W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > November 2011

MAGE-TAB in RDF

From: James Malone <malone@ebi.ac.uk>
Date: Wed, 30 Nov 2011 17:23:09 +0000
Message-ID: <4ED6667D.7@ebi.ac.uk>
To: HCLS <public-semweb-lifesci@w3.org>
CC: Marco Brandizi <brandizi@ebi.ac.uk>
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



sdrf.png
(image/png attachment: sdrf.png)

idf.png
(image/png attachment: idf.png)

Received on Wednesday, 30 November 2011 17:24:13 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:04 GMT