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From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 30 Nov 2011 12:13:03 -0800
Message-ID: <e486913c3836fbb648647567c40cabb7@mail.gmail.com>
To: James Malone <malone@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>
Cc: Marco Brandizi <brandizi@ebi.ac.uk>
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!):

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
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


> -----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

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Received on Wednesday, 30 November 2011 20:13:38 UTC

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