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

From: <sarala@ebi.ac.uk>
Date: Tue, 26 Jun 2012 20:49:38 +0100
Message-ID: <f497d06d0fd048fb02e88d03a42a0d44.squirrel@webmail.ebi.ac.uk>
To: "Oliver Ruebenacker" <curoli@gmail.com>
Cc: sarala@ebi.ac.uk, "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
Hi Oliver,

Thanks for the link. I'll have a look and get back to you soon.

Many thanks
Sarala

>      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 19:50:14 GMT

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