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Re: MAGE-TAB in RDF

From: Marco Brandizi <brandizi@ebi.ac.uk>
Date: Wed, 30 Nov 2011 18:04:01 +0000
Message-ID: <4ED67011.50405@ebi.ac.uk>
To: public-semweb-lifesci@w3.org
CC: Drashtti Vasant <vasant@ebi.ac.uk>
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<brandizi@ebi.ac.uk>

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
Received on Wednesday, 30 November 2011 18:04:38 GMT

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