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 MedicalResearch Data Acquisition

• Data lifecycle solution for research medical data instruments.Based on the REDCap platform.

• Design, adapt and implement surveys and questionnaires forselected 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: Dependenciessteps

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:MultiStepmedred: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:demographicsex:baseline_dataex: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_section3ex: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_2ex:Morethanonceaweek_3ex: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

gracias! ¿tienes preguntas?

Jean-Paul Calbimonte

University of Applied Sciences and Arts Western Switzerland

HES-SO Valais-Wallis

@jpcik