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.

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. For the latest release, you would need BASE 2.4.6. See the documentation section for more details.

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 – Required for loading raw data and import values associated to BASE rawBioassays. This is a critical requirement, for multi-channel experiments, before running the Tab2MageImporter. Users must ensure that raw data import plugin has been properly configured and is able to import a raw datafile of the type of the submission.

The definition for the above plug-ins is available by default in Base 2. The plugins should be configured by a Base 2 administrator and shared to everyone or a suitable group of target users.

​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.

Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. For simplicity, the Annotation Type Cv Importer Plugin is included in the Tab2MageImporter.jar file. Read the README file in the documentation section for further details.

Click ​AnnotationTypeCvImporter for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation.

Also, do make sure that Array Design(s) corresponding to the one(s) referenced in the Array[accession] field of the tab2mage file have been properly created in BASE2. If not, the plugin will fail. For all non-Affymetrix Array Designs,this means that Reporters have been loaded and Feature to Reporter Map have been attached to Array Designs. Those tasks can be only be achieved if the above plugins have been properly set up and configured.

Optional

​AffyArrayDesignBatchImporter 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 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.

Sample Tab2Mage Import Work Flow: ​Affymetrix

FAQs

​Tab2Mage Import FAQ.

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 ( bloader.jar), is used and adapted as a dependent jar for this tab2mage importer implementation.

Misha Bayer <sbrn@…> at the Plant Bioinformatics Group, Scottish Crop Research Institute for allowing us use some code from his batchimporter for the tab2mage importer.

Last but not least, the BASE 2 team at Lund, keep up the good work guys.

Download

plugin jar file: ​Tab2MageImporter.jar

Sample archives: ​Genepix, Agilent and Affymetrix