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Meaninging

Meaninging. Mike Cooling March 2012. Missing Semantics. <variable name=“ Cai ” …… Intracellular calcium? <variable name=“ ic ”…… Free calcium? Cytosolic? A person might be able to find out… Even for a small model this can be tricky. Example. ‘System Models’. 1. 2.

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Meaninging

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  1. Meaninging Mike Cooling March 2012

  2. Missing Semantics <variable name=“Cai” …… • Intracellular calcium? <variable name=“ic”…… • Free calcium? Cytosolic? • A person might be able to find out… • Even for a small model this can be tricky

  3. Example ‘System Models’ 1 2 ‘SVPs’ -Physical things or processes ‘Templates’ – Mathematical structures Adapted from Cooling et al. (2010) Bioinf. Fig 1.

  4. Computer assisted…. • Searching • Composition • Visualisation • Analysis

  5. Searching • Existing PMR2 – tags • Standardised tags?

  6. Ontologies • Set of defined terms • Relationships between the terms • Most software packages embody an ontology • But is what Alan means by ‘ion channel’ is same as what I mean by ‘ion channel’? • Do they relate the same way to ‘heart’ • ‘local’ ontologiesvrs reference ontologies

  7. Metadata Specifications • Syntax for connecting model elements • variable • components • …to reference ontologies • In RDF/XML

  8. bqbiol:is “The biological entity represented by the model component is the subject of the referenced resource” one.cellml Model: m1 Component: c bqbiol:is "urn:miriam:uniprot:P04551" Variable: a

  9. Metadata Specification 1.1 • 1.0 –never used? • 1.1 – removing a lot of things • Could already do a lot with existing technologies • URL : http://www.cellml.org/specifications/metadata/mcdraft

  10. Main features • cmeta:ids • Not limited to this • Can annotate, say an attribute of an element ie ‘initial_value’ • Annotations don’t have to be in the CellML file • I don’t have to modify Poul to frighten 1st years • Modular structure – can develop more specs for different domains as needed • Comments • Authorship • License information • Citation information • Biological information

  11. Practical Issues • Good tool for adding annotation in as painless a way as possible • Link to ontologies • Lack of good use cases – motivation • Good idea for the future…maybe?… • Would be nice if someone else did it…. • …or would it?

  12. Further (Research?) Issues • “Annotate your model” • “Yes sir” • Which bits? • How much? • Against what? • Probably depends on what you’re going to do with the annotations • But if we are hosting a repository….

  13. Which Bits? • variables? • components? • To what extent to annotations of contents adhere to the elements above? • Unit definitions? • Connections? • Import statements? • Everything? • All attributes?

  14. How Much? • Can have multiple annotations • How many different annotations needed? • To what level of detail? • model is_a thingy • such-and-such is_a protein • As specific as you can?

  15. Against What? • Guidance on ontologies for the relationships given in the metadata specs • ‘examples’ probably better • Ontologies for the RHS? • OBO ? • Upper ontologies • Come out in the wash… • Tend to mean biological. What about mathematical? Thermodynamic? ‘is’ "P04551"

  16. Annotating an existing model • Annotate it according to what you think ‘most people’ would mean? • Annotate it according to what you thought the author meant? • Annotate it according to what the author actually thought he/she meant? • Annotate it according to what it actually is? • What we think it is…views on this can change over time…

  17. Exciting times ahead • Research: • If we knew exactly what we were doing we shouldn’t be working on it  • More engagement with ontologists • Bit wary of modelling tech • Clearer idea of what we want to do with models • Construction / aggregation • Have a syntax, • Need some examples….

  18. Acknowledgements Metadata specs: • Randall Britten • David Brooks • Richard Christie • James Lawson • Caton Little • Catherine Lloyd • Andrew Miller • David Nickerson • Poul Nielsen • Tommy Yu European Commission, grant agreement number 248502 • BOA Group • m.cooling@auckland.ac.nz

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