedRed: Dependencies
steps
provenance
constraints

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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

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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

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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

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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

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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

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

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We are in LOV

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Also in Zenodo

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