JERM Templates Update Transcriptomics by yurtgc548

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									JERM Templates Update
         Tools to Help
                                     Tools Update

Auto generation of templates
 ISA Creator and ISA configurator (beta)

 MAGE-TAB Generator



Help with annotating experiments
 Ontology annotator
     Orcha (it needs a new name!)
                                     ISA Creator


   Generates ISA-TAB compliant templates to help
    with submission of ISA format data
   Stand-alone java tool available for download
    from:
    http://isatab.sourceforge.net/isacreator.html
                             Testing Orcha Out



   Auto-generate a new MIAME compliant file from
    ArrayExpress
   Use Orcha to set particular cells to particular
    ontology terms
                                 MIAME Compliance

   Data
       Raw data, processed data
   Metadata
       sample annotations (experimental factors),
        experiment design (including sample-data
        relationships), array design, experiment and data
        processing protocols
                                     MIAME Files


   IDF: Investigation Description Format
   SDRF: Sample and Data Relationship Format
   ADF: Array Design Format
   Raw and processed data files, including "data
    matrix" files
Taken from the ArrayExpress Website
http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cg
                  Orcha Ontology Annotator


   Helps keep templates consistent
   Makes filling in the metadata easier
   Keeps data MIAME (or other MIBBI) compliant
                                                                     Practical
   Go to http://www.cs.man.ac.uk/~katy/taverna
   Download the Orcha file: orcha-0.9.0(2).zip
   Unzip it and click run
   Auto generate a MIAME file from
http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi

   Or download one I made earlier from
http://www.cs.manchester.ac.uk/~katy/taverna/kwolst_MAGE-TAB_testSysmo_format.xls

   Load this file into Orcha by selecting File -> Open
    Workbook
   Load the Microarray Experimental Conditions
    ontology from the BioPortal (File -> Open from
    BioPortal)

								
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