- From: James Malone <malone@ebi.ac.uk>
- Date: Wed, 30 Nov 2011 20:48:30 +0000
- To: Michael Miller <Michael.Miller@systemsbiology.org>
- CC: HCLS <public-semweb-lifesci@w3.org>, Marco Brandizi <brandizi@ebi.ac.uk>
Thanks Michael for sending on Jim's figure. I'll look into making the server public. James On 30/11/2011 20:13, Michael Miller wrote: > hi james, > > thanks for the example, it looks very promising. > > i believe this is jim's link to his illustration of his work (in no way > reflects any effort on my part!): > http://dl.dropbox.com/u/9752413/IRWG/carpt-00469.png > > not seeing the formal owl definition but just looking at the png, it looks > like if the owl ontology was a realization of the MAGE-TAB object model > (http://wwwdev.ebi.ac.uk/microarray-srv/magetab/generated-doc/objectmodel. > html or ftp://smd-ftp.stanford.edu/smd/transfers/magetab/magetab.xml -- > see attachments) a lot of the attributes and relations can be in a super > term like Material and the realizable terms like Source, Sample, ..., can > have 'is_a' or similar to OBI and EFO. > > in terms of making the site public, that would be great so that the W3C > note could reference it and it could joined into LODD > > cheers, > michael > >> -----Original Message----- >> From: James Malone [mailto:malone@ebi.ac.uk] >> Sent: Wednesday, November 30, 2011 9:23 AM >> To: HCLS >> Cc: Marco Brandizi >> Subject: MAGE-TAB in RDF >> >> All, >> >> I had promised to send something on regarding the work our student >> (Drashtti Vasant) had been doing on producing RDF from our MAGE-TAB >> experiments in ArrayExpress. So here are some bits. We started this a >> couple of months back before a model was sent around by Jim or Michael >> (apologies, not sure who it was exactly - for whatever reason I can not >> find the email and diagram that was sent round - could someone resend >> it >> please!). Interesting to see the things that align/different, I seem to >> recall they aren't a million miles off. >> >> Anyway, I've attached the graphs we used as our baseline and the table >> of nodes we included as rdf and the triples we formed in this rdf - >> note >> we do not include everything in the graphs attached. For factor values, >> we ran our Zooma term matching across the values to try and mine these >> against matches in EFO and for those that we matched we formed triples >> (e.g. liver, cancer). For those we couldn't match automatically we >> added >> some default high level triples (which are less useful) just to say >> this >> has some factor values and we captured it as a literal text string. I'm >> simplifying a bit as it was a bit more complicated but more or less >> that >> is what we did. As well as the triples in the doc I've attached we also >> added some "convenience" triples to each of these nodes directly to the >> experiment using part_of relation so you can do simple queries on the >> experiment without having to traverse the whole graph. >> >> The store is sitting on an internal server at the moment but we may >> open >> it up if there is any interest in using it. Otherwise, we have some >> internal (interesting) stuff we're doing with it as well expanding and >> refining what we have. We focused on things we wanted to ask questions >> about explicitly based on a set of competency questions we had formed. >> It's not perfect but I'm of the school of release early, often, refine. >> >> Cheers, >> >> James >> >> PS credit for work is to Drashtti Vasant who did most of this >> implementation, myself and Tony Burdett supervised with some guidance >> on >> RDF matters from Marco Brandizi. >> >> >> -- >> European Bioinformatics Institute, >> Wellcome Trust Genome Campus, >> Cambridge, CB10 1SD, >> United Kingdom >> Tel: + 44 (0) 1223 494 676 >> Fax: + 44 (0) 1223 494 468 -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468
Received on Wednesday, 30 November 2011 20:49:06 UTC