- From: <sarala@ebi.ac.uk>
- Date: Tue, 26 Jun 2012 10:17:45 +0100
- 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 UTC