mike cooling march 2012. missing semantics publish duane mccarthy, ...
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Meaninging
Mike Cooling March 2012
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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
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Example2
‘Templates’ – Mathematical structures
‘SVPs’ -Physical things or processes
‘System Models’
1
Adapted from Cooling et al. (2010) Bioinf. Fig 1.
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Computer assisted….SearchingCompositionVisualisationAnalysis
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SearchingExisting PMR2 – tags
Standardised tags?
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OntologiesSet of defined termsRelationships between the termsMost 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’ ontologies vrs reference ontologies
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Metadata SpecificationsSyntax for connecting model elements
variablecomponents
…to reference ontologies
In RDF/XML
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one.cellml
Component: c
caxdt
dx
Variable: a
Model: m1
bqbiol:is “The biological entity represented by the model component is the subject of the referenced resource”
bqbiol:is"urn:miriam:uniprot:P04551"
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Metadata Specification 1.11.0 –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
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Main featurescmeta:ids
Not limited to thisCan 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 yearsModular structure – can develop more specs for different
domains as neededComments AuthorshipLicense informationCitation informationBiological information
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Practical IssuesGood tool for adding annotation in as painless
a way as possibleLink to ontologies
Lack of good use cases – motivationGood idea for the future…maybe?…Would be nice if someone else did it….
…or would it?
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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….
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Which Bits?variables?components?
To what extent to annotations of contents adhere to the elements above?
Unit definitions?Connections?Import statements?Everything?
All attributes?
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How Much?Can have multiple annotations
How many different annotations needed?To what level of detail?
model is_a thingysuch-and-such is_a proteinAs specific as you can?
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Against What?Guidance on ontologies for the relationships
given in the metadata specs‘examples’ probably better
Ontologies for the RHS?OBO ?Upper ontologiesCome out in the wash…
Tend to mean biological. What about mathematical? Thermodynamic?
caxdt
dx
‘is’"P04551"
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Annotating an existing modelAnnotate 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…
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Exciting times aheadResearch:
If we knew exactly what we were doing we shouldn’t be working on it
More engagement with ontologistsBit wary of modelling tech
Clearer idea of what we want to do with modelsConstruction / aggregation
Have a syntax,Need some examples….
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AcknowledgementsMetadata specs:Randall BrittenDavid BrooksRichard ChristieJames LawsonCaton LittleCatherine Lloyd Andrew MillerDavid NickersonPoul NielsenTommy Yu
European Commission, grant agreement number 248502