Mode odel s semantics cs f for or di discover ery, com ompos - - PowerPoint PPT Presentation

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Mode odel s semantics cs f for or di discover ery, com ompos - - PowerPoint PPT Presentation

May 21, 2023 26 likes •167 views

https://doi.org/10.17608/k6.auckland.6790676 Mode odel s semantics cs f for or di discover ery, com ompos position on, a and nd pe person onal alisation on David Nickerson, Koray Atalag, Reza Kalbasi, Dewan Sarwar, Tommy Yu,

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Mode

  • del s

semantics cs f for

  • r di

discover ery, com

  • mpos

position

  • n, a

and nd pe person

  • nal

alisation

  • n

David Nickerson, Koray Atalag, Reza Kalbasi, Dewan Sarwar, Tommy Yu, Peter Hunter

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Big Picture: Linking Com putational Models to Data

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Standards

  • Sharing, archiving, reuse, reproducibility
  • Bond graph-based modelling frameworks
  • going beyond the math, capture the physics
  • essential for cross-domain modelling
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Core Standards

Standards for Visual Representation Standards for Models and their Analyses Standards for Knowledge Representation

Associated Standards

Used by core standards Controlled Vocabularies Infrastructure Projects BioModels.net qualifiers

BioPAX

http:/ / co.m bine.org/

Meeting in Boston this October: http: / / co.mbine.org/ events/ COMBINE_2018 (travel grants available for US-based students!)

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Collaboration & comprehension

  • Modularity and reuse
  • Versioning, provenance, capturing key decisions
  • Describing the model
  • Common approaches for annotation – speak the “same” language
  • cross-repository discovery
  • cross-standard reuse and merging
  • common software tools
  • Discovering relevant information
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Physiome Model Repository (PMR)

https://models.physiomeproject.org

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Semantic annotation

From Neal ML et al. PLoS Comp Bio, 2014.

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https://travis.cs.ox.ac.uk/FunctionalCuration/db

Simulation experiments

  • Annotate simulation experiments
  • common similarity tools
  • discover suitable protocols to test models
  • “continuous integration”
  • automated model validation?
  • Cardiac Electrophysiology Web Lab
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Clinical data annotations

mindmap representation of openEHR Archetype

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Clinical data annotations

OPB:Chemical concentration property_of CHEBI:potassium (1+) part_of FMA:Portion of blood

AQL

SPARQL

Clinical data Repository Clinical data annotations (SNOMED CT, LOINC) Manual Ontology Mapping Model annotation (composite annotation) Model Repository

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Result: Experimental & Simulation Data Integration

Extended prototype cardiac electrophysiology web lab to link to experimental data described in an

  • penEHR database.
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Acknowledgements

  • Cardiac electrophysiology web lab team
  • John Gennari, Max Neal, Dan Cook, Graham Kim @ University of Washington,

Seattle, USA

  • Centre for Reproducible Biomedical Modeling
  • http://reproduciblebiomodels.org/
  • Aotearoa Foundation

Koray Atalag Reza Kalbasi Dewan Sarwar Tommy Yu Peter Hunter