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

From: <sarala@ebi.ac.uk>
Date: Tue, 26 Jun 2012 10:17:45 +0100
Message-ID: <f698d68b4ddca110e4281caaf21f88b9.squirrel@webmail.ebi.ac.uk>
To: "Michel Dumontier" <michel.dumontier@gmail.com>
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
Hi Michel,

Not at the moment but we are hopping to address this as well.

Cheers,
Sarala

> 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 11:59:03 GMT

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