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Re: MAGE-TAB in RDF

From: James Malone <malone@ebi.ac.uk>
Date: Wed, 30 Nov 2011 20:48:30 +0000
Message-ID: <4ED6969E.9080901@ebi.ac.uk>
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 GMT

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