- From: <sarala@ebi.ac.uk>
- Date: Tue, 26 Jun 2012 20:49:38 +0100
- 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 UTC