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Re: Michel Dumontier @ Systems Biology Telco - today at 11AM EST

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Mon, 25 Jun 2012 22:45:46 -0400
Message-ID: <CALcEXf6=YZxfXLGLg0H7a+0obM2nUcYtuG9dOW7tTj5SBe1JHg@mail.gmail.com>
To: sarala@ebi.ac.uk
Cc: Helena Deus <helenadeus@gmail.com>, pierregrenon@gmail.com, Michael Hucka <mhucka@caltech.edu>, HCLS hcls <public-semweb-lifesci@w3.org>, laleh.kazemzadeh@deri.org
Sarala,
  Do you convert/extract the (MathML) kinetic expressions?

m.

On Mon, Jun 25, 2012 at 10:12 PM, <sarala@ebi.ac.uk> wrote:

> Hi Lena,
>
> We are interested in querying the underlying model representation as well.
> We want to be able to run SPARQL queries on different types of model/data
> repositories eg. cellml. It is not always possible to convert some of the
> model/data we work with to BioPAX. Our rdf schema consists of a general
> model representation followed by more specific representations for each
> standard.
>
> Cheers,
> Sarala
>
> > Hello Sarala,
> >
> > This is great - naive question: is there a reason why you didn't go with
> > the biopax representation?
> > Best,
> > Lena
> >
> > On Mon, Jun 25, 2012 at 10:46 AM, <sarala@ebi.ac.uk> wrote:
> >
> >> Hi Lena,
> >>
> >> I'm working on semantic interoperability of data and models. As part of
> >> this work, I have converted all curated sbml models in biomodels into
> >> RDF.
> >> It would be good to see what you have done, may be see were we can
> >> collaborate. I'm in the process of documenting my work but you can find
> >> the rdf models and the schema at
> >> https://sites.google.com/site/ricordowp4/file-cabinet/sbmltordf. These
> >> models are stored in a RDF store and can be queried via ws eg.
> >> http://wwwdev.ebi.ac.uk/ricordo-rdfstore-ws/service/search/getResources
> .
> >> A
> >> bit more documentation on this can be found at
> >> https://github.com/sarala/ricordo-rdfstore-ws. I will be uploading the
> >> converter code to github soon. Please let me know if your work is
> >> available to access online.
> >>
> >> Cheers,
> >> Sarala
> >>
> >> > Mike,
> >> >   This might be of interest to harmony/combine folks - which mailing
> >> lists
> >> > might Lena post to do indicate she will be presenting on this topic?
> >> >
> >> > m.
> >> >
> >> > On Fri, Jun 22, 2012 at 12:09 PM, Me <helenadeus@gmail.com> wrote:
> >> >
> >> >> Hi Michael,
> >> >>
> >> >> My plan for the next telco is to have a much MUCH  more hands-on
> >> focus
> >> >> than what we've had so far. Me and Laleh (my PhD student) are
> >> creating
> >> >> RDF
> >> >> representations of SBML models so that we can visualize with google
> >> >> fusion
> >> >> tables. We hope to have something to show by next telco.
> >> >>
> >> >> Best,
> >> >> Lena
> >> >>
> >> >>
> >> > --
> >> > Michel Dumontier
> >> > Associate Professor of Bioinformatics, Carleton University
> >> > Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> >> > Group
> >> > http://dumontierlab.com
> >> >
> >>
> >>
> >
> >
> > --
> > Helena F. Deus
> > Post-Doctoral Researcher at DERI/NUIG
> > http://lenadeus.info/
> >
>
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Tuesday, 26 June 2012 02:46:35 GMT

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