Hi Rupali,
On 6 févr. 06, at 22:08, Rupali Patwardhan wrote:
Hi,
This is regarding MAGE-ML export that can be accepted by ArrayExpress
(again)! I did see Kjell's email a couple of weeks back where he
mentioned that stable code will be available in the CVS later this
month.
I assume it be necessary to upgrade to a new version of 1.2.x to get
these MAGE-ML corrections? or would something like a patch be provided
which we can apply to an existing 1.2.x installation?
you will have to upgrade your installation
Also, has anyone used the Tab2MAGE utility from ArrayExpress to
convert tab delimited data exported from BASE into MAGEML? Any inputs
on this will be greatly appreciated.
yes. I generate TAB2MAGE and ADF file from BASE but the result of this
really depends on how you configured your installation. The ADF file is
not a problem but the TAB2MAGE one can be.
1. do your sample annotations match with MIAME required annotations?
2. And if so, do you use MO terms whenever posssible for sample
annotations and other places like exp design , ....?
3. BioSource concept is one of the trickiest issue to automate : this
really depends on how you use the SampleOrign in BASE
4. Other problems is that concepts are missing in BASE like Factor
Value and few annotation fields on the level of extract and
labeledextract (like ExtractMaterial, ...)
It is possible to generate a "draft" TAB2MAGE from BASE that you'll
have to manually adapt (or do little bit of coding if you are a
programmer). Depending on how "compliant" is your BASE and how big is
your experiment, you might want to assemble the TAB2MAGE by hand or
spend a couple of day to write code fitting with your BASE
installation.
Hopefully the next BASE release will also ease TAB2MAGE export a lot.
Hope this helps
Charles
Thanks,
Rupali
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Best regards,
Charles
=====================
Charles Girardot
EMBL
C. Boulin and E. Furlong Groups
Tel: +49-(0)6221-387-8426 (or 8516)
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