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

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, Peter Hunter

https://doi.org/10.17608/k6.auckland.6790676 Big Picture: Linking Com putational Models to Data

https://doi.org/10.17608/k6.auckland.6790676 Standards • Sharing, archiving, reuse, reproducibility • Bond graph-based modelling frameworks • going beyond the math, capture the physics • essential for cross-domain modelling

https://doi.org/10.17608/k6.auckland.6790676 Standards for Knowledge Standards for Visual Standards for Models Representation Representation and their Analyses Core Standards BioPAX Associated Controlled Projects Infrastructure Vocabularies Standards BioModels.net Used by core qualifiers standards http:/ / co.m bine.org/ Meeting in Boston this October: http: / / co.mbine.org/ events/ COMBINE_2018 (travel grants available for US-based students!)

https://doi.org/10.17608/k6.auckland.6790676 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

https://doi.org/10.17608/k6.auckland.6790676 Physiome Model Repository (PMR) https://models.physiomeproject.org

https://doi.org/10.17608/k6.auckland.6790676

https://doi.org/10.17608/k6.auckland.6790676 Semantic annotation From Neal ML et al. PLoS Comp Bio, 2014.

https://doi.org/10.17608/k6.auckland.6790676

https://doi.org/10.17608/k6.auckland.6790676 Simulation experiments • Annotate simulation experiments • common similarity tools • discover suitable protocols to test models • “continuous integration” • automated model validation? • Cardiac Electrophysiology Web Lab https://travis.cs.ox.ac.uk/FunctionalCuration/db

https://doi.org/10.17608/k6.auckland.6790676 Clinical data annotations mindmap representation of openEHR Archetype

https://doi.org/10.17608/k6.auckland.6790676 Clinical data annotations OPB:Chemical concentration property_of AQL SPARQL CHEBI:potassium (1+) part_of FMA:Portion of blood Manual Model Clinical data Clinical data annotations Model annotation Ontology Repository Repository (SNOMED CT, LOINC) (composite annotation) Mapping

https://doi.org/10.17608/k6.auckland.6790676 Result: Experimental & Simulation Data Integration Extended prototype cardiac electrophysiology web lab to link to experimental data described in an openEHR database.

https://doi.org/10.17608/k6.auckland.6790676 Acknowledgements Koray Atalag Reza Kalbasi Dewan Sarwar Tommy Yu Peter Hunter • 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