Hi all,
just a few things.
We are adding a very similar export of data from the SampleTAB format
(http://nar.oxfordjournals.org/content/early/2011/11/16/nar.gkr937.full), with
the idea to integrate these two sources of data in a unified
representation.
I've seen the diagram in the mail titled 'SWAN-myExp-OBI-ISA' and my
understanding is we are talking about similar things, i.e., representing
experiment meta-data in RDF with models (possibly one...) that can
accommodate most popular formats (ISA-Tab, MAGETAB, etc) and also can be
linked to other models, such as SWAN.
So, it should be interesting to try to put things together.
Cheers,
Marco.
On 30/11/2011 17:23, James Malone wrote:
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.
--
===============================================================================
Marco Brandizi, PhD<[email protected]>
Microarray Group - Sr Software Engineer
http://www.ebi.ac.uk/microarray
European Bioinformatics Institute
Hinxton, CB10 1SD, United Kingdom
Office A3141
Tel.: +44 (0)1223 492 613
Fax: +44 (0)1223 492 620
http://www.marcobrandizi.info
