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Re: MAGE-TAB in RDF

From: Jim McCusker <james.mccusker@yale.edu>
Date: Wed, 30 Nov 2011 16:02:07 -0500
Message-ID: <CAAtgn=R=fLYfkMQubVJ+QmRUTP7D4wb+N0VVnm0ea=kHw2iapw@mail.gmail.com>
To: James Malone <malone@ebi.ac.uk>
Cc: Michael Miller <Michael.Miller@systemsbiology.org>, HCLS <public-semweb-lifesci@w3.org>, Marco Brandizi <brandizi@ebi.ac.uk>
All, this has been an extension of my work on magetab2rdf (
http://magetab2rdf.googlecode.com) for the caBIG Information Representation
Working Group, which has been looking at mapping the caBIG Life Sciences
Domain Analysis Model (LS-DAM) into existing ontologies. We chose a use
case that had its experiment already represented in MAGE-TAB, so I took
that and updated the representation to use PROV and to improve the
representation based on what I've learned about OBI et al. since the last
time I ran magetab2rdf.

Jim

On Wed, Nov 30, 2011 at 3:48 PM, James Malone <malone@ebi.ac.uk> wrote:

> 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<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<http://wwwdev.ebi.ac.uk/microarray-srv/magetab/generated-doc/objectmodel>
>> .
>> html or ftp://smd-ftp.stanford.edu/**smd/transfers/magetab/magetab.**xml<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
>
>
>


-- 
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Wednesday, 30 November 2011 21:03:02 GMT

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