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

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Tue, 26 Jun 2012 10:01:37 -0400
Message-ID: <CAA=X4OCfyEUC0JcTSg47stssS4v-AgxTq4UusU31VZfXDf2w=A@mail.gmail.com>
To: sarala@ebi.ac.uk
Cc: Michel Dumontier <michel.dumontier@gmail.com>, Helena Deus <helenadeus@gmail.com>, pierregrenon@gmail.com, Michael Hucka <mhucka@caltech.edu>, HCLS hcls <public-semweb-lifesci@w3.org>, laleh.kazemzadeh@deri.org
     Hello Sarala,

  We created SBPAX, an extension to BioPAX to integrate quantitative
data and build a bridge to modeling. SBPAX is in line to become part
of BioPAX, and is supported by two popular databases and by upcoming
versions of the Virtual Cell.

  If there is anything you need that SBPAX does not have, then we
would be happy to hear about it and maybe we can extend SBPAX to serve
your needs.

  Please check out http://www.sbpax.org

     Take care
     Oliver

On Tue, Jun 26, 2012 at 5:17 AM,  <sarala@ebi.ac.uk> wrote:
> 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
>>
>
>
>
>



-- 
Oliver Ruebenacker, Bioinformatics and Network Analysis Consultant
President and Founder of Knowomics
(http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Consultant at Predictive Medicine
(http://predmed.com/people/oliverruebenacker.html)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
Received on Tuesday, 26 June 2012 14:02:09 GMT

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