Hello,

I want to revive an old base-users thread about MAGE-ML export (or MAGE-Tab).

If we consider that I have gathering and import all my data in base2.
Now I will need to export them in order to submit our arrays to ArrayExpress 
and/or GEO.

I already test Tab2Mage_exporter but there is a problem with the pooling of 
Labaled Extract or Extract.

Are there other methods to generate submission files from Base2 to ArrayExpress 
or GEO ?
I searched on the forum but it seems that it's still in debate.


Best regards

G.



Hi Chris,

Thanks for your post.
ArrayExpress is now relying on MAGE-TAB format (a evolution of tab2mage
format allowing a bit more flexibility in terms of annotation).
There are currently 2 plugins supporting tab2mage format for BASE2 but
they only work with base246. We are working to bring those plugins in line
with the latest version of base2 api.
We also have an alpha version of a MAGE-TAB importer, which requires more
work. There have been slight changes to the MAGE-TAB specifications,which
we need to implement. The code is not committed to the svn.
Converting the tab2mage to MAGE-TAB can be made with a perl script but of
course having a plugin in BASE would be nice.
We are currently working with Micha Bayer at SCRI and Duccio Cavallieri
group at University of Florence,who are also very keen to have such
functionality.

All the best

Philippe




I'm looking for a way to get
 lots of data into a BASE2 repository from ArrayExpress and GEO so I can
 run code against it and find interesting biology.<br>
 <br>
 I notice that MAGE-ML is an OMG standard that ArrayExpress supports for
 export and there is some Java code from MGED
 (<a class="moz-txt-link-freetext"

 href="http://www.mged.org/Workgroups/MAGE/mage-ml.html";  
<http://www.mged.org/Workgroups/MAGE/mage-ml.html%22>;>http://www.mged.org/Workgroups/MAGE/mage-ml.html</a>)
 already for reading files.<br>
 <br>
 Is there a plugin to get data into or out of BASE2 in MAGE-ML format?
 Is there a workaround using Tab2MAGE?<br>
 <br>
 I'm an experienced programmer (Java/Python/Perl/C++ etc) willing to
 contribute such plugins if it's feasible. Unfortunately, I'm a bit new
 to the microarray side of gene expression (worked previously with SAGE
 data).<br>
 <br>
 I noticed several posts about MAGE-ML in BASE1 but it seems to have
 disappeared for MAGE2.<br>
 <br>
 I would really appreciate any guidance and I'm willing to contribute
 significantly to the codebase if this is feasible.<br>
 <br>
 Cheers,<br>
 -Chris</font><br>
 <pre class="moz-signature" cols="72">--
 -------------------------------------------------
 Chris Fjell
 Post-doctoral fellow
 CMDR (Centre for Microbial Diseases and Immunity Research)
 University of British Columbia
 Vancouver, BC, Canada

 <a class="moz-txt-link-abbreviated"
  href="[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>
 </pre>
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