[cellml-discussion] Suggestions regarding search and browse utility for CellML Repository

[Dagmar Koehn]

Hello Ely,

I have been looking at model composition a bit as well and I would be 
interested in your work :-)
Unfortunately, I don't know any Brazilian, but do you think you might 
provide me with some English information?
Is the implementation available somewhere?

Thanks a lot,
Dagmar


Ely Edison Matos wrote:
> Hello all,
> James, my Msc. dissertation, recently concluded, was about the use of 
> ontologies to enrich semantically the CellML Models. I've proposed a initial 
> ontology represented in OWL-DL and using SWRL, called CelO (Cell Component 
> Ontology) with 3 "sub-ontologies": one to represent SI units and quantities, 
> other to represent the biological domain terms and another to represent the 
> model.
>
> My proposal was exactly to have "atomic components" (models with a single 
> component or, at least, a single "interface" - when a component "encapsules" 
> other components and only it is visible to external world). Each "atomic 
> model" owns a interface (input/output variables) semantically annoted to let 
> one to make "semantic queries" about models (using SPARQL). This let me to 
> do questions as "which are the components related with SodiumIonChannel?", 
> taked in account that this "knowledge" is extracted from the names of 
> variables in CellML Model (like "I_Na") and some inferences (like "I" is the 
> symbol of "ampere" that measures "eletric_current", then this variable is 
> associated with eletric_current; as it is defined inside the component 
> "mebrane" and "Na" is the symbol of "Sodium", it can be associated with 
> .SodiumIonChannel). This is a very simple example.
> .
> Each "CelO Model" has a reference to the correspondent CellML Model, to let 
> compose "atomic components" and create a "composed model", with components 
> of diverse models (as a rough example, a SodiumChannel of Hodking_Huxley 
> inside a Noble model). The CelO Models are stored in a relational database 
> and inference engines can be used to do queries.
>
> I've implemented a "framework" (as web service) that offers all this 
> services (registry, query, "execute", compose models).
>
> This work is very incipient, given my "almost null" knowlegde about 
> intrinsics of biological domain. As my Master Program is about Computational 
> Modeling, my focus was strongly directed to the "modelling" part, not the 
> "biological" part. My objective was provide a "high level" view of CellML 
> Models.
>
> Unfortunately my dissertation is written only in brazilian portuguese. I've 
> submmited some papers but I didn't get success. However, if there is some 
> curiosity I can try to translate the main ideas.
>
> Sorry by intromission and the bad english,
>
> Ely Matos
> Computational Modeling Master Program
> UFJF/Brazil
>   

-- 
Dagmar Köhn, EMBL - European Bioinformatics Institute, Computational Neurobiology Group, Hinxton, Cambridge, CB10 1DS, UK, http://www.ebi.ac.uk/compneur-srv/, dagmar at ebi.ac.uk, Tel: +441223494418