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


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  • From: ely.matos at ufjf.edu.br (Ely Edison Matos)
  • Subject: [cellml-discussion] Suggestions regarding search and browse utility for CellML Repository
  • Date: Fri, 16 May 2008 23:24:50 -0300
Hello all,
Just to say that i'm trying to write a little draft in english that resumes
the ideas. And yes, there is a initial prototype application.

Ely Matos
Computational Modeling Master Program
UFJF/Brazil

----- Original Message -----
From: "Dagmar Koehn" <dagmar at ebi.ac.uk>
To: "CellML Discussion List" <cellml-discussion at cellml.org>
Sent: Friday, May 16, 2008 4:48 AM
Subject: Re: [cellml-discussion] Suggestions regarding search and browse
utility for CellML Repository


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 K?hn, 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

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