Tab2MageImporter

Short description

Imports into BASE 2, raw data files and experimental metadata from a zipped archive containing a tab2mage formatted description of the experiment and a set of raw data files.

Long description

The Tab2MageImporter plugin batch loads raw data files and inserts all experimental descriptors in BASE2 by parsing a tab2mage file and raw data files from a zipped archive. The tab2mage specifications is provided by the Microarray Informatics Team at the EBI, at the EBI, Cambridge and are available from ​http://tab2mage.sourceforge.net/.

The Tab2MageImporter plugin is started from the Experiment Item View Page. This means that the user needs to create an experiment first and then execute the plugin from this page by clicking on the Import tab. The displayed wizards asked for the zip file containing the meta- data i.e. tab2mage file and the raw data files. Furthermore, the user’s email server name could be specified to received notices of success or failure of the uploading or can be omitted to receive no message.

Please read the next section to ensure the BASE environment has been properly set up before trying to run Tab2MageImporter plugin.

Prerequisites

Base 2.2 and above
AnnotationTypeCvImporter Plugin – Required for loading annotation types. The plugin must have a proper configuration defined to import an annotation type file created by the Tab2MageImporter plugin when parsing the tab2mage file.

Reporter Importer Plugin - Required for loading Reporters

Reporter Map Importer Plugin – Required for mapping features to Reporters when defining an Array Design

Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files.

The definition for the plug-in is available by default. The configuration should be done by administrator and shared to everyone or a suitable group that all the target users belong.

Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Further information on AnnotationTypeCvImporter Plugin is available on Base2plugin website and for other plugins, please read base2 documentation.

Optional

​AffyArrayDesignImproter Plugin . – for batch uploading affymetrix array designs. Useful to upload all array designs used in an experiment in one go before running the Tab2Mage Importer.

If you want to use messaging, mail.jar and activation. jar for messaging is required- these jar files should be downloaded and copied to your base installation class path /web-inf/lib folder.

Documentation

The ​README.txt contains information on how to install and use the plug-in.

FAQs

Sample Tab2Mage Spreadsheets

​Affymetrix, ​Agilent and ​Genepix

Maintenance plan

Bugs will be fixed. Volunteers welcome to help extend the plug-in.

License

​GNU General Public License version 2.

Author

Dominic Oyeniran – European Bioinformatics Institute, Cambridge, UK
​http://www.ebi.ac.uk
​Project Page
email: oyeniran@…

Philippe Rocca-Serra – European Bioinformatics Institute, Cambridge, UK, Net-Project technical coordinator.
email: rocca@…

Credits

We would like to thank:

Charles Girardot <charles.girardot@…> and Sajoscha Sauer <sauer@…> at EMBL, Germany whose tab2mage Base1Loader code, were used and adapted for this tab2mage importer implementation.

Misha Bayer <sbrn@…> at the Plant Bioinformatics Group, Scottish Crop Research Institute whose batchimporter was also used and adapted to develop the tab2mage importer.

Download

plugin jar file: ​Tab2MageImporter.jar