Welcome Jeremy! Sounds interesting! Many of us are having this very conversation about naming and scaling offlist, and we'll bring you into it. The time slot for the clinical pgx was changed from 11am to 1015am EDT to accomodate my teaching requirements for this term and european participants. The last lab I run in this time slot will be April 3, after which we can schedule that works for more participants. With the linked life data group, we're trying to figure out how to accomodate japan and australia into the mix... (soon i will also be on the west coast). suggestions welcome!
m. On Mar 15, 2013, at 5:34 PM, Jeremy J Carroll <j...@syapse.com> wrote: > > While it doesn't seem to be the convention in this group, now that I have > graduated from lurking to participating, I thought I should say why I am here. > > I have a new job with a genomics company in Silicon Valley, and my remit is > to work out how best to represent both scientific knowledge about genomics, > and also the per-patient knowledge found in say a VCF file …. > > Having been working in SemWeb for over a decade now (RDF Concepts, OWL Tests, > Jena, Named Graphs, TopBraid Suite), my bias is to use SemWeb technologies; > but, particularly with the variant information, the back-of-an-envelope > numbers look fairly large, see: > > http://lists.w3.org/Archives/Public/semantic-web/2013Mar/0048.html > > (That's 1B triples for science, and 1B triples per vcf file uploaded) > > The Clinical Pharmacogenomics TF seems like the most relevant part, > unfortunately the 7.15 - 8.15 slot for the call coincides with some parental > duties for me … > > I am still on the look out for some documentation by people who have been > tackling similar problems. > > As far as I can tell, many people in the field are bought into an ontological > approach, but the penetration of even pretty basic SemWeb good practices is > low: e.g. use of URIs for concepts, RDF and OWL … and interoperating with > various large datasets (e.g. dbsnp) is necessary, but most are not natively > OWL > > Any thoughts or suggestions would be very welcome > > Jeremy > >
