Hi Paulo, There is a plugin called the Tab2MageExporter and it exports an entire experiment in a spreadsheet format called Tab2Mage (http://tab2mage.sourceforge.net/) which is accepted by ArrayExpress as a one possible route of submission. However, the EBI are planning to substitute this format with MAGE-TAB in the longer term, which is why things are moving away from Tab2Mage currently.
I am not sure about the compatibility of the plugin with the current version of BASE as I haven't touched it or even BASE itself for some time now but you may as well try it: http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageExporter My understanding is that it is not actively maintained at the moment anyway. A MAGE-TAB export plugin is under development at EBI but I am not sure when it will be ready. The plan is for this to replace the current Tab2MageExporter plugin eventually. Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer ================================== > -----Original Message----- > From: Paulo Almeida [mailto:[EMAIL PROTECTED] > Sent: 31 October 2008 16:22 > To: basedb-users@lists.sourceforge.net > Subject: [base] Array Express submissions > > Hi, > > I know that there is work being done in a MAGE-Tab plugin, but other > than > that, does Base have any way to make it easier to submit data to > ArrayExpress? I'm particularly worried about protocol formats (can they > just > be codes or should the field contain the entire protocol?) and > biosource > details (right now I think there is only one big field for biosource > description, but I was told ArrayExpress needs specific fields for > that, > which vary depending on certain parameteres, like whether it is an > animal or > plant sample). > > It would be helpful to know about the experience of anyone who > currently uses > Base as a tool to prepare ArrayExpress submissions. > > Thanks, > Paulo Almeida > > > ----------------------------------------------------------------------- > -- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the > world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ ______________________________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________________________ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
