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

Example2

‘Templates’ – Mathematical structures

‘SVPs’ -Physical things or processes

‘System Models’

1

Adapted from Cooling et al. (2010) Bioinf. Fig 1.

Computer assisted….SearchingCompositionVisualisationAnalysis

SearchingExisting PMR2 – tags

Standardised tags?

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

Metadata SpecificationsSyntax for connecting model elements

variablecomponents

…to reference ontologies

In RDF/XML

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"

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

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

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?

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….

Which Bits?variables?components?

To what extent to annotations of contents adhere to the elements above?

Unit definitions?Connections?Import statements?Everything?

All attributes?

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?

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"

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…

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….

AcknowledgementsMetadata specs:Randall BrittenDavid BrooksRichard ChristieJames LawsonCaton LittleCatherine Lloyd Andrew MillerDavid NickersonPoul NielsenTommy Yu

BOA Groupm.cooling@auckland.ac.nz

European Commission, grant agreement number 248502