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 PhilippeI'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> </body> </html>
------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com
_______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
