Re: Action Items from call today

Thanks, Helen.

To make it more concrete. I've been thinking about some example queries 
that I hope can be answered by the RDF data once converted. I wonder if 
the following example quereis can be answered:

Retrieve a list of differentially expressed genes between different 
brain regions (e.g., hippocampus and entorhinal cortex) for normally 
aged human subjects.

Retrieve a list of differentially expressed genes for the same brain 
region of normal human subjects and AD patients.

Using these lists of genes one can issue (federated) queries to retrieve 
addtional information about the genes for various types of analyses 
(e.g., GO term enrichment).

Just a thought.

Cheers,

-Kei



Helen Parkinson wrote:

> Hi
>
> here are my action items from the call today
>
> 1. MAGE-TAB->RDF, Lena requested details.
>
> Code here: https://sourceforge.net/projects/limpopo/
>
> Java Parser for MAGE-TAB developed by EBI, used by several groups. 
> Contact Tony Burdett tburdett@ebi.ac.uk for details. Tony estimates 
> for a simple RDF dump a few days work. Lena if you are interested in 
> working on this java code please contact Tony as he's already 
> designed  with rdf export in mind
>
> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>
> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
> Pretty much all public MAGE-ML comes from AE and is available from 
> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's 
> mage-ml importer, and non public data
>
>
> 3. EBI experimental factor ontology (EFO) slides, attached
> see also www.ebi.ac.uk/efo
>
> 4. Noted that an RDF dump of atlas data and triple store access will 
> be useful, we'll announce when these are available
>
> thanks
>
> Helen
>
>
>

Received on Thursday, 15 October 2009 02:04:32 UTC