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Re: GXA triples

From: Helen Parkinson <parkinson@ebi.ac.uk>
Date: Fri, 08 Jul 2011 15:44:05 +0100
Message-ID: <4E1717B5.2010603@ebi.ac.uk>
To: Michael Miller <Michael.Miller@systemsbiology.org>
CC: tomasz.adamusiak@ebi.ac.uk, public-semweb-lifesci@w3.org
Hi Michael

it would help to prioritize what to represent if we had a set of 
concrete use cases for the points you mention. We can generate RDF for 
lots of elements of the experiments of course -

cheers

Helen

On 08/07/2011 15:37, Michael Miller wrote:
> hi tomasz,
>
> thanks for the update, nice!  and again to jun for hosting.
>
> the documentation is appreciated, interestingly enough, in the diagram, it
> looks like it is only the relationship between the experiment, the set of
> sequences and their differential measurements per experimental factor
> value.  is there an overall, across the factors, differential measurement
> (e.g. limma) or am i missing something?
>
> are you also planning on RDFizing the information on the experiment (the
> idf and sdrf info) that is in ArrayExpress?
>
> cheers,
> michael
>
> Michael Miller
> Software Engineer
> Institute for Systems Biology
>
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>> lifesci-request@w3.org] On Behalf Of Tomasz Adamusiak
>> Sent: Friday, July 08, 2011 3:57 AM
>> To: public-semweb-lifesci@w3.org
>> Subject: GXA triples
>>
>> Hi,
>>
>> [Resending as my original email seems to be lost in moderation.]
>>
>> Jun has kindly reloaded a new batch of Atlas triples that James and I
>> generated. In this release there are up to 500 top differentially
>> expressed genes per experiment available and a total number of triples
>> increased from ~37 to ~170 million.
>>
>> More information is available at:
>> http://www.ebi.ac.uk/efo/semanticweb/atlas
>>
>> SPARQL examples are collated at:
>> http://code.google.com/p/open-biomed/wiki/GeneExpressionAtlas
>>
>> We've also deployed a secondary endpoint that mirrors the data:
>> http://wwwdev.ebi.ac.uk/microarray-srv/openrdf-sesame/repositories/gxa
>>
>> Feedback very much welcome.
>>
>> Cheers
>> Tomasz
>>
>>
>> --
>> Tomasz Adamusiak, MD, PhD
>> European Bioinformatics Institute
>> +44 (0) 1223 492 562
>> tomasz.adamusiak@ebi.ac.uk
>>

-- 
Helen Parkinson, PhD
Team Leader
Functional Genomics Group
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi
www.ebi.ac.uk/fgpt/
Received on Friday, 8 July 2011 14:44:49 GMT

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