Bringing Things Together and Linking to Health Information using openEHR

Biomedical Informatics whats the point?

Bringing Things Together and Linking to Health Information using openEHR

Koray Atalag, MD, PhD, FACHISenior Research Fellow (ABI & NIHI)[email protected]

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cell-cell connections

proteins

genomicsequenceamino acidsequence

torsoExample: The Heart Physiome

3D cell

tissue

heartcellular processes

nmm=109nmHunter PJ, Pullan AJ, Smaill, BH. Modeling total heart function. Annual Review of Biomedical Engineering, 5:147-177, 2003LeGrice IJ, Hunter PJ, Smaill BH. Am.J.Physiol. 272:H2466-H2476, 1997

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Myocardial activation Ventricular wall mechanics Ventricular blood flowHeart valve mechanicsCoronary blood flowNeural control Torso modelComposite lumped parameter cell modelHodgkin-Huxley type ion channel model

Markov ion channel model

3D protein model (KCNQ1+KCNE1) Coarse grained MD modelQuantum mechanics modelMolecular dynamics model

Continuum tissue model Organ model

Discrete tissue structure model

Calcium transport modelsMyofilament mechanicsSignal pathway modelsMetabolic pathway modelsGene regulation models

3D cell model

Tissue

OsteonNephronAcinusLiver lobuleLymph nodeCardiac sheetsOrgan

HeartLungsDiaphragmColonEyeKneeLiverEnvironmentOrgan systemOrganism

Cell

ProteinGeneAtomNetworkx 1million20 generations

The challenge: organs to proteins

(www.cellml.org)Cuellar AA, Lloyd CM, Nielsen PF, Halstead MDB, Bullivant DP, Nickerson DP, Hunter PJ. An overview of CellML 1.1, a biological model description language.SIMULATION: Transactions of the Society for Modeling and Simulation, 79(12):740-747, 2003 Physiome Standards: CellML, SBML, FieldML,

Why the need for clinical data?Biophysical models (geometric/mathematical) define real-world biological entities/processesMulti-scale biomedical integration requires understanding of normal and pathological phenomenaClinical records are sinks of valuable knowledgeEmbody effects of environment/random phenomenaTherefore clinical data will allow forBetter understanding (geno-pheno-enviro)Model validationModel customisation (e.g. personal parameters)Predictive tools & advanced decision support

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Patient Avatar:digital representation of all health-related data that is available for the individual, as the general basis for the construction of Virtual Physiological Human workflows

VPH-Share Clinical WorkflowMedical recordsPatient imagesPopulation data

Images/Data

ProcessSegmentMeshBCs

10%

Surgical planningetcRisk of SomethingOutputIndividualised risk scoreSurgical strategyTherapy

NetworksMultiple sources/types

CloudScalable

ComputingFast processing

Remote VizEfficient graphicsClinicalICTSimulationVisualisationAnalysisAnalysis

Integrating Physiome/Biomedical InformaticsCurrent Physiome / VPH data and model integration work is mostly underpinned by Semantic WebTheres limited uptake of Semantic Web technologies in healthcare delivery (e.g. EHRs, HIS, CIS etc.)openEHR is a key medical informatics standard to link the two worlds;Models of how to capture/represent clinical informationSupports data creation, validation, storage etc.Supports explicit semantics via terminology bindings to formal ontologiesUsed by many real-world systems today

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The Science Domains10

PhD Research (Aleksandar Zivaljevic):Annotation of clinical datasets using openEHR ArchetypesExtending the RICORDO* Framework

Bono B de, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P. The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Research Notes. 2011 Aug 30;4(1):313.

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ConclusionLinked Data is a necessityPhenotypes (e.g. diseases, findings, behaviour)Genotype (e.g. Omics data)Environment (e.g. physical, food, psychological)Physiological (models, simulations, visualisations)Physiome / VPH needs to link to real world dataShared resources & annotations key to linkageTODO: clinical data platform w/ common meta-data

has been utilised by VPH-Share (Avatars)

HL7s is also a key standard for exchange

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