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

From: <sarala@ebi.ac.uk>
Date: Tue, 26 Jun 2012 03:12:11 +0100
Message-ID: <51d4e9d0947de0e9badcc7f9f8b6df3f.squirrel@webmail.ebi.ac.uk>
To: "Helena Deus" <helenadeus@gmail.com>
Cc: pierregrenon@gmail.com, "Michel Dumontier" <michel.dumontier@gmail.com>, "Michael Hucka" <mhucka@caltech.edu>, "HCLS hcls" <public-semweb-lifesci@w3.org>, laleh.kazemzadeh@deri.org
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/
>
Received on Tuesday, 26 June 2012 11:59:00 GMT

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